Starting phenix.real_space_refine on Mon Jul 22 21:35:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oaf_3773/07_2024/5oaf_3773_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oaf_3773/07_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_3773/07_2024/5oaf_3773.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oaf_3773/07_2024/5oaf_3773.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oaf_3773/07_2024/5oaf_3773_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oaf_3773/07_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 Residue "A ARG 14": "NH1" <-> "NH2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B ARG 54": "NH1" <-> "NH2" Residue "B ARG 64": "NH1" <-> "NH2" Residue "B ARG 71": "NH1" <-> "NH2" Residue "B ARG 124": "NH1" <-> "NH2" Residue "B ARG 334": "NH1" <-> "NH2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B ARG 392": "NH1" <-> "NH2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B ARG 428": "NH1" <-> "NH2" Residue "B PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 438": "NH1" <-> "NH2" Residue "C ARG 14": "NH1" <-> "NH2" Residue "C ARG 46": "NH1" <-> "NH2" Residue "C ARG 117": "NH1" <-> "NH2" Residue "C ARG 118": "NH1" <-> "NH2" Residue "C ARG 276": "NH1" <-> "NH2" Residue "C ARG 333": "NH1" <-> "NH2" Residue "C ARG 339": "NH1" <-> "NH2" Residue "D ARG 18": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "D ARG 64": "NH1" <-> "NH2" Residue "D ARG 71": "NH1" <-> "NH2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D ARG 253": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D ARG 284": "NH1" <-> "NH2" Residue "D ARG 334": "NH1" <-> "NH2" Residue "D ARG 374": "NH1" <-> "NH2" Residue "D ARG 400": "NH1" <-> "NH2" Residue "D ARG 428": "NH1" <-> "NH2" Residue "E ARG 14": "NH1" <-> "NH2" Residue "E ARG 46": "NH1" <-> "NH2" Residue "E ARG 117": "NH1" <-> "NH2" Residue "E ARG 118": "NH1" <-> "NH2" Residue "E ARG 276": "NH1" <-> "NH2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E ARG 362": "NH1" <-> "NH2" Residue "E ARG 378": "NH1" <-> "NH2" Residue "E ARG 404": "NH1" <-> "NH2" Residue "F ARG 18": "NH1" <-> "NH2" Residue "F ARG 21": "NH1" <-> "NH2" Residue "F ARG 53": "NH1" <-> "NH2" Residue "F ARG 54": "NH1" <-> "NH2" Residue "F ARG 64": "NH1" <-> "NH2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F ARG 314": "NH1" <-> "NH2" Residue "F ARG 353": "NH1" <-> "NH2" Residue "F ARG 374": "NH1" <-> "NH2" Residue "F ARG 400": "NH1" <-> "NH2" Residue "F ARG 438": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 10.07, per 1000 atoms: 0.51 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 - 3.50 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: 7.42 Conformation dependent library (CDL) restraints added in 3.3 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: 2.37 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: 5.92 Time building geometry restraints manager: 8.13 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: 100.44 - 107.59: 581 107.59 - 114.75: 12558 114.75 - 121.90: 9560 121.90 - 129.05: 4181 129.05 - 136.21: 70 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 2.440 nonbonded pdb=" O TYR B 387 " pdb=" OG1 THR B 391 " model vdw 2.201 2.440 nonbonded pdb=" O TYR D 387 " pdb=" OG1 THR D 391 " model vdw 2.209 2.440 nonbonded pdb=" NH1 ARG F 400 " pdb=" O2A ADP F 501 " model vdw 2.212 2.520 nonbonded pdb=" OG SER E 99 " pdb=" OG SER F 310 " model vdw 2.235 2.440 ... (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 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: 11.300 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 47.720 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.360 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 6 poor density : 759 time to evaluate : 2.600 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: 0.3483 time to fit residues: 384.5779 Evaluate side-chains 405 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 402 time to evaluate : 2.365 ------------------------------------------------------------------------------- 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: 7.9990 chunk 190 optimal weight: 0.0980 chunk 105 optimal weight: 0.6980 chunk 64 optimal weight: 0.4980 chunk 128 optimal weight: 0.7980 chunk 101 optimal weight: 10.0000 chunk 196 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 146 optimal weight: 10.0000 chunk 227 optimal weight: 0.0570 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN 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 156 HIS C 229 HIS C 414 ASN E 34 GLN E 305 HIS F 78 GLN ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19990 Z= 0.161 Angle : 0.600 8.117 26950 Z= 0.295 Chirality : 0.043 0.176 3170 Planarity : 0.004 0.099 3434 Dihedral : 9.275 161.765 2788 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % 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: -1.26 (0.14), residues: 2512 helix: -1.05 (0.14), residues: 1034 sheet: 0.17 (0.21), residues: 440 loop : -0.88 (0.17), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 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 489 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 489 time to evaluate : 2.387 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: A 184 ARG cc_start: 0.7006 (mpt180) cc_final: 0.6538 (mtp180) REVERT: A 215 LEU cc_start: 0.7275 (mt) cc_final: 0.6701 (mt) REVERT: A 259 MET cc_start: 0.2873 (mtt) cc_final: 0.2434 (mtm) REVERT: A 260 MET cc_start: 0.6440 (ptm) cc_final: 0.5864 (ppp) REVERT: B 46 MET cc_start: 0.8326 (mmm) cc_final: 0.7905 (mmm) REVERT: B 117 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7939 (tm-30) REVERT: B 443 MET cc_start: 0.7484 (mmp) cc_final: 0.7084 (ppp) REVERT: C 28 GLU cc_start: 0.7635 (tp30) cc_final: 0.7386 (tp30) REVERT: C 271 ILE cc_start: 0.8293 (mm) cc_final: 0.8056 (mm) REVERT: C 323 ILE cc_start: 0.7259 (pt) cc_final: 0.7044 (mm) REVERT: C 341 THR cc_start: 0.8090 (p) cc_final: 0.7838 (t) REVERT: C 359 MET cc_start: 0.6942 (mtp) cc_final: 0.6738 (mtt) REVERT: D 81 THR cc_start: 0.8818 (p) cc_final: 0.8573 (p) REVERT: D 141 GLU cc_start: 0.8376 (tt0) cc_final: 0.8101 (tp30) REVERT: D 176 THR cc_start: 0.6846 (p) cc_final: 0.6329 (t) REVERT: D 223 LYS cc_start: 0.7366 (mptt) cc_final: 0.6282 (tttp) REVERT: E 47 GLU cc_start: 0.7427 (pt0) cc_final: 0.7030 (pt0) REVERT: E 100 GLU cc_start: 0.8212 (mp0) cc_final: 0.7716 (mp0) REVERT: E 102 TYR cc_start: 0.7489 (m-80) cc_final: 0.7106 (m-10) REVERT: E 308 ASP cc_start: 0.7391 (t0) cc_final: 0.6911 (t0) REVERT: E 376 LYS cc_start: 0.8972 (tptp) cc_final: 0.8757 (tppt) REVERT: E 380 GLN cc_start: 0.8425 (tt0) cc_final: 0.8181 (tp-100) REVERT: F 168 MET cc_start: 0.5692 (ptp) cc_final: 0.5338 (ptm) REVERT: F 368 LYS cc_start: 0.7731 (tttt) cc_final: 0.7329 (tttt) outliers start: 0 outliers final: 0 residues processed: 489 average time/residue: 0.3350 time to fit residues: 243.0804 Evaluate side-chains 328 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 328 time to evaluate : 2.189 ------------------------------------------------------------------------------- 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: 8.9990 chunk 70 optimal weight: 0.7980 chunk 189 optimal weight: 9.9990 chunk 155 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 228 optimal weight: 0.0870 chunk 246 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 226 optimal weight: 0.0370 chunk 77 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 203 GLN ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 GLN B 302 HIS 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 27 HIS F 245 HIS F 277 ASN ** F 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19990 Z= 0.153 Angle : 0.589 7.533 26950 Z= 0.286 Chirality : 0.043 0.168 3170 Planarity : 0.004 0.052 3434 Dihedral : 8.820 156.081 2788 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.35 % Favored : 97.61 % Rotamer: Outliers : 0.05 % Allowed : 2.24 % Favored : 97.71 % 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: -0.55 (0.15), residues: 2512 helix: -0.22 (0.15), residues: 1039 sheet: 0.56 (0.22), residues: 446 loop : -0.80 (0.17), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 283 HIS 0.012 0.001 HIS F 245 PHE 0.020 0.001 PHE D 261 TYR 0.017 0.001 TYR E 314 ARG 0.006 0.001 ARG A 276 *********************** 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 430 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 429 time to evaluate : 2.392 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: A 184 ARG cc_start: 0.6994 (mpt180) cc_final: 0.6539 (mtp180) REVERT: A 203 GLN cc_start: 0.5944 (tp-100) cc_final: 0.5726 (tp40) REVERT: A 259 MET cc_start: 0.3037 (mtt) cc_final: 0.2724 (mtm) REVERT: A 260 MET cc_start: 0.6584 (ptm) cc_final: 0.6031 (ppp) REVERT: B 46 MET cc_start: 0.8358 (mmm) cc_final: 0.7874 (mmm) REVERT: B 401 TYR cc_start: 0.7653 (t80) cc_final: 0.7293 (t80) REVERT: B 443 MET cc_start: 0.7394 (mmp) cc_final: 0.6964 (ppp) REVERT: C 341 THR cc_start: 0.8028 (p) cc_final: 0.7768 (t) REVERT: D 223 LYS cc_start: 0.7372 (mptt) cc_final: 0.6198 (tttp) REVERT: D 254 THR cc_start: 0.7719 (p) cc_final: 0.7514 (p) REVERT: D 262 SER cc_start: 0.6549 (p) cc_final: 0.6289 (t) REVERT: E 47 GLU cc_start: 0.7379 (pt0) cc_final: 0.7072 (pt0) REVERT: E 100 GLU cc_start: 0.8204 (mp0) cc_final: 0.7334 (mp0) REVERT: E 102 TYR cc_start: 0.7327 (m-80) cc_final: 0.6939 (m-10) REVERT: E 308 ASP cc_start: 0.7384 (t0) cc_final: 0.6833 (t0) REVERT: E 380 GLN cc_start: 0.8518 (tt0) cc_final: 0.8161 (tp-100) REVERT: F 168 MET cc_start: 0.5466 (ptp) cc_final: 0.5180 (ptm) REVERT: F 311 PHE cc_start: 0.7708 (t80) cc_final: 0.7297 (t80) REVERT: F 314 ARG cc_start: 0.6541 (ptp-110) cc_final: 0.6100 (ttm-80) outliers start: 1 outliers final: 0 residues processed: 429 average time/residue: 0.3285 time to fit residues: 214.0505 Evaluate side-chains 318 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 318 time to evaluate : 2.282 ------------------------------------------------------------------------------- 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: 10.0000 chunk 171 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 25 optimal weight: 8.9990 chunk 108 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 229 optimal weight: 2.9990 chunk 242 optimal weight: 0.0070 chunk 119 optimal weight: 6.9990 chunk 217 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 HIS C 229 HIS C 414 ASN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN F 404 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 19990 Z= 0.157 Angle : 0.581 9.513 26950 Z= 0.281 Chirality : 0.043 0.163 3170 Planarity : 0.003 0.034 3434 Dihedral : 8.482 149.696 2788 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.75 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % 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: -0.22 (0.16), residues: 2512 helix: 0.17 (0.16), residues: 1047 sheet: 0.73 (0.23), residues: 440 loop : -0.76 (0.18), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 283 HIS 0.008 0.001 HIS E 316 PHE 0.018 0.001 PHE D 309 TYR 0.019 0.001 TYR C 150 ARG 0.004 0.000 ARG C 404 *********************** REFINEMENT MACRO_CYCLE 4 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 413 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 413 time to evaluate : 2.152 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: A 132 GLU cc_start: 0.8198 (pm20) cc_final: 0.7513 (pp20) REVERT: A 184 ARG cc_start: 0.7107 (mpt180) cc_final: 0.6579 (mtp180) REVERT: A 203 GLN cc_start: 0.5833 (tp-100) cc_final: 0.5609 (tp40) REVERT: A 259 MET cc_start: 0.3702 (mtt) cc_final: 0.3458 (mtm) REVERT: A 260 MET cc_start: 0.6625 (ptm) cc_final: 0.6087 (ppp) REVERT: B 46 MET cc_start: 0.8306 (mmm) cc_final: 0.7898 (mmm) REVERT: B 443 MET cc_start: 0.7611 (mmp) cc_final: 0.6915 (ppp) REVERT: C 311 CYS cc_start: 0.8459 (m) cc_final: 0.8246 (m) REVERT: C 341 THR cc_start: 0.8068 (p) cc_final: 0.7751 (t) REVERT: D 141 GLU cc_start: 0.8401 (tt0) cc_final: 0.7960 (tp30) REVERT: E 47 GLU cc_start: 0.7552 (pt0) cc_final: 0.7224 (pt0) REVERT: E 100 GLU cc_start: 0.8338 (mp0) cc_final: 0.7829 (mp0) REVERT: E 102 TYR cc_start: 0.7295 (m-80) cc_final: 0.6964 (m-10) REVERT: E 308 ASP cc_start: 0.7780 (t0) cc_final: 0.7074 (t0) REVERT: E 380 GLN cc_start: 0.8367 (tt0) cc_final: 0.8149 (tp-100) REVERT: F 168 MET cc_start: 0.5296 (ptp) cc_final: 0.5071 (ptm) REVERT: F 311 PHE cc_start: 0.7648 (t80) cc_final: 0.7360 (t80) REVERT: F 314 ARG cc_start: 0.6768 (ptp-110) cc_final: 0.6330 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 413 average time/residue: 0.3487 time to fit residues: 220.9495 Evaluate side-chains 298 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 2.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 202 optimal weight: 0.0670 chunk 137 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 100 optimal weight: 0.0980 chunk 207 optimal weight: 0.6980 chunk 167 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 217 optimal weight: 0.7980 chunk 61 optimal weight: 0.4980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 HIS C 229 HIS C 247 ASN ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN F 344 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19990 Z= 0.141 Angle : 0.580 8.623 26950 Z= 0.278 Chirality : 0.043 0.168 3170 Planarity : 0.003 0.057 3434 Dihedral : 8.043 142.741 2788 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.95 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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: 0.06 (0.16), residues: 2512 helix: 0.45 (0.16), residues: 1045 sheet: 0.83 (0.23), residues: 450 loop : -0.66 (0.18), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 283 HIS 0.012 0.001 HIS C 156 PHE 0.026 0.001 PHE D 123 TYR 0.016 0.001 TYR E 314 ARG 0.007 0.000 ARG F 372 *********************** REFINEMENT MACRO_CYCLE 5 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 405 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 405 time to evaluate : 2.359 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: A 132 GLU cc_start: 0.8139 (pm20) cc_final: 0.7505 (pp20) REVERT: A 184 ARG cc_start: 0.7096 (mpt180) cc_final: 0.6557 (mtm180) REVERT: A 203 GLN cc_start: 0.5859 (tp-100) cc_final: 0.5656 (tp40) REVERT: A 259 MET cc_start: 0.3803 (mtt) cc_final: 0.3430 (mtm) REVERT: A 260 MET cc_start: 0.6758 (ptm) cc_final: 0.6154 (ppp) REVERT: B 46 MET cc_start: 0.8249 (mmm) cc_final: 0.8037 (mmm) REVERT: B 443 MET cc_start: 0.7594 (mmp) cc_final: 0.6854 (ppp) REVERT: C 247 ASN cc_start: 0.7693 (t160) cc_final: 0.7427 (m-40) REVERT: D 141 GLU cc_start: 0.8386 (tt0) cc_final: 0.8027 (tp30) REVERT: D 314 ARG cc_start: 0.7105 (mmt180) cc_final: 0.6859 (mmt90) REVERT: E 47 GLU cc_start: 0.7427 (pt0) cc_final: 0.7058 (pt0) REVERT: E 100 GLU cc_start: 0.8386 (mp0) cc_final: 0.7896 (mp0) REVERT: E 102 TYR cc_start: 0.7183 (m-80) cc_final: 0.6795 (m-10) REVERT: E 168 LYS cc_start: 0.7857 (tttt) cc_final: 0.7547 (mptt) REVERT: E 308 ASP cc_start: 0.7673 (t0) cc_final: 0.6983 (t0) REVERT: E 359 MET cc_start: 0.8521 (ttt) cc_final: 0.8014 (ttt) REVERT: E 380 GLN cc_start: 0.8363 (tt0) cc_final: 0.8010 (tp-100) REVERT: F 168 MET cc_start: 0.5356 (ptp) cc_final: 0.4969 (ppp) REVERT: F 314 ARG cc_start: 0.6606 (ptp-110) cc_final: 0.6271 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 405 average time/residue: 0.3196 time to fit residues: 197.3505 Evaluate side-chains 298 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 81 optimal weight: 4.9990 chunk 218 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 142 optimal weight: 5.9990 chunk 59 optimal weight: 0.2980 chunk 242 optimal weight: 2.9990 chunk 201 optimal weight: 0.0770 chunk 112 optimal weight: 0.7980 chunk 20 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 overall best weight: 1.0340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 HIS C 229 HIS C 247 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.5268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19990 Z= 0.176 Angle : 0.600 10.607 26950 Z= 0.290 Chirality : 0.043 0.163 3170 Planarity : 0.003 0.031 3434 Dihedral : 7.639 133.487 2788 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.07 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: 0.09 (0.16), residues: 2512 helix: 0.52 (0.16), residues: 1050 sheet: 0.69 (0.23), residues: 467 loop : -0.65 (0.19), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 283 HIS 0.011 0.001 HIS C 156 PHE 0.018 0.002 PHE A 312 TYR 0.026 0.001 TYR B 401 ARG 0.007 0.000 ARG F 53 *********************** REFINEMENT MACRO_CYCLE 6 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 391 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 2.187 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: A 99 SER cc_start: 0.8698 (p) cc_final: 0.8492 (p) REVERT: A 132 GLU cc_start: 0.8189 (pm20) cc_final: 0.7541 (pp20) REVERT: A 203 GLN cc_start: 0.5644 (tp-100) cc_final: 0.5408 (tp40) REVERT: A 259 MET cc_start: 0.4371 (mtt) cc_final: 0.3840 (mtm) REVERT: A 260 MET cc_start: 0.6821 (ptm) cc_final: 0.6278 (ppp) REVERT: B 443 MET cc_start: 0.7391 (mmp) cc_final: 0.6779 (ppp) REVERT: C 247 ASN cc_start: 0.7737 (t160) cc_final: 0.7417 (m-40) REVERT: C 264 MET cc_start: 0.4044 (ppp) cc_final: 0.3729 (ppp) REVERT: D 141 GLU cc_start: 0.8352 (tt0) cc_final: 0.7788 (tp30) REVERT: D 314 ARG cc_start: 0.7207 (mmt180) cc_final: 0.6988 (mmt90) REVERT: D 404 GLN cc_start: 0.7915 (mt0) cc_final: 0.7688 (mt0) REVERT: E 47 GLU cc_start: 0.7603 (pt0) cc_final: 0.7178 (pt0) REVERT: E 102 TYR cc_start: 0.7267 (m-80) cc_final: 0.6832 (m-10) REVERT: E 181 GLN cc_start: 0.8450 (tp40) cc_final: 0.8122 (tp40) REVERT: E 308 ASP cc_start: 0.7656 (t0) cc_final: 0.7153 (t0) REVERT: E 359 MET cc_start: 0.8641 (ttt) cc_final: 0.8387 (ttp) REVERT: E 380 GLN cc_start: 0.8403 (tt0) cc_final: 0.7986 (tp-100) REVERT: F 168 MET cc_start: 0.5514 (ptp) cc_final: 0.4887 (ppp) REVERT: F 301 VAL cc_start: 0.8327 (t) cc_final: 0.8038 (t) REVERT: F 311 PHE cc_start: 0.7575 (t80) cc_final: 0.7317 (t80) REVERT: F 314 ARG cc_start: 0.6782 (ptp-110) cc_final: 0.6426 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 391 average time/residue: 0.2992 time to fit residues: 179.9911 Evaluate side-chains 299 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 2.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 234 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 138 optimal weight: 0.9980 chunk 177 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 204 optimal weight: 0.6980 chunk 135 optimal weight: 8.9990 chunk 241 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 HIS ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 HIS C 229 HIS C 247 ASN C 316 HIS D 302 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.5512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19990 Z= 0.167 Angle : 0.602 10.172 26950 Z= 0.290 Chirality : 0.043 0.234 3170 Planarity : 0.003 0.032 3434 Dihedral : 7.285 129.425 2788 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.58 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % 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: 0.07 (0.16), residues: 2512 helix: 0.59 (0.16), residues: 1048 sheet: 0.61 (0.23), residues: 458 loop : -0.70 (0.18), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 283 HIS 0.011 0.001 HIS C 156 PHE 0.015 0.002 PHE D 224 TYR 0.012 0.001 TYR B 401 ARG 0.005 0.000 ARG C 404 *********************** REFINEMENT MACRO_CYCLE 7 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 380 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 380 time to evaluate : 2.215 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: A 132 GLU cc_start: 0.8204 (pm20) cc_final: 0.7510 (pp20) REVERT: A 180 LEU cc_start: 0.8373 (mm) cc_final: 0.8163 (tp) REVERT: A 259 MET cc_start: 0.4302 (mtt) cc_final: 0.3831 (mtm) REVERT: A 260 MET cc_start: 0.6889 (ptm) cc_final: 0.6475 (ppp) REVERT: B 117 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7782 (tm-30) REVERT: B 303 MET cc_start: 0.7802 (ppp) cc_final: 0.6731 (ppp) REVERT: B 401 TYR cc_start: 0.7877 (t80) cc_final: 0.7655 (t80) REVERT: C 264 MET cc_start: 0.3881 (ppp) cc_final: 0.3540 (ppp) REVERT: D 113 MET cc_start: 0.6981 (ptp) cc_final: 0.6757 (ptp) REVERT: D 141 GLU cc_start: 0.8355 (tt0) cc_final: 0.7779 (tp30) REVERT: D 167 GLU cc_start: 0.7787 (tp30) cc_final: 0.7075 (pm20) REVERT: D 303 MET cc_start: 0.7485 (tpt) cc_final: 0.7255 (tmm) REVERT: D 314 ARG cc_start: 0.7243 (mmt180) cc_final: 0.6886 (mmt90) REVERT: D 404 GLN cc_start: 0.7912 (mt0) cc_final: 0.7698 (mt0) REVERT: E 47 GLU cc_start: 0.7654 (pt0) cc_final: 0.7232 (pt0) REVERT: E 102 TYR cc_start: 0.7198 (m-80) cc_final: 0.6713 (m-10) REVERT: E 181 GLN cc_start: 0.8458 (tp40) cc_final: 0.8168 (tp40) REVERT: E 308 ASP cc_start: 0.7506 (t0) cc_final: 0.7152 (t0) REVERT: E 359 MET cc_start: 0.8684 (ttt) cc_final: 0.8415 (ttp) REVERT: E 380 GLN cc_start: 0.8498 (tt0) cc_final: 0.8153 (tp-100) REVERT: F 168 MET cc_start: 0.5562 (ptp) cc_final: 0.5149 (ptm) REVERT: F 311 PHE cc_start: 0.7507 (t80) cc_final: 0.7272 (t80) REVERT: F 314 ARG cc_start: 0.6680 (ptp-110) cc_final: 0.6428 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 380 average time/residue: 0.2830 time to fit residues: 168.0810 Evaluate side-chains 290 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 149 optimal weight: 0.0770 chunk 96 optimal weight: 4.9990 chunk 144 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 153 optimal weight: 0.6980 chunk 164 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 overall best weight: 0.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS C 156 HIS C 229 HIS C 247 ASN ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.5692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19990 Z= 0.154 Angle : 0.598 9.874 26950 Z= 0.287 Chirality : 0.043 0.312 3170 Planarity : 0.003 0.033 3434 Dihedral : 7.023 128.320 2788 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.54 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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: 0.12 (0.16), residues: 2512 helix: 0.63 (0.16), residues: 1051 sheet: 0.60 (0.24), residues: 455 loop : -0.66 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 283 HIS 0.011 0.001 HIS C 156 PHE 0.014 0.001 PHE B 261 TYR 0.024 0.001 TYR E 405 ARG 0.008 0.000 ARG F 29 *********************** REFINEMENT MACRO_CYCLE 8 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 380 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 380 time to evaluate : 2.341 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: A 132 GLU cc_start: 0.8118 (pm20) cc_final: 0.7538 (pp20) REVERT: A 180 LEU cc_start: 0.8373 (mm) cc_final: 0.8155 (tp) REVERT: A 184 ARG cc_start: 0.7040 (mpt180) cc_final: 0.6543 (mtp180) REVERT: A 259 MET cc_start: 0.3987 (mtt) cc_final: 0.3559 (mtm) REVERT: A 260 MET cc_start: 0.6778 (ptm) cc_final: 0.6507 (ppp) REVERT: B 117 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7697 (tm-30) REVERT: B 193 ILE cc_start: 0.7104 (mm) cc_final: 0.6900 (mm) REVERT: B 411 LEU cc_start: 0.8435 (mt) cc_final: 0.7552 (mt) REVERT: C 254 GLN cc_start: 0.7556 (tp-100) cc_final: 0.7318 (mm-40) REVERT: C 264 MET cc_start: 0.4072 (ppp) cc_final: 0.3760 (ppp) REVERT: D 113 MET cc_start: 0.7022 (ptp) cc_final: 0.6816 (ptp) REVERT: D 167 GLU cc_start: 0.7823 (tp30) cc_final: 0.7190 (pm20) REVERT: D 303 MET cc_start: 0.7533 (tpt) cc_final: 0.7153 (tmm) REVERT: D 314 ARG cc_start: 0.7057 (mmt180) cc_final: 0.6834 (mmt90) REVERT: D 404 GLN cc_start: 0.7922 (mt0) cc_final: 0.7690 (mt0) REVERT: E 102 TYR cc_start: 0.7175 (m-80) cc_final: 0.6726 (m-10) REVERT: E 181 GLN cc_start: 0.8464 (tp40) cc_final: 0.8183 (tp40) REVERT: E 308 ASP cc_start: 0.7589 (t0) cc_final: 0.7190 (t0) REVERT: E 380 GLN cc_start: 0.8445 (tt0) cc_final: 0.8094 (tp-100) REVERT: F 168 MET cc_start: 0.5528 (ptp) cc_final: 0.4822 (ppp) outliers start: 0 outliers final: 0 residues processed: 380 average time/residue: 0.2893 time to fit residues: 170.9404 Evaluate side-chains 294 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 2.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 220 optimal weight: 1.9990 chunk 231 optimal weight: 0.8980 chunk 211 optimal weight: 5.9990 chunk 225 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 203 optimal weight: 2.9990 chunk 213 optimal weight: 7.9990 chunk 224 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 HIS C 229 HIS ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.5991 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= 0.201 Angle : 0.638 10.018 26950 Z= 0.310 Chirality : 0.045 0.295 3170 Planarity : 0.004 0.061 3434 Dihedral : 7.049 127.781 2788 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.94 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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: -0.00 (0.16), residues: 2512 helix: 0.55 (0.16), residues: 1046 sheet: 0.45 (0.24), residues: 456 loop : -0.70 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 283 HIS 0.011 0.001 HIS C 156 PHE 0.017 0.002 PHE F 311 TYR 0.027 0.002 TYR D 172 ARG 0.008 0.000 ARG F 29 *********************** REFINEMENT MACRO_CYCLE 9 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 368 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 368 time to evaluate : 2.573 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: A 132 GLU cc_start: 0.8264 (pm20) cc_final: 0.7673 (pp20) REVERT: A 180 LEU cc_start: 0.8394 (mm) cc_final: 0.8193 (tp) REVERT: A 203 GLN cc_start: 0.6116 (tp40) cc_final: 0.5814 (tp40) REVERT: A 259 MET cc_start: 0.4203 (mtt) cc_final: 0.3952 (mtt) REVERT: A 260 MET cc_start: 0.6985 (ptm) cc_final: 0.6646 (ppp) REVERT: B 46 MET cc_start: 0.8366 (mmm) cc_final: 0.8161 (mmm) REVERT: B 117 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7833 (tm-30) REVERT: C 264 MET cc_start: 0.3783 (ppp) cc_final: 0.3466 (ppp) REVERT: D 167 GLU cc_start: 0.7866 (tp30) cc_final: 0.7215 (pm20) REVERT: D 314 ARG cc_start: 0.7239 (mmt180) cc_final: 0.6962 (mmt90) REVERT: E 102 TYR cc_start: 0.7326 (m-80) cc_final: 0.6908 (m-10) REVERT: E 181 GLN cc_start: 0.8510 (tp40) cc_final: 0.8291 (tp40) REVERT: E 308 ASP cc_start: 0.7698 (t0) cc_final: 0.7223 (t0) REVERT: E 359 MET cc_start: 0.8441 (ttt) cc_final: 0.8147 (ttt) REVERT: E 380 GLN cc_start: 0.8497 (tt0) cc_final: 0.8133 (tp-100) REVERT: F 272 VAL cc_start: 0.8478 (t) cc_final: 0.8225 (p) outliers start: 0 outliers final: 0 residues processed: 368 average time/residue: 0.2846 time to fit residues: 165.0379 Evaluate side-chains 292 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 148 optimal weight: 6.9990 chunk 238 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 165 optimal weight: 8.9990 chunk 250 optimal weight: 5.9990 chunk 230 optimal weight: 7.9990 chunk 199 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 275 GLN C 156 HIS C 229 HIS ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 HIS D 441 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.6504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19990 Z= 0.288 Angle : 0.732 12.418 26950 Z= 0.361 Chirality : 0.047 0.175 3170 Planarity : 0.004 0.034 3434 Dihedral : 7.439 129.650 2788 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.58 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % 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: -0.38 (0.16), residues: 2512 helix: 0.28 (0.16), residues: 1040 sheet: 0.13 (0.23), residues: 492 loop : -0.90 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 283 HIS 0.011 0.002 HIS C 156 PHE 0.021 0.002 PHE A 116 TYR 0.031 0.002 TYR B 401 ARG 0.012 0.001 ARG B 374 ********************** REFINEMENT MACRO_CYCLE 10 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 339 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 2.493 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: A 203 GLN cc_start: 0.5902 (tp40) cc_final: 0.5624 (tp40) REVERT: A 209 TYR cc_start: 0.7153 (m-80) cc_final: 0.6552 (m-10) REVERT: A 259 MET cc_start: 0.3775 (mtt) cc_final: 0.3467 (mtt) REVERT: A 260 MET cc_start: 0.6982 (ptm) cc_final: 0.6711 (ppp) REVERT: B 46 MET cc_start: 0.8449 (mmm) cc_final: 0.8185 (mmm) REVERT: C 311 CYS cc_start: 0.8417 (m) cc_final: 0.8205 (m) REVERT: C 359 MET cc_start: 0.7372 (mtt) cc_final: 0.6783 (mtt) REVERT: D 141 GLU cc_start: 0.8292 (tt0) cc_final: 0.8032 (tt0) REVERT: D 167 GLU cc_start: 0.7930 (tp30) cc_final: 0.7198 (pm20) REVERT: D 224 PHE cc_start: 0.5472 (p90) cc_final: 0.4885 (p90) REVERT: E 21 VAL cc_start: 0.7140 (p) cc_final: 0.6924 (p) REVERT: E 102 TYR cc_start: 0.7630 (m-80) cc_final: 0.7174 (m-10) REVERT: E 113 MET cc_start: 0.7913 (tmm) cc_final: 0.7697 (tmm) REVERT: E 308 ASP cc_start: 0.7953 (t0) cc_final: 0.7674 (t0) REVERT: E 359 MET cc_start: 0.8477 (ttt) cc_final: 0.8107 (ttt) REVERT: E 380 GLN cc_start: 0.8590 (tt0) cc_final: 0.8170 (tp-100) REVERT: F 246 GLU cc_start: 0.8870 (pm20) cc_final: 0.8663 (pm20) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.2791 time to fit residues: 149.6150 Evaluate side-chains 276 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 2.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 158 optimal weight: 0.5980 chunk 212 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 183 optimal weight: 0.0570 chunk 29 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 199 optimal weight: 0.0870 chunk 83 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 GLN C 247 ASN ** C 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 ASN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 233 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.130758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.115195 restraints weight = 44771.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.117521 restraints weight = 27290.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.119129 restraints weight = 18652.342| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3857 r_free = 0.3857 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3858 r_free = 0.3858 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.6479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19990 Z= 0.162 Angle : 0.643 9.734 26950 Z= 0.309 Chirality : 0.044 0.177 3170 Planarity : 0.003 0.042 3434 Dihedral : 7.026 124.190 2788 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.18 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: -0.20 (0.16), residues: 2512 helix: 0.45 (0.16), residues: 1051 sheet: 0.19 (0.23), residues: 487 loop : -0.84 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 283 HIS 0.006 0.001 HIS A 316 PHE 0.017 0.001 PHE B 261 TYR 0.029 0.001 TYR B 401 ARG 0.008 0.000 ARG F 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4423.35 seconds wall clock time: 80 minutes 19.51 seconds (4819.51 seconds total)