Starting phenix.real_space_refine on Fri Feb 16 02:53:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ogr_12886/02_2024/7ogr_12886.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ogr_12886/02_2024/7ogr_12886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ogr_12886/02_2024/7ogr_12886.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ogr_12886/02_2024/7ogr_12886.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ogr_12886/02_2024/7ogr_12886.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ogr_12886/02_2024/7ogr_12886.pdb" } resolution = 3.0 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= 0.004 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 Zn 1 6.06 5 S 73 5.16 5 C 9010 2.51 5 N 2432 2.21 5 O 2619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 303": "OD1" <-> "OD2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "B ASP 346": "OD1" <-> "OD2" Residue "B GLU 440": "OE1" <-> "OE2" Residue "B ASP 484": "OD1" <-> "OD2" Residue "C ARG 7": "NH1" <-> "NH2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "C ARG 92": "NH1" <-> "NH2" Residue "C GLU 118": "OE1" <-> "OE2" Residue "C GLU 144": "OE1" <-> "OE2" Residue "C GLU 182": "OE1" <-> "OE2" Residue "C ARG 194": "NH1" <-> "NH2" Residue "C ARG 209": "NH1" <-> "NH2" Residue "C PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 234": "NH1" <-> "NH2" Residue "C ARG 243": "NH1" <-> "NH2" Residue "C ARG 257": "NH1" <-> "NH2" Residue "C ARG 264": "NH1" <-> "NH2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "C ASP 280": "OD1" <-> "OD2" Residue "C ARG 285": "NH1" <-> "NH2" Residue "C ARG 288": "NH1" <-> "NH2" Residue "C TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 314": "NH1" <-> "NH2" Residue "C ARG 321": "NH1" <-> "NH2" Residue "C ARG 326": "NH1" <-> "NH2" Residue "C ARG 327": "NH1" <-> "NH2" Residue "C ASP 329": "OD1" <-> "OD2" Residue "C ARG 339": "NH1" <-> "NH2" Residue "C ASP 352": "OD1" <-> "OD2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 359": "NH1" <-> "NH2" Residue "C ARG 362": "NH1" <-> "NH2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C ARG 370": "NH1" <-> "NH2" Residue "C ARG 414": "NH1" <-> "NH2" Residue "C ARG 426": "NH1" <-> "NH2" Residue "C ARG 427": "NH1" <-> "NH2" Residue "C ARG 432": "NH1" <-> "NH2" Residue "C ARG 443": "NH1" <-> "NH2" Residue "C ASP 444": "OD1" <-> "OD2" Residue "C ARG 450": "NH1" <-> "NH2" Residue "C GLU 452": "OE1" <-> "OE2" Residue "C ASP 477": "OD1" <-> "OD2" Residue "C ARG 543": "NH1" <-> "NH2" Residue "C ARG 552": "NH1" <-> "NH2" Residue "C ASP 563": "OD1" <-> "OD2" Residue "C GLU 652": "OE1" <-> "OE2" Residue "D TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 72": "NH1" <-> "NH2" Residue "D GLU 85": "OE1" <-> "OE2" Residue "D ARG 88": "NH1" <-> "NH2" Residue "D ASP 114": "OD1" <-> "OD2" Residue "D TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "D ARG 216": "NH1" <-> "NH2" Residue "D ASP 225": "OD1" <-> "OD2" Residue "D GLU 248": "OE1" <-> "OE2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D GLU 261": "OE1" <-> "OE2" Residue "D ARG 264": "NH1" <-> "NH2" Residue "D ARG 282": "NH1" <-> "NH2" Residue "D ASP 287": "OD1" <-> "OD2" Residue "D ARG 322": "NH1" <-> "NH2" Residue "D ARG 356": "NH1" <-> "NH2" Residue "E ARG 33": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ARG 80": "NH1" <-> "NH2" Residue "E ARG 86": "NH1" <-> "NH2" Residue "E ARG 121": "NH1" <-> "NH2" Residue "E PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "E GLU 345": "OE1" <-> "OE2" Residue "E GLU 346": "OE1" <-> "OE2" Residue "E GLU 444": "OE1" <-> "OE2" Residue "E ARG 510": "NH1" <-> "NH2" Residue "E GLU 527": "OE1" <-> "OE2" Residue "E ARG 530": "NH1" <-> "NH2" Residue "E ARG 541": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14135 Number of models: 1 Model: "" Number of chains: 7 Chain: "X" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 160 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "A" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1527 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 11, 'TRANS': 178} Chain breaks: 1 Chain: "B" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1565 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 9, 'TRANS': 187} Chain breaks: 1 Chain: "C" Number of atoms: 4875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4875 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 35, 'TRANS': 576} Chain breaks: 1 Chain: "D" Number of atoms: 3023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 3023 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 14, 'TRANS': 358} Chain breaks: 2 Chain: "E" Number of atoms: 2984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2984 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 16, 'TRANS': 354} Chain breaks: 2 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10491 SG CYS D 288 16.948 82.058 18.253 1.00 82.42 S ATOM 10896 SG CYS D 341 17.363 79.547 21.885 1.00 84.63 S ATOM 10918 SG CYS D 350 19.774 82.408 19.784 1.00 76.18 S ATOM 10939 SG CYS D 353 17.808 83.449 21.085 1.00 67.76 S Time building chain proxies: 8.53, per 1000 atoms: 0.60 Number of scatterers: 14135 At special positions: 0 Unit cell: (107.1, 135.15, 114.75, 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) Zn 1 29.99 S 73 16.00 O 2619 8.00 N 2432 7.00 C 9010 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: 4.90 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 288 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 341 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 353 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 350 " Number of angles added : 6 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3346 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 17 sheets defined 41.5% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'X' and resid 4 through 12 Processing helix chain 'X' and resid 18 through 25 Processing helix chain 'A' and resid 313 through 321 removed outlier: 3.670A pdb=" N GLN A 319 " --> pdb=" O GLY A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 332 removed outlier: 3.664A pdb=" N ASN A 327 " --> pdb=" O TYR A 323 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS A 328 " --> pdb=" O HIS A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 347 removed outlier: 3.657A pdb=" N ASN A 347 " --> pdb=" O PHE A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 365 Processing helix chain 'A' and resid 430 through 437 removed outlier: 3.604A pdb=" N THR A 434 " --> pdb=" O ASP A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 474 removed outlier: 3.902A pdb=" N ILE A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TRP A 472 " --> pdb=" O THR A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 removed outlier: 3.604A pdb=" N LEU A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 322 removed outlier: 3.673A pdb=" N ALA B 322 " --> pdb=" O TYR B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 331 Processing helix chain 'B' and resid 337 through 346 removed outlier: 3.544A pdb=" N ILE B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 353 removed outlier: 3.532A pdb=" N THR B 351 " --> pdb=" O CYS B 347 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR B 353 " --> pdb=" O ALA B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 367 removed outlier: 3.504A pdb=" N ILE B 361 " --> pdb=" O TYR B 357 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 380 removed outlier: 3.551A pdb=" N PHE B 377 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER B 378 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE B 380 " --> pdb=" O PHE B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 399 removed outlier: 3.617A pdb=" N HIS B 387 " --> pdb=" O ASN B 383 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER B 394 " --> pdb=" O ALA B 390 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.809A pdb=" N MET B 408 " --> pdb=" O ALA B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 442 removed outlier: 3.733A pdb=" N GLU B 440 " --> pdb=" O ASP B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 474 removed outlier: 4.114A pdb=" N ALA B 465 " --> pdb=" O ILE B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 490 Processing helix chain 'B' and resid 504 through 520 Processing helix chain 'C' and resid 16 through 20 Processing helix chain 'C' and resid 27 through 38 removed outlier: 3.647A pdb=" N MET C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL C 35 " --> pdb=" O GLY C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 removed outlier: 3.651A pdb=" N GLU C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 138 Processing helix chain 'C' and resid 189 through 193 removed outlier: 3.664A pdb=" N LYS C 193 " --> pdb=" O LYS C 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 189 through 193' Processing helix chain 'C' and resid 249 through 254 Processing helix chain 'C' and resid 255 through 261 removed outlier: 3.676A pdb=" N ARG C 260 " --> pdb=" O PRO C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 327 removed outlier: 3.629A pdb=" N TYR C 305 " --> pdb=" O GLN C 301 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N HIS C 308 " --> pdb=" O LYS C 304 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR C 312 " --> pdb=" O HIS C 308 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU C 317 " --> pdb=" O TYR C 313 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG C 326 " --> pdb=" O GLY C 322 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG C 327 " --> pdb=" O LEU C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 348 removed outlier: 3.604A pdb=" N ARG C 339 " --> pdb=" O GLU C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 422 No H-bonds generated for 'chain 'C' and resid 420 through 422' Processing helix chain 'C' and resid 423 through 428 Processing helix chain 'C' and resid 430 through 453 removed outlier: 3.592A pdb=" N TYR C 434 " --> pdb=" O TYR C 430 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA C 453 " --> pdb=" O LEU C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 470 removed outlier: 3.630A pdb=" N ASN C 467 " --> pdb=" O GLN C 463 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER C 468 " --> pdb=" O GLN C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 491 removed outlier: 3.696A pdb=" N VAL C 476 " --> pdb=" O ASN C 472 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR C 478 " --> pdb=" O GLN C 474 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE C 489 " --> pdb=" O GLY C 485 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE C 490 " --> pdb=" O PHE C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 498 Processing helix chain 'C' and resid 504 through 512 removed outlier: 3.581A pdb=" N VAL C 508 " --> pdb=" O PRO C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 538 Processing helix chain 'C' and resid 634 through 640 Processing helix chain 'C' and resid 643 through 656 Processing helix chain 'D' and resid 15 through 20 Processing helix chain 'D' and resid 40 through 49 removed outlier: 3.858A pdb=" N LEU D 46 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU D 49 " --> pdb=" O LYS D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 51 No H-bonds generated for 'chain 'D' and resid 50 through 51' Processing helix chain 'D' and resid 52 through 56 removed outlier: 3.658A pdb=" N HIS D 56 " --> pdb=" O PRO D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 67 removed outlier: 3.564A pdb=" N HIS D 66 " --> pdb=" O PRO D 63 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS D 67 " --> pdb=" O SER D 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 63 through 67' Processing helix chain 'D' and resid 92 through 109 removed outlier: 3.536A pdb=" N HIS D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU D 98 " --> pdb=" O MET D 94 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER D 109 " --> pdb=" O ILE D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 137 removed outlier: 3.665A pdb=" N LEU D 118 " --> pdb=" O ASP D 114 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL D 135 " --> pdb=" O ASN D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 153 removed outlier: 4.011A pdb=" N ILE D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA D 150 " --> pdb=" O MET D 146 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU D 151 " --> pdb=" O PHE D 147 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL D 152 " --> pdb=" O ASP D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 161 removed outlier: 3.538A pdb=" N ALA D 161 " --> pdb=" O LYS D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 174 Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.778A pdb=" N VAL D 180 " --> pdb=" O SER D 176 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL D 183 " --> pdb=" O LYS D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 201 Processing helix chain 'D' and resid 205 through 214 removed outlier: 3.515A pdb=" N LEU D 209 " --> pdb=" O LYS D 205 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA D 212 " --> pdb=" O GLN D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 261 removed outlier: 4.240A pdb=" N THR D 253 " --> pdb=" O SER D 249 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS D 254 " --> pdb=" O ARG D 250 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA D 255 " --> pdb=" O SER D 251 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU D 256 " --> pdb=" O GLY D 252 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR D 258 " --> pdb=" O LYS D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 277 removed outlier: 4.170A pdb=" N ASN D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG D 271 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LYS D 272 " --> pdb=" O TYR D 268 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER D 273 " --> pdb=" O PHE D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 307 removed outlier: 3.606A pdb=" N LYS D 307 " --> pdb=" O LYS D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 355 Processing helix chain 'D' and resid 356 through 361 removed outlier: 3.631A pdb=" N ILE D 359 " --> pdb=" O ARG D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 381 removed outlier: 3.828A pdb=" N LYS D 378 " --> pdb=" O SER D 374 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE D 379 " --> pdb=" O MET D 375 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR D 380 " --> pdb=" O GLY D 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 13 Processing helix chain 'E' and resid 18 through 23 Processing helix chain 'E' and resid 25 through 30 Processing helix chain 'E' and resid 40 through 53 removed outlier: 3.784A pdb=" N ILE E 52 " --> pdb=" O SER E 48 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 56 No H-bonds generated for 'chain 'E' and resid 54 through 56' Processing helix chain 'E' and resid 70 through 79 Processing helix chain 'E' and resid 323 through 337 removed outlier: 4.233A pdb=" N ASN E 327 " --> pdb=" O LYS E 323 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS E 331 " --> pdb=" O ASN E 327 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN E 337 " --> pdb=" O HIS E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 366 removed outlier: 3.804A pdb=" N LEU E 361 " --> pdb=" O ILE E 357 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET E 365 " --> pdb=" O LEU E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 372 removed outlier: 3.523A pdb=" N HIS E 371 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU E 372 " --> pdb=" O ALA E 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 368 through 372' Processing helix chain 'E' and resid 394 through 410 Processing helix chain 'E' and resid 417 through 429 Processing helix chain 'E' and resid 488 through 493 Processing helix chain 'E' and resid 518 through 522 removed outlier: 3.574A pdb=" N GLY E 521 " --> pdb=" O GLY E 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 540 Processing sheet with id=AA1, first strand: chain 'A' and resid 294 through 300 removed outlier: 7.591A pdb=" N ILE A 404 " --> pdb=" O ARG A 295 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL A 297 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N MET A 406 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N THR A 299 " --> pdb=" O MET A 406 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE A 312 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL A 395 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN A 388 " --> pdb=" O PHE A 376 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET A 372 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 296 " --> pdb=" O LEU A 423 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 410 through 412 removed outlier: 3.961A pdb=" N TRP B 478 " --> pdb=" O LEU B 499 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AA4, first strand: chain 'C' and resid 52 through 53 Processing sheet with id=AA5, first strand: chain 'C' and resid 67 through 68 removed outlier: 3.667A pdb=" N VAL C 67 " --> pdb=" O ILE C 152 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 111 through 116 removed outlier: 6.672A pdb=" N THR C 98 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL C 78 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE C 100 " --> pdb=" O LEU C 76 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 119 through 123 removed outlier: 4.614A pdb=" N HIS C 122 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N PHE C 126 " --> pdb=" O HIS C 122 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 184 through 188 removed outlier: 6.915A pdb=" N PHE C 185 " --> pdb=" O CYS C 398 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N VAL C 400 " --> pdb=" O PHE C 185 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA C 187 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LYS C 386 " --> pdb=" O LEU C 575 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 198 through 206 removed outlier: 6.374A pdb=" N ARG C 370 " --> pdb=" O ILE C 283 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE C 283 " --> pdb=" O ARG C 370 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLU C 372 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE C 281 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR C 374 " --> pdb=" O ILE C 279 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 211 through 213 removed outlier: 3.566A pdb=" N VAL C 270 " --> pdb=" O ILE C 239 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ALA C 241 " --> pdb=" O ARG C 268 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG C 268 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 357 through 358 Processing sheet with id=AB3, first strand: chain 'C' and resid 550 through 552 Processing sheet with id=AB4, first strand: chain 'D' and resid 4 through 7 removed outlier: 6.005A pdb=" N ASN D 4 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N GLU D 30 " --> pdb=" O ASN D 4 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR D 6 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER D 39 " --> pdb=" O HIS D 27 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 294 through 297 removed outlier: 3.517A pdb=" N ALA D 294 " --> pdb=" O PHE D 335 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 67 through 68 removed outlier: 3.756A pdb=" N TYR E 96 " --> pdb=" O LEU E 116 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 126 through 127 Processing sheet with id=AB8, first strand: chain 'E' and resid 144 through 145 removed outlier: 4.199A pdb=" N ILE E 152 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU E 159 " --> pdb=" O ILE E 152 " (cutoff:3.500A) 451 hydrogen bonds defined for protein. 1275 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: 3.82 Time building geometry restraints manager: 5.38 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: 4599 1.34 - 1.46: 3122 1.46 - 1.58: 6606 1.58 - 1.70: 0 1.70 - 1.81: 130 Bond restraints: 14457 Sorted by residual: bond pdb=" N ARG E 541 " pdb=" CA ARG E 541 " ideal model delta sigma weight residual 1.466 1.501 -0.035 1.36e-02 5.41e+03 6.47e+00 bond pdb=" C ASN C 290 " pdb=" N PRO C 291 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.15e+00 bond pdb=" C PHE E 540 " pdb=" N ARG E 541 " ideal model delta sigma weight residual 1.334 1.366 -0.032 1.58e-02 4.01e+03 4.08e+00 bond pdb=" C ALA C 141 " pdb=" N PRO C 142 " ideal model delta sigma weight residual 1.337 1.353 -0.016 9.80e-03 1.04e+04 2.67e+00 bond pdb=" CA ASP C 125 " pdb=" CB ASP C 125 " ideal model delta sigma weight residual 1.530 1.551 -0.021 1.54e-02 4.22e+03 1.81e+00 ... (remaining 14452 not shown) Histogram of bond angle deviations from ideal: 99.81 - 106.92: 493 106.92 - 114.02: 8147 114.02 - 121.12: 6853 121.12 - 128.23: 3987 128.23 - 135.33: 122 Bond angle restraints: 19602 Sorted by residual: angle pdb=" C GLN D 281 " pdb=" N ARG D 282 " pdb=" CA ARG D 282 " ideal model delta sigma weight residual 120.82 127.00 -6.18 1.47e+00 4.63e-01 1.77e+01 angle pdb=" N VAL B 367 " pdb=" CA VAL B 367 " pdb=" C VAL B 367 " ideal model delta sigma weight residual 110.21 105.81 4.40 1.13e+00 7.83e-01 1.52e+01 angle pdb=" CA GLN C 3 " pdb=" CB GLN C 3 " pdb=" CG GLN C 3 " ideal model delta sigma weight residual 114.10 121.62 -7.52 2.00e+00 2.50e-01 1.41e+01 angle pdb=" C ILE C 239 " pdb=" N PHE C 240 " pdb=" CA PHE C 240 " ideal model delta sigma weight residual 121.54 128.71 -7.17 1.91e+00 2.74e-01 1.41e+01 angle pdb=" C VAL B 367 " pdb=" N MET B 368 " pdb=" CA MET B 368 " ideal model delta sigma weight residual 122.36 127.57 -5.21 1.42e+00 4.96e-01 1.35e+01 ... (remaining 19597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 7854 17.85 - 35.71: 714 35.71 - 53.56: 96 53.56 - 71.41: 12 71.41 - 89.26: 10 Dihedral angle restraints: 8686 sinusoidal: 3500 harmonic: 5186 Sorted by residual: dihedral pdb=" CA ALA A 413 " pdb=" C ALA A 413 " pdb=" N PRO A 414 " pdb=" CA PRO A 414 " ideal model delta harmonic sigma weight residual 180.00 152.03 27.97 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA PHE E 540 " pdb=" C PHE E 540 " pdb=" N ARG E 541 " pdb=" CA ARG E 541 " ideal model delta harmonic sigma weight residual 180.00 -153.82 -26.18 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA ARG E 510 " pdb=" C ARG E 510 " pdb=" N LEU E 511 " pdb=" CA LEU E 511 " ideal model delta harmonic sigma weight residual -180.00 -154.63 -25.37 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 8683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1571 0.046 - 0.092: 442 0.092 - 0.137: 141 0.137 - 0.183: 20 0.183 - 0.229: 3 Chirality restraints: 2177 Sorted by residual: chirality pdb=" CA PHE C 240 " pdb=" N PHE C 240 " pdb=" C PHE C 240 " pdb=" CB PHE C 240 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA ASN C 290 " pdb=" N ASN C 290 " pdb=" C ASN C 290 " pdb=" CB ASN C 290 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ASP C 125 " pdb=" N ASP C 125 " pdb=" C ASP C 125 " pdb=" CB ASP C 125 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.21e-01 ... (remaining 2174 not shown) Planarity restraints: 2515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE E 540 " -0.037 2.00e-02 2.50e+03 7.19e-02 5.16e+01 pdb=" C PHE E 540 " 0.124 2.00e-02 2.50e+03 pdb=" O PHE E 540 " -0.047 2.00e-02 2.50e+03 pdb=" N ARG E 541 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 141 " -0.040 5.00e-02 4.00e+02 6.08e-02 5.91e+00 pdb=" N PRO C 142 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 142 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 142 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 255 " 0.040 5.00e-02 4.00e+02 6.00e-02 5.75e+00 pdb=" N PRO C 256 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO C 256 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 256 " 0.033 5.00e-02 4.00e+02 ... (remaining 2512 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4292 2.83 - 3.35: 11704 3.35 - 3.86: 22749 3.86 - 4.38: 26495 4.38 - 4.90: 45733 Nonbonded interactions: 110973 Sorted by model distance: nonbonded pdb=" OE1 GLU D 166 " pdb=" OG1 THR D 168 " model vdw 2.309 2.440 nonbonded pdb=" O ALA D 161 " pdb=" OG SER D 176 " model vdw 2.324 2.440 nonbonded pdb=" OH TYR C 434 " pdb=" O ILE D 236 " model vdw 2.343 2.440 nonbonded pdb=" OH TYR C 82 " pdb=" O ILE C 281 " model vdw 2.347 2.440 nonbonded pdb=" OH TYR B 480 " pdb=" O PRO B 483 " model vdw 2.355 2.440 ... (remaining 110968 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.710 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: 0.010 Extract box with map and model: 4.400 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 39.190 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 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:10.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 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 : 0.003 0.048 14457 Z= 0.201 Angle : 0.690 10.328 19602 Z= 0.393 Chirality : 0.048 0.229 2177 Planarity : 0.006 0.072 2515 Dihedral : 13.646 89.265 5340 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.69 (0.14), residues: 1749 helix: -3.84 (0.10), residues: 700 sheet: -1.71 (0.40), residues: 146 loop : -2.72 (0.16), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 445 HIS 0.011 0.001 HIS C 436 PHE 0.028 0.002 PHE E 151 TYR 0.015 0.001 TYR D 311 ARG 0.005 0.000 ARG D 159 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 318 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 327 ASN cc_start: 0.7738 (t0) cc_final: 0.7409 (t0) REVERT: B 467 GLN cc_start: 0.7808 (tp40) cc_final: 0.7448 (mt0) REVERT: B 476 SER cc_start: 0.8637 (t) cc_final: 0.8317 (t) REVERT: B 498 VAL cc_start: 0.8232 (t) cc_final: 0.7958 (p) REVERT: C 504 PRO cc_start: 0.6326 (Cg_endo) cc_final: 0.5943 (Cg_exo) REVERT: D 237 ASP cc_start: 0.7688 (p0) cc_final: 0.7180 (p0) REVERT: D 312 GLN cc_start: 0.6001 (tm-30) cc_final: 0.5329 (tp40) REVERT: D 351 MET cc_start: 0.8276 (tpp) cc_final: 0.8073 (mmm) REVERT: D 375 MET cc_start: 0.8259 (ttm) cc_final: 0.7993 (ttp) REVERT: D 377 ASP cc_start: 0.7689 (m-30) cc_final: 0.7331 (m-30) outliers start: 0 outliers final: 1 residues processed: 318 average time/residue: 1.4417 time to fit residues: 496.0363 Evaluate side-chains 194 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 502 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 159 optimal weight: 8.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 HIS A 311 HIS A 319 GLN A 347 ASN ** A 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 ASN B 342 GLN ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN C 65 HIS C 245 HIS C 345 GLN C 474 GLN C 643 ASN D 66 HIS D 71 ASN D 83 ASN D 104 ASN D 127 ASN D 155 HIS D 189 GLN D 208 GLN D 274 GLN D 278 GLN ** D 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 ASN E 123 ASN E 537 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14457 Z= 0.215 Angle : 0.575 14.248 19602 Z= 0.296 Chirality : 0.043 0.164 2177 Planarity : 0.004 0.048 2515 Dihedral : 5.039 23.603 1933 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.69 % Allowed : 12.97 % Favored : 84.35 % 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: -3.09 (0.17), residues: 1749 helix: -1.99 (0.16), residues: 690 sheet: -1.22 (0.42), residues: 143 loop : -2.23 (0.17), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 22 HIS 0.006 0.001 HIS C 436 PHE 0.027 0.002 PHE C 240 TYR 0.014 0.001 TYR C 487 ARG 0.005 0.000 ARG E 525 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 201 time to evaluate : 1.746 Fit side-chains revert: symmetry clash REVERT: A 327 ASN cc_start: 0.8164 (t0) cc_final: 0.7833 (t0) REVERT: B 472 SER cc_start: 0.8475 (OUTLIER) cc_final: 0.8216 (m) REVERT: B 476 SER cc_start: 0.8748 (t) cc_final: 0.8490 (t) REVERT: B 492 GLN cc_start: 0.6990 (OUTLIER) cc_final: 0.6467 (tt0) REVERT: B 498 VAL cc_start: 0.8042 (t) cc_final: 0.7718 (p) REVERT: C 160 LYS cc_start: 0.7651 (mtpt) cc_final: 0.7446 (ttpp) REVERT: C 498 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.6480 (ptp) REVERT: D 237 ASP cc_start: 0.7793 (p0) cc_final: 0.7182 (p0) REVERT: D 302 THR cc_start: 0.7476 (p) cc_final: 0.7264 (t) REVERT: D 312 GLN cc_start: 0.5973 (tm-30) cc_final: 0.5283 (tp40) REVERT: D 351 MET cc_start: 0.8304 (tpp) cc_final: 0.8014 (mmm) REVERT: D 375 MET cc_start: 0.8360 (ttm) cc_final: 0.8128 (ttp) outliers start: 41 outliers final: 16 residues processed: 224 average time/residue: 1.4053 time to fit residues: 343.0939 Evaluate side-chains 197 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 178 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 492 GLN Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 418 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 0.9980 chunk 49 optimal weight: 0.0970 chunk 133 optimal weight: 0.0770 chunk 108 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 160 optimal weight: 0.6980 chunk 172 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 158 optimal weight: 8.9990 chunk 54 optimal weight: 0.0770 chunk 128 optimal weight: 8.9990 overall best weight: 0.3894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN ** A 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 ASN B 467 GLN B 492 GLN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 436 HIS C 463 GLN D 71 ASN D 104 ASN D 208 GLN D 274 GLN ** D 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14457 Z= 0.118 Angle : 0.476 10.988 19602 Z= 0.245 Chirality : 0.041 0.147 2177 Planarity : 0.003 0.053 2515 Dihedral : 4.452 22.014 1929 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.96 % Allowed : 16.11 % Favored : 81.93 % 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: -2.03 (0.18), residues: 1749 helix: -0.84 (0.19), residues: 692 sheet: -0.54 (0.44), residues: 136 loop : -1.88 (0.18), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 103 HIS 0.005 0.000 HIS C 436 PHE 0.020 0.001 PHE C 240 TYR 0.012 0.001 TYR E 96 ARG 0.005 0.000 ARG E 427 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 204 time to evaluate : 1.432 Fit side-chains revert: symmetry clash REVERT: A 327 ASN cc_start: 0.7853 (t0) cc_final: 0.7600 (t0) REVERT: B 467 GLN cc_start: 0.7925 (tp40) cc_final: 0.7543 (mt0) REVERT: B 472 SER cc_start: 0.8564 (p) cc_final: 0.8346 (m) REVERT: B 476 SER cc_start: 0.8617 (t) cc_final: 0.8367 (t) REVERT: B 498 VAL cc_start: 0.8029 (t) cc_final: 0.7717 (p) REVERT: C 217 TYR cc_start: 0.7454 (m-80) cc_final: 0.7252 (m-80) REVERT: D 237 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.7068 (p0) REVERT: D 312 GLN cc_start: 0.6016 (tm-30) cc_final: 0.5316 (tp40) REVERT: D 375 MET cc_start: 0.8320 (ttm) cc_final: 0.8073 (ttp) outliers start: 30 outliers final: 10 residues processed: 220 average time/residue: 1.2715 time to fit residues: 306.2766 Evaluate side-chains 193 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 182 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 349 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 8.9990 chunk 120 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 160 optimal weight: 2.9990 chunk 170 optimal weight: 8.9990 chunk 152 optimal weight: 0.0000 chunk 45 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 overall best weight: 1.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 453 HIS ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 GLN C 472 ASN C 474 GLN C 538 ASN D 13 ASN D 71 ASN D 104 ASN D 208 GLN D 274 GLN ** D 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14457 Z= 0.188 Angle : 0.530 10.352 19602 Z= 0.270 Chirality : 0.042 0.155 2177 Planarity : 0.004 0.051 2515 Dihedral : 4.594 22.376 1929 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.21 % Allowed : 15.98 % Favored : 80.81 % 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: -1.69 (0.19), residues: 1749 helix: -0.47 (0.19), residues: 705 sheet: -0.35 (0.44), residues: 134 loop : -1.79 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 103 HIS 0.006 0.001 HIS C 436 PHE 0.024 0.001 PHE C 240 TYR 0.013 0.001 TYR A 477 ARG 0.003 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 187 time to evaluate : 1.607 Fit side-chains revert: symmetry clash REVERT: B 476 SER cc_start: 0.8764 (t) cc_final: 0.8538 (t) REVERT: B 492 GLN cc_start: 0.6910 (OUTLIER) cc_final: 0.6532 (tt0) REVERT: B 498 VAL cc_start: 0.8052 (t) cc_final: 0.7670 (p) REVERT: C 160 LYS cc_start: 0.7820 (mtpt) cc_final: 0.7561 (ttpp) REVERT: C 217 TYR cc_start: 0.7858 (m-80) cc_final: 0.7654 (m-80) REVERT: D 25 GLU cc_start: 0.6550 (OUTLIER) cc_final: 0.6091 (pm20) REVERT: D 304 LYS cc_start: 0.7231 (mmtt) cc_final: 0.6667 (mtpt) REVERT: D 375 MET cc_start: 0.8425 (ttm) cc_final: 0.8183 (ttp) REVERT: D 377 ASP cc_start: 0.7564 (m-30) cc_final: 0.7267 (m-30) outliers start: 49 outliers final: 21 residues processed: 213 average time/residue: 1.2824 time to fit residues: 299.4523 Evaluate side-chains 191 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 168 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 492 GLN Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 365 MET Chi-restraints excluded: chain E residue 389 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 117 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 86 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 chunk 42 optimal weight: 0.0670 chunk 57 optimal weight: 4.9990 overall best weight: 1.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 471 ASN B 467 GLN B 481 HIS ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 GLN C 3 GLN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 HIS C 463 GLN C 474 GLN D 13 ASN D 71 ASN D 208 GLN D 274 GLN ** D 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14457 Z= 0.224 Angle : 0.556 9.678 19602 Z= 0.283 Chirality : 0.043 0.165 2177 Planarity : 0.004 0.048 2515 Dihedral : 4.752 22.975 1929 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.41 % Allowed : 17.35 % Favored : 79.24 % 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: -1.55 (0.19), residues: 1749 helix: -0.35 (0.20), residues: 705 sheet: -0.51 (0.42), residues: 139 loop : -1.68 (0.19), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 240 HIS 0.007 0.001 HIS C 436 PHE 0.026 0.001 PHE C 240 TYR 0.014 0.001 TYR D 311 ARG 0.007 0.000 ARG C 543 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 172 time to evaluate : 1.628 Fit side-chains revert: symmetry clash REVERT: B 476 SER cc_start: 0.8788 (t) cc_final: 0.8529 (t) REVERT: B 498 VAL cc_start: 0.8047 (t) cc_final: 0.7643 (p) REVERT: C 160 LYS cc_start: 0.7826 (mtpt) cc_final: 0.7550 (ttpp) REVERT: C 217 TYR cc_start: 0.7908 (m-80) cc_final: 0.7699 (m-80) REVERT: D 25 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.5991 (pm20) REVERT: D 237 ASP cc_start: 0.7837 (p0) cc_final: 0.7260 (p0) REVERT: D 304 LYS cc_start: 0.7268 (mmtt) cc_final: 0.6673 (mtpt) REVERT: D 375 MET cc_start: 0.8353 (ttm) cc_final: 0.8129 (ttp) REVERT: D 377 ASP cc_start: 0.7650 (m-30) cc_final: 0.7389 (m-30) outliers start: 52 outliers final: 25 residues processed: 206 average time/residue: 1.3147 time to fit residues: 297.1598 Evaluate side-chains 188 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 162 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain E residue 17 MET Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 365 MET Chi-restraints excluded: chain E residue 389 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 170 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 14 optimal weight: 0.0470 chunk 56 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 164 optimal weight: 8.9990 overall best weight: 1.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 471 ASN B 467 GLN B 481 HIS B 492 GLN C 3 GLN C 474 GLN D 71 ASN D 208 GLN D 274 GLN ** D 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14457 Z= 0.157 Angle : 0.513 9.247 19602 Z= 0.262 Chirality : 0.042 0.167 2177 Planarity : 0.004 0.050 2515 Dihedral : 4.519 22.093 1929 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.88 % Allowed : 18.93 % Favored : 78.19 % 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: -1.20 (0.19), residues: 1749 helix: 0.06 (0.20), residues: 689 sheet: -0.52 (0.43), residues: 139 loop : -1.53 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 26 HIS 0.005 0.001 HIS C 436 PHE 0.023 0.001 PHE C 240 TYR 0.013 0.001 TYR D 311 ARG 0.008 0.000 ARG C 543 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 170 time to evaluate : 1.589 Fit side-chains revert: symmetry clash REVERT: A 327 ASN cc_start: 0.8145 (t0) cc_final: 0.7832 (t0) REVERT: B 467 GLN cc_start: 0.7923 (tp40) cc_final: 0.7557 (mt0) REVERT: B 476 SER cc_start: 0.8799 (t) cc_final: 0.8526 (t) REVERT: B 498 VAL cc_start: 0.8057 (t) cc_final: 0.7643 (p) REVERT: C 160 LYS cc_start: 0.7758 (mtpt) cc_final: 0.7465 (ttpp) REVERT: C 217 TYR cc_start: 0.7818 (m-80) cc_final: 0.7546 (m-80) REVERT: C 406 MET cc_start: 0.8741 (mmm) cc_final: 0.8211 (mmt) REVERT: D 25 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.5959 (pm20) REVERT: D 304 LYS cc_start: 0.7266 (mmtt) cc_final: 0.6675 (mtpt) REVERT: D 375 MET cc_start: 0.8341 (ttm) cc_final: 0.8096 (ttp) outliers start: 44 outliers final: 24 residues processed: 199 average time/residue: 1.2817 time to fit residues: 280.0256 Evaluate side-chains 188 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 163 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 514 ASP Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain E residue 17 MET Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 365 MET Chi-restraints excluded: chain E residue 389 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 96 optimal weight: 0.2980 chunk 143 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 169 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 103 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 471 ASN B 481 HIS B 492 GLN C 3 GLN C 474 GLN D 71 ASN D 104 ASN D 208 GLN D 274 GLN ** D 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14457 Z= 0.145 Angle : 0.503 9.037 19602 Z= 0.255 Chirality : 0.042 0.154 2177 Planarity : 0.003 0.051 2515 Dihedral : 4.361 21.511 1929 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.49 % Allowed : 19.32 % Favored : 78.19 % 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: -0.97 (0.20), residues: 1749 helix: 0.31 (0.20), residues: 691 sheet: -0.31 (0.44), residues: 136 loop : -1.46 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 26 HIS 0.005 0.001 HIS C 436 PHE 0.022 0.001 PHE C 240 TYR 0.016 0.001 TYR C 478 ARG 0.008 0.000 ARG C 543 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 174 time to evaluate : 1.593 Fit side-chains revert: symmetry clash REVERT: A 327 ASN cc_start: 0.8066 (t0) cc_final: 0.7756 (t0) REVERT: B 476 SER cc_start: 0.8785 (t) cc_final: 0.8517 (t) REVERT: B 498 VAL cc_start: 0.8064 (t) cc_final: 0.7627 (p) REVERT: C 160 LYS cc_start: 0.7767 (mtpt) cc_final: 0.7473 (ttpp) REVERT: C 217 TYR cc_start: 0.7745 (m-80) cc_final: 0.7483 (m-80) REVERT: C 406 MET cc_start: 0.8790 (mmm) cc_final: 0.8200 (mmt) REVERT: D 25 GLU cc_start: 0.6586 (OUTLIER) cc_final: 0.5938 (pm20) REVERT: D 304 LYS cc_start: 0.7282 (mmtt) cc_final: 0.6699 (mtpt) REVERT: D 375 MET cc_start: 0.8347 (ttm) cc_final: 0.8113 (ttp) outliers start: 38 outliers final: 24 residues processed: 197 average time/residue: 1.2752 time to fit residues: 275.4249 Evaluate side-chains 190 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 165 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 514 ASP Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 365 MET Chi-restraints excluded: chain E residue 389 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 0.4980 chunk 101 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 107 optimal weight: 0.4980 chunk 115 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 chunk 154 optimal weight: 8.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 388 GLN A 471 ASN B 467 GLN B 481 HIS B 492 GLN C 3 GLN C 463 GLN C 474 GLN D 71 ASN D 208 GLN D 274 GLN ** D 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14457 Z= 0.204 Angle : 0.553 10.164 19602 Z= 0.281 Chirality : 0.043 0.163 2177 Planarity : 0.004 0.048 2515 Dihedral : 4.611 22.530 1929 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.62 % Allowed : 19.52 % Favored : 77.87 % 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: -1.08 (0.20), residues: 1749 helix: 0.24 (0.20), residues: 696 sheet: -0.63 (0.41), residues: 151 loop : -1.52 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 240 HIS 0.007 0.001 HIS C 436 PHE 0.025 0.001 PHE C 240 TYR 0.013 0.001 TYR D 311 ARG 0.007 0.000 ARG C 543 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 173 time to evaluate : 1.762 Fit side-chains revert: symmetry clash REVERT: B 476 SER cc_start: 0.8786 (t) cc_final: 0.8513 (t) REVERT: B 498 VAL cc_start: 0.8094 (t) cc_final: 0.7656 (p) REVERT: C 160 LYS cc_start: 0.7813 (mtpt) cc_final: 0.7476 (ttpp) REVERT: C 406 MET cc_start: 0.8726 (mmm) cc_final: 0.8165 (mmt) REVERT: D 25 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6098 (pm20) REVERT: D 304 LYS cc_start: 0.7302 (mmtt) cc_final: 0.6756 (mtpt) REVERT: D 375 MET cc_start: 0.8311 (ttm) cc_final: 0.8090 (ttp) outliers start: 40 outliers final: 26 residues processed: 198 average time/residue: 1.3008 time to fit residues: 282.5353 Evaluate side-chains 193 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 166 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 488 LYS Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 514 ASP Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 365 MET Chi-restraints excluded: chain E residue 389 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 158 optimal weight: 0.0010 chunk 95 optimal weight: 0.9980 chunk 68 optimal weight: 0.0670 chunk 124 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 chunk 157 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.6128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 471 ASN B 467 GLN B 481 HIS B 492 GLN C 3 GLN C 474 GLN D 71 ASN D 208 GLN D 274 GLN ** D 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14457 Z= 0.211 Angle : 0.559 11.876 19602 Z= 0.284 Chirality : 0.043 0.163 2177 Planarity : 0.004 0.048 2515 Dihedral : 4.652 22.721 1929 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.36 % Allowed : 19.91 % Favored : 77.73 % 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: -1.05 (0.20), residues: 1749 helix: 0.28 (0.20), residues: 691 sheet: -0.49 (0.44), residues: 137 loop : -1.52 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 26 HIS 0.007 0.001 HIS C 436 PHE 0.026 0.001 PHE C 240 TYR 0.015 0.001 TYR C 478 ARG 0.009 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 172 time to evaluate : 1.667 Fit side-chains revert: symmetry clash REVERT: B 476 SER cc_start: 0.8783 (t) cc_final: 0.8499 (t) REVERT: B 498 VAL cc_start: 0.8115 (t) cc_final: 0.7768 (p) REVERT: C 406 MET cc_start: 0.8746 (mmm) cc_final: 0.8151 (mmt) REVERT: D 25 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6287 (pm20) REVERT: D 304 LYS cc_start: 0.7299 (mmtt) cc_final: 0.6738 (mtpt) REVERT: D 375 MET cc_start: 0.8290 (ttm) cc_final: 0.8068 (ttp) outliers start: 36 outliers final: 27 residues processed: 197 average time/residue: 1.2680 time to fit residues: 274.0092 Evaluate side-chains 194 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 166 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 488 LYS Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 514 ASP Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 365 MET Chi-restraints excluded: chain E residue 389 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 116 optimal weight: 6.9990 chunk 175 optimal weight: 0.8980 chunk 161 optimal weight: 0.2980 chunk 139 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 107 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 327 ASN A 471 ASN B 467 GLN B 481 HIS B 492 GLN C 94 ASN C 474 GLN C 495 HIS D 71 ASN D 208 GLN D 274 GLN ** D 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 14457 Z= 0.159 Angle : 0.529 10.477 19602 Z= 0.267 Chirality : 0.042 0.155 2177 Planarity : 0.004 0.050 2515 Dihedral : 4.440 22.012 1929 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.29 % Allowed : 20.24 % Favored : 77.47 % 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: -0.89 (0.20), residues: 1749 helix: 0.46 (0.20), residues: 691 sheet: -0.56 (0.40), residues: 164 loop : -1.45 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 26 HIS 0.005 0.001 HIS C 436 PHE 0.024 0.001 PHE C 240 TYR 0.014 0.001 TYR C 217 ARG 0.008 0.000 ARG E 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 172 time to evaluate : 1.607 Fit side-chains revert: symmetry clash REVERT: B 476 SER cc_start: 0.8764 (t) cc_final: 0.8479 (t) REVERT: B 498 VAL cc_start: 0.8046 (t) cc_final: 0.7599 (p) REVERT: D 25 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.6259 (pm20) REVERT: D 304 LYS cc_start: 0.7287 (mmtt) cc_final: 0.6752 (mtpt) REVERT: D 375 MET cc_start: 0.8308 (ttm) cc_final: 0.8057 (ttp) outliers start: 35 outliers final: 23 residues processed: 193 average time/residue: 1.2808 time to fit residues: 270.6468 Evaluate side-chains 190 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 166 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 488 LYS Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 514 ASP Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 365 MET Chi-restraints excluded: chain E residue 389 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.2980 chunk 42 optimal weight: 3.9990 chunk 128 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 143 optimal weight: 2.9990 chunk 17 optimal weight: 0.0040 chunk 25 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 327 ASN A 471 ASN B 467 GLN B 481 HIS B 492 GLN C 3 GLN C 94 ASN C 474 GLN D 71 ASN D 208 GLN D 274 GLN ** D 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.147993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.116563 restraints weight = 16746.336| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.66 r_work: 0.3244 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14457 Z= 0.179 Angle : 0.541 10.432 19602 Z= 0.274 Chirality : 0.042 0.156 2177 Planarity : 0.003 0.049 2515 Dihedral : 4.478 21.753 1929 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.16 % Allowed : 20.43 % Favored : 77.41 % 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: -0.90 (0.20), residues: 1749 helix: 0.43 (0.20), residues: 697 sheet: -0.58 (0.40), residues: 164 loop : -1.45 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 26 HIS 0.006 0.001 HIS C 436 PHE 0.024 0.001 PHE C 240 TYR 0.014 0.001 TYR C 217 ARG 0.008 0.000 ARG D 250 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5412.70 seconds wall clock time: 97 minutes 3.00 seconds (5823.00 seconds total)