Starting phenix.real_space_refine on Sat Aug 3 22:59:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k7a_36936/08_2024/8k7a_36936.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k7a_36936/08_2024/8k7a_36936.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k7a_36936/08_2024/8k7a_36936.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k7a_36936/08_2024/8k7a_36936.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k7a_36936/08_2024/8k7a_36936.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k7a_36936/08_2024/8k7a_36936.cif" } resolution = 4.2 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 28 5.16 5 C 5732 2.51 5 N 1464 2.21 5 O 1686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 614": "OE1" <-> "OE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 460": "OE1" <-> "OE2" Residue "B TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 576": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8918 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4427 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 12, 'TRANS': 550} Chain: "B" Number of atoms: 4427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4427 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 12, 'TRANS': 550} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.04, per 1000 atoms: 0.57 Number of scatterers: 8918 At special positions: 0 Unit cell: (82.368, 80.652, 141.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 28 16.00 P 6 15.00 Mg 2 11.99 O 1686 8.00 N 1464 7.00 C 5732 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: 3.87 Conformation dependent library (CDL) restraints added in 1.5 seconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2124 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 4 sheets defined 67.1% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 158 through 162 Processing helix chain 'A' and resid 168 through 173 removed outlier: 4.322A pdb=" N VAL A 172 " --> pdb=" O ILE A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 188 removed outlier: 3.686A pdb=" N THR A 179 " --> pdb=" O THR A 175 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 251 removed outlier: 4.430A pdb=" N LEU A 218 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN A 219 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL A 232 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASP A 240 " --> pdb=" O ARG A 236 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TYR A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 246 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 260 removed outlier: 4.371A pdb=" N PHE A 257 " --> pdb=" O PRO A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 272 removed outlier: 3.945A pdb=" N ARG A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE A 269 " --> pdb=" O ILE A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 292 removed outlier: 4.528A pdb=" N ILE A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASP A 277 " --> pdb=" O ASN A 273 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A 280 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL A 290 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 304 removed outlier: 3.973A pdb=" N LEU A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'A' and resid 313 through 325 removed outlier: 4.309A pdb=" N ILE A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE A 325 " --> pdb=" O ILE A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 352 removed outlier: 4.540A pdb=" N GLU A 330 " --> pdb=" O MET A 326 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N MET A 332 " --> pdb=" O PRO A 328 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASP A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N MET A 337 " --> pdb=" O ASN A 333 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLU A 338 " --> pdb=" O ARG A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 361 removed outlier: 4.162A pdb=" N ILE A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 416 removed outlier: 3.919A pdb=" N ARG A 366 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL A 412 " --> pdb=" O TRP A 408 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU A 413 " --> pdb=" O MET A 409 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 414 " --> pdb=" O GLY A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 444 removed outlier: 3.964A pdb=" N TYR A 433 " --> pdb=" O THR A 429 " (cutoff:3.500A) Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 444 through 461 removed outlier: 3.767A pdb=" N THR A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL A 461 " --> pdb=" O ARG A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 531 removed outlier: 3.627A pdb=" N ALA A 527 " --> pdb=" O LYS A 523 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL A 531 " --> pdb=" O ALA A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 559 removed outlier: 3.759A pdb=" N LEU A 556 " --> pdb=" O ASP A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 Processing helix chain 'A' and resid 588 through 598 Processing helix chain 'A' and resid 623 through 638 removed outlier: 3.879A pdb=" N THR A 638 " --> pdb=" O ARG A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 665 removed outlier: 3.502A pdb=" N ILE A 665 " --> pdb=" O VAL A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 683 removed outlier: 4.339A pdb=" N ALA A 681 " --> pdb=" O ARG A 677 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU A 682 " --> pdb=" O LEU A 678 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG A 683 " --> pdb=" O THR A 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 677 through 683' Processing helix chain 'A' and resid 700 through 707 Processing helix chain 'A' and resid 709 through 717 removed outlier: 3.524A pdb=" N HIS A 713 " --> pdb=" O GLY A 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 164 removed outlier: 3.910A pdb=" N LYS B 163 " --> pdb=" O PRO B 159 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 190 removed outlier: 3.983A pdb=" N ILE B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL B 172 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA B 174 " --> pdb=" O ASN B 170 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR B 179 " --> pdb=" O THR B 175 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASN B 182 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN B 190 " --> pdb=" O SER B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 195 Processing helix chain 'B' and resid 201 through 251 removed outlier: 3.959A pdb=" N ASP B 240 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR B 245 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE B 246 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE B 250 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N HIS B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 260 removed outlier: 4.186A pdb=" N PHE B 257 " --> pdb=" O PRO B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 272 removed outlier: 4.053A pdb=" N VAL B 266 " --> pdb=" O THR B 262 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG B 268 " --> pdb=" O GLU B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 304 removed outlier: 5.005A pdb=" N SER B 291 " --> pdb=" O PHE B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 311 Processing helix chain 'B' and resid 314 through 326 removed outlier: 4.044A pdb=" N TYR B 318 " --> pdb=" O ALA B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 353 removed outlier: 4.078A pdb=" N LYS B 331 " --> pdb=" O LYS B 327 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA B 339 " --> pdb=" O ASP B 335 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY B 353 " --> pdb=" O GLU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 361 removed outlier: 3.871A pdb=" N ILE B 357 " --> pdb=" O GLY B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 417 removed outlier: 3.603A pdb=" N ARG B 366 " --> pdb=" O SER B 362 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP B 376 " --> pdb=" O LYS B 372 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR B 377 " --> pdb=" O GLU B 373 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU B 378 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 387 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS B 395 " --> pdb=" O GLN B 391 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS B 396 " --> pdb=" O LYS B 392 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL B 397 " --> pdb=" O ALA B 393 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE B 406 " --> pdb=" O LEU B 402 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B 407 " --> pdb=" O ASN B 403 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL B 412 " --> pdb=" O TRP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 444 removed outlier: 3.855A pdb=" N TYR B 433 " --> pdb=" O THR B 429 " (cutoff:3.500A) Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 444 through 460 removed outlier: 3.580A pdb=" N LEU B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL B 453 " --> pdb=" O GLN B 449 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 532 removed outlier: 4.096A pdb=" N MET B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL B 531 " --> pdb=" O ALA B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 559 removed outlier: 3.510A pdb=" N LEU B 556 " --> pdb=" O ASP B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 579 removed outlier: 3.875A pdb=" N ASN B 577 " --> pdb=" O THR B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 598 removed outlier: 3.652A pdb=" N ALA B 598 " --> pdb=" O ALA B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 638 removed outlier: 3.945A pdb=" N THR B 638 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 665 removed outlier: 3.758A pdb=" N ILE B 665 " --> pdb=" O VAL B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 684 removed outlier: 4.300A pdb=" N ALA B 681 " --> pdb=" O ARG B 677 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU B 682 " --> pdb=" O LEU B 678 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG B 683 " --> pdb=" O THR B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 708 removed outlier: 3.876A pdb=" N GLY B 708 " --> pdb=" O LEU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 716 Processing sheet with id=AA1, first strand: chain 'A' and resid 500 through 503 removed outlier: 5.818A pdb=" N SER A 501 " --> pdb=" O TYR A 491 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N TYR A 491 " --> pdb=" O SER A 501 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N PHE A 486 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N SER A 542 " --> pdb=" O PHE A 486 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLN A 488 " --> pdb=" O GLU A 540 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLU A 540 " --> pdb=" O GLN A 488 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 560 through 561 removed outlier: 6.026A pdb=" N ASN A 561 " --> pdb=" O ILE A 644 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 672 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL A 513 " --> pdb=" O PHE A 673 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LYS A 512 " --> pdb=" O LYS A 686 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N VAL A 688 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA A 514 " --> pdb=" O VAL A 688 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU A 690 " --> pdb=" O ALA A 514 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL A 516 " --> pdb=" O LEU A 690 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL A 687 " --> pdb=" O GLU A 698 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU A 698 " --> pdb=" O VAL A 687 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL A 689 " --> pdb=" O VAL A 696 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 500 through 503 removed outlier: 5.935A pdb=" N SER B 501 " --> pdb=" O TYR B 491 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N TYR B 491 " --> pdb=" O SER B 501 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 503 " --> pdb=" O VAL B 489 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER B 542 " --> pdb=" O THR B 485 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL B 489 " --> pdb=" O GLN B 538 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN B 538 " --> pdb=" O VAL B 489 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 560 through 561 removed outlier: 5.822A pdb=" N ASN B 561 " --> pdb=" O ILE B 644 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B 643 " --> pdb=" O THR B 670 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 672 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS B 686 " --> pdb=" O LYS B 512 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY B 699 " --> pdb=" O VAL B 687 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU B 697 " --> pdb=" O VAL B 689 " (cutoff:3.500A) 475 hydrogen bonds defined for protein. 1416 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: 2.66 Time building geometry restraints manager: 4.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1709 1.33 - 1.45: 2015 1.45 - 1.57: 5260 1.57 - 1.70: 10 1.70 - 1.82: 56 Bond restraints: 9050 Sorted by residual: bond pdb=" O5' ATP B 801 " pdb=" PA ATP B 801 " ideal model delta sigma weight residual 1.579 1.672 -0.093 1.10e-02 8.26e+03 7.14e+01 bond pdb=" O5' ATP A 801 " pdb=" PA ATP A 801 " ideal model delta sigma weight residual 1.579 1.671 -0.092 1.10e-02 8.26e+03 7.01e+01 bond pdb=" C2 ATP A 801 " pdb=" N1 ATP A 801 " ideal model delta sigma weight residual 1.334 1.415 -0.081 1.00e-02 1.00e+04 6.53e+01 bond pdb=" C2 ATP B 801 " pdb=" N1 ATP B 801 " ideal model delta sigma weight residual 1.334 1.415 -0.081 1.00e-02 1.00e+04 6.49e+01 bond pdb=" C5 ATP B 801 " pdb=" C6 ATP B 801 " ideal model delta sigma weight residual 1.409 1.340 0.069 1.00e-02 1.00e+04 4.72e+01 ... (remaining 9045 not shown) Histogram of bond angle deviations from ideal: 96.39 - 104.02: 106 104.02 - 111.66: 3739 111.66 - 119.29: 3915 119.29 - 126.92: 4448 126.92 - 134.56: 70 Bond angle restraints: 12278 Sorted by residual: angle pdb=" PA ATP B 801 " pdb=" O3A ATP B 801 " pdb=" PB ATP B 801 " ideal model delta sigma weight residual 136.83 123.40 13.43 1.00e+00 1.00e+00 1.80e+02 angle pdb=" PA ATP A 801 " pdb=" O3A ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 136.83 123.41 13.42 1.00e+00 1.00e+00 1.80e+02 angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 127.31 12.56 1.00e+00 1.00e+00 1.58e+02 angle pdb=" PB ATP B 801 " pdb=" O3B ATP B 801 " pdb=" PG ATP B 801 " ideal model delta sigma weight residual 139.87 127.34 12.53 1.00e+00 1.00e+00 1.57e+02 angle pdb=" N1 ATP B 801 " pdb=" C2 ATP B 801 " pdb=" N3 ATP B 801 " ideal model delta sigma weight residual 128.69 117.83 10.86 1.00e+00 1.00e+00 1.18e+02 ... (remaining 12273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 4896 17.20 - 34.39: 495 34.39 - 51.59: 100 51.59 - 68.79: 20 68.79 - 85.99: 7 Dihedral angle restraints: 5518 sinusoidal: 2224 harmonic: 3294 Sorted by residual: dihedral pdb=" CA GLU A 349 " pdb=" C GLU A 349 " pdb=" N ASP A 350 " pdb=" CA ASP A 350 " ideal model delta harmonic sigma weight residual 180.00 152.99 27.01 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA LEU B 444 " pdb=" C LEU B 444 " pdb=" N GLN B 445 " pdb=" CA GLN B 445 " ideal model delta harmonic sigma weight residual -180.00 -153.79 -26.21 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" C THR A 613 " pdb=" N THR A 613 " pdb=" CA THR A 613 " pdb=" CB THR A 613 " ideal model delta harmonic sigma weight residual -122.00 -109.05 -12.95 0 2.50e+00 1.60e-01 2.68e+01 ... (remaining 5515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 1409 0.128 - 0.256: 82 0.256 - 0.383: 6 0.383 - 0.511: 0 0.511 - 0.639: 1 Chirality restraints: 1498 Sorted by residual: chirality pdb=" CB ILE A 158 " pdb=" CA ILE A 158 " pdb=" CG1 ILE A 158 " pdb=" CG2 ILE A 158 " both_signs ideal model delta sigma weight residual False 2.64 2.01 0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" CB VAL A 531 " pdb=" CA VAL A 531 " pdb=" CG1 VAL A 531 " pdb=" CG2 VAL A 531 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CB ILE A 674 " pdb=" CA ILE A 674 " pdb=" CG1 ILE A 674 " pdb=" CG2 ILE A 674 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 1495 not shown) Planarity restraints: 1522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 514 " -0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C ALA A 514 " 0.063 2.00e-02 2.50e+03 pdb=" O ALA A 514 " -0.024 2.00e-02 2.50e+03 pdb=" N PHE A 515 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 331 " -0.017 2.00e-02 2.50e+03 3.47e-02 1.20e+01 pdb=" C LYS B 331 " 0.060 2.00e-02 2.50e+03 pdb=" O LYS B 331 " -0.023 2.00e-02 2.50e+03 pdb=" N MET B 332 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 587 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.09e+00 pdb=" C THR A 587 " 0.046 2.00e-02 2.50e+03 pdb=" O THR A 587 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN A 588 " -0.016 2.00e-02 2.50e+03 ... (remaining 1519 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.29: 7 2.29 - 2.94: 3703 2.94 - 3.60: 13877 3.60 - 4.25: 19929 4.25 - 4.90: 32777 Nonbonded interactions: 70293 Sorted by model distance: nonbonded pdb=" NZ LYS A 523 " pdb=" CE1 HIS A 676 " model vdw 1.638 3.340 nonbonded pdb=" O2B ATP B 801 " pdb="MG MG B 802 " model vdw 1.952 2.170 nonbonded pdb=" O2B ATP A 801 " pdb="MG MG A 802 " model vdw 1.953 2.170 nonbonded pdb=" NE2 GLN A 647 " pdb=" NE2 HIS A 676 " model vdw 2.042 3.200 nonbonded pdb=" O3G ATP A 801 " pdb="MG MG A 802 " model vdw 2.090 2.170 ... (remaining 70288 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.930 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: 25.910 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 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 : 0.007 0.093 9050 Z= 0.435 Angle : 1.456 14.748 12278 Z= 0.796 Chirality : 0.067 0.639 1498 Planarity : 0.007 0.076 1522 Dihedral : 14.726 85.987 3394 Min Nonbonded Distance : 1.638 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.71 % Allowed : 5.97 % Favored : 93.32 % Rotamer: Outliers : 0.30 % Allowed : 0.91 % Favored : 98.79 % Cbeta Deviations : 0.19 % 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: -3.62 (0.20), residues: 1122 helix: -2.23 (0.16), residues: 672 sheet: -0.22 (1.13), residues: 24 loop : -2.61 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 408 HIS 0.005 0.001 HIS A 490 PHE 0.028 0.002 PHE A 374 TYR 0.023 0.002 TYR A 384 ARG 0.018 0.001 ARG B 627 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 137 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ILE cc_start: 0.9638 (pt) cc_final: 0.9272 (mm) REVERT: A 526 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9046 (tp) REVERT: A 649 THR cc_start: 0.8848 (p) cc_final: 0.8397 (t) REVERT: B 269 PHE cc_start: 0.9310 (t80) cc_final: 0.9099 (t80) REVERT: B 308 PHE cc_start: 0.8864 (t80) cc_final: 0.8593 (t80) REVERT: B 326 MET cc_start: 0.5150 (ptt) cc_final: 0.4269 (ptt) REVERT: B 484 MET cc_start: 0.8908 (tpt) cc_final: 0.8481 (tpp) outliers start: 3 outliers final: 0 residues processed: 139 average time/residue: 0.1723 time to fit residues: 35.0321 Evaluate side-chains 94 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 45 optimal weight: 0.0170 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 HIS ** B 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN ** B 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9050 Z= 0.144 Angle : 0.666 7.475 12278 Z= 0.338 Chirality : 0.041 0.222 1498 Planarity : 0.004 0.045 1522 Dihedral : 8.361 81.243 1280 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.10 % Favored : 95.63 % Rotamer: Outliers : 0.20 % Allowed : 6.67 % Favored : 93.13 % 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: -1.79 (0.23), residues: 1122 helix: -0.62 (0.19), residues: 680 sheet: -0.00 (1.19), residues: 24 loop : -2.11 (0.25), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 408 HIS 0.005 0.001 HIS A 490 PHE 0.031 0.001 PHE B 309 TYR 0.011 0.001 TYR A 559 ARG 0.004 0.000 ARG B 627 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 128 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 ASN cc_start: 0.9696 (t0) cc_final: 0.9483 (t0) REVERT: A 607 MET cc_start: 0.7625 (tmm) cc_final: 0.7330 (tmm) REVERT: B 308 PHE cc_start: 0.8841 (t80) cc_final: 0.8526 (t80) REVERT: B 409 MET cc_start: 0.8797 (ppp) cc_final: 0.8324 (ppp) outliers start: 2 outliers final: 2 residues processed: 130 average time/residue: 0.1720 time to fit residues: 33.3038 Evaluate side-chains 95 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 101 optimal weight: 0.2980 chunk 110 optimal weight: 20.0000 chunk 90 optimal weight: 30.0000 chunk 34 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 HIS ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 ASN ** B 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9050 Z= 0.199 Angle : 0.678 7.263 12278 Z= 0.351 Chirality : 0.042 0.183 1498 Planarity : 0.004 0.037 1522 Dihedral : 8.250 87.494 1280 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.99 % Favored : 94.74 % Rotamer: Outliers : 0.20 % Allowed : 5.05 % Favored : 94.75 % 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: -1.10 (0.24), residues: 1122 helix: -0.05 (0.20), residues: 674 sheet: 0.25 (1.24), residues: 24 loop : -1.82 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 408 HIS 0.004 0.001 HIS A 676 PHE 0.027 0.002 PHE B 309 TYR 0.014 0.001 TYR A 562 ARG 0.003 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 117 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ILE cc_start: 0.9644 (pt) cc_final: 0.9318 (mm) REVERT: A 310 MET cc_start: 0.3895 (ttt) cc_final: 0.3254 (tpt) REVERT: A 409 MET cc_start: 0.9044 (tmm) cc_final: 0.8798 (ppp) REVERT: A 607 MET cc_start: 0.7888 (tmm) cc_final: 0.7425 (tmm) REVERT: B 269 PHE cc_start: 0.9420 (t80) cc_final: 0.9212 (t80) REVERT: B 310 MET cc_start: 0.5269 (ptp) cc_final: 0.5019 (ptm) REVERT: B 357 ILE cc_start: 0.9781 (mm) cc_final: 0.9552 (tp) REVERT: B 409 MET cc_start: 0.8773 (ppp) cc_final: 0.8381 (ppp) REVERT: B 690 LEU cc_start: 0.9308 (tp) cc_final: 0.8954 (tp) outliers start: 2 outliers final: 0 residues processed: 119 average time/residue: 0.1592 time to fit residues: 28.7144 Evaluate side-chains 93 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 5.9990 chunk 52 optimal weight: 0.1980 chunk 11 optimal weight: 4.9990 chunk 48 optimal weight: 20.0000 chunk 68 optimal weight: 8.9990 chunk 102 optimal weight: 0.0770 chunk 108 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.4544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9050 Z= 0.139 Angle : 0.636 7.856 12278 Z= 0.320 Chirality : 0.041 0.181 1498 Planarity : 0.004 0.036 1522 Dihedral : 7.591 89.287 1280 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.99 % Favored : 94.74 % Rotamer: Outliers : 0.20 % Allowed : 3.74 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.25), residues: 1122 helix: 0.34 (0.21), residues: 670 sheet: 0.49 (1.23), residues: 24 loop : -1.66 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 408 HIS 0.004 0.001 HIS A 490 PHE 0.028 0.001 PHE B 309 TYR 0.025 0.001 TYR A 559 ARG 0.002 0.000 ARG B 386 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 121 time to evaluate : 1.123 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 239 ILE cc_start: 0.9624 (pt) cc_final: 0.9293 (mm) REVERT: A 310 MET cc_start: 0.4009 (ttt) cc_final: 0.3056 (tpt) REVERT: A 409 MET cc_start: 0.9038 (tmm) cc_final: 0.8774 (ppp) REVERT: A 607 MET cc_start: 0.7745 (tmm) cc_final: 0.7052 (tmm) REVERT: B 196 TYR cc_start: 0.8042 (m-80) cc_final: 0.7682 (m-80) REVERT: B 229 LEU cc_start: 0.9681 (mm) cc_final: 0.9431 (pp) REVERT: B 269 PHE cc_start: 0.9396 (t80) cc_final: 0.9191 (t80) REVERT: B 308 PHE cc_start: 0.8842 (t80) cc_final: 0.8614 (t80) REVERT: B 310 MET cc_start: 0.5154 (ptp) cc_final: 0.4902 (ptm) REVERT: B 357 ILE cc_start: 0.9751 (mm) cc_final: 0.9513 (tp) REVERT: B 409 MET cc_start: 0.8657 (ppp) cc_final: 0.8327 (ppp) REVERT: B 484 MET cc_start: 0.8825 (tpt) cc_final: 0.8283 (tpp) REVERT: B 690 LEU cc_start: 0.9267 (tp) cc_final: 0.8967 (tp) outliers start: 2 outliers final: 1 residues processed: 123 average time/residue: 0.1619 time to fit residues: 30.2678 Evaluate side-chains 94 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 0.4980 chunk 97 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9050 Z= 0.150 Angle : 0.632 8.075 12278 Z= 0.320 Chirality : 0.041 0.183 1498 Planarity : 0.003 0.035 1522 Dihedral : 7.217 83.724 1280 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.08 % Favored : 94.65 % Rotamer: Outliers : 0.20 % Allowed : 3.13 % Favored : 96.67 % 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: -0.36 (0.25), residues: 1122 helix: 0.56 (0.21), residues: 668 sheet: 0.54 (1.23), residues: 24 loop : -1.52 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 408 HIS 0.004 0.001 HIS A 490 PHE 0.027 0.001 PHE B 309 TYR 0.010 0.001 TYR A 493 ARG 0.002 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 121 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 GLU cc_start: 0.9140 (mp0) cc_final: 0.8902 (pm20) REVERT: A 310 MET cc_start: 0.3948 (ttt) cc_final: 0.2984 (tpt) REVERT: A 409 MET cc_start: 0.9076 (tmm) cc_final: 0.8773 (ppp) REVERT: A 607 MET cc_start: 0.7861 (tmm) cc_final: 0.7071 (tmm) REVERT: B 196 TYR cc_start: 0.8046 (m-80) cc_final: 0.7669 (m-80) REVERT: B 269 PHE cc_start: 0.9418 (t80) cc_final: 0.9211 (t80) REVERT: B 308 PHE cc_start: 0.8824 (t80) cc_final: 0.8611 (t80) REVERT: B 310 MET cc_start: 0.5350 (ptp) cc_final: 0.5079 (ptm) REVERT: B 357 ILE cc_start: 0.9757 (mm) cc_final: 0.9512 (tp) REVERT: B 409 MET cc_start: 0.8629 (ppp) cc_final: 0.8324 (ppp) outliers start: 2 outliers final: 0 residues processed: 123 average time/residue: 0.1590 time to fit residues: 29.5819 Evaluate side-chains 93 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 0.0030 chunk 56 optimal weight: 20.0000 chunk 104 optimal weight: 2.9990 overall best weight: 3.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 HIS ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9050 Z= 0.193 Angle : 0.682 8.170 12278 Z= 0.350 Chirality : 0.042 0.180 1498 Planarity : 0.004 0.035 1522 Dihedral : 6.827 79.414 1280 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.15 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % 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: -0.37 (0.25), residues: 1122 helix: 0.54 (0.20), residues: 670 sheet: 0.51 (1.21), residues: 24 loop : -1.50 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 408 HIS 0.005 0.001 HIS A 490 PHE 0.026 0.002 PHE B 309 TYR 0.022 0.001 TYR A 559 ARG 0.004 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.4284 (ttt) cc_final: 0.3386 (tpt) REVERT: A 409 MET cc_start: 0.9128 (tmm) cc_final: 0.8822 (ppp) REVERT: A 607 MET cc_start: 0.8010 (tmm) cc_final: 0.7189 (tmm) REVERT: B 196 TYR cc_start: 0.8152 (m-80) cc_final: 0.7803 (m-80) REVERT: B 310 MET cc_start: 0.5875 (ptp) cc_final: 0.5555 (ptm) REVERT: B 357 ILE cc_start: 0.9776 (mm) cc_final: 0.9490 (tp) REVERT: B 367 TYR cc_start: 0.9261 (t80) cc_final: 0.8667 (t80) REVERT: B 409 MET cc_start: 0.8632 (ppp) cc_final: 0.8391 (ppp) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1623 time to fit residues: 28.7505 Evaluate side-chains 89 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 91 optimal weight: 30.0000 chunk 60 optimal weight: 4.9990 chunk 107 optimal weight: 0.0000 chunk 67 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 overall best weight: 2.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 GLN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9050 Z= 0.163 Angle : 0.658 7.482 12278 Z= 0.334 Chirality : 0.042 0.172 1498 Planarity : 0.003 0.038 1522 Dihedral : 6.697 88.436 1280 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.08 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % 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: -0.24 (0.25), residues: 1122 helix: 0.63 (0.20), residues: 672 sheet: 0.61 (1.18), residues: 24 loop : -1.44 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 408 HIS 0.005 0.001 HIS A 490 PHE 0.025 0.001 PHE B 309 TYR 0.011 0.001 TYR A 493 ARG 0.002 0.000 ARG A 557 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.4164 (ttt) cc_final: 0.3173 (tpt) REVERT: A 357 ILE cc_start: 0.9695 (mp) cc_final: 0.9236 (tp) REVERT: A 409 MET cc_start: 0.9182 (tmm) cc_final: 0.8962 (tmm) REVERT: A 607 MET cc_start: 0.7949 (tmm) cc_final: 0.7109 (tmm) REVERT: B 196 TYR cc_start: 0.8083 (m-80) cc_final: 0.7744 (m-80) REVERT: B 308 PHE cc_start: 0.8826 (t80) cc_final: 0.8582 (t80) REVERT: B 310 MET cc_start: 0.5102 (ptp) cc_final: 0.4800 (ptm) REVERT: B 357 ILE cc_start: 0.9770 (mm) cc_final: 0.9475 (tp) REVERT: B 367 TYR cc_start: 0.9223 (t80) cc_final: 0.8643 (t80) REVERT: B 409 MET cc_start: 0.8584 (ppp) cc_final: 0.8365 (ppp) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1685 time to fit residues: 29.2830 Evaluate side-chains 89 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 20 optimal weight: 0.0570 chunk 68 optimal weight: 7.9990 chunk 73 optimal weight: 0.2980 chunk 53 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 chunk 84 optimal weight: 20.0000 chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 overall best weight: 2.0704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 HIS ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9050 Z= 0.152 Angle : 0.672 9.616 12278 Z= 0.340 Chirality : 0.042 0.162 1498 Planarity : 0.003 0.037 1522 Dihedral : 6.620 88.685 1280 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.08 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % 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: -0.19 (0.25), residues: 1122 helix: 0.65 (0.20), residues: 672 sheet: 0.77 (1.18), residues: 24 loop : -1.39 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 408 HIS 0.005 0.001 HIS A 490 PHE 0.027 0.001 PHE B 309 TYR 0.020 0.001 TYR A 559 ARG 0.002 0.000 ARG B 260 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 GLU cc_start: 0.9250 (mp0) cc_final: 0.8917 (mp0) REVERT: A 310 MET cc_start: 0.4155 (ttt) cc_final: 0.3101 (tpt) REVERT: A 409 MET cc_start: 0.9133 (tmm) cc_final: 0.8914 (tmm) REVERT: A 607 MET cc_start: 0.7966 (tmm) cc_final: 0.7665 (tmm) REVERT: B 196 TYR cc_start: 0.8057 (m-80) cc_final: 0.7766 (m-80) REVERT: B 308 PHE cc_start: 0.8779 (t80) cc_final: 0.8577 (t80) REVERT: B 310 MET cc_start: 0.5036 (ptp) cc_final: 0.4743 (ptm) REVERT: B 357 ILE cc_start: 0.9767 (mm) cc_final: 0.9465 (tp) REVERT: B 367 TYR cc_start: 0.9206 (t80) cc_final: 0.8621 (t80) REVERT: B 384 TYR cc_start: 0.9088 (t80) cc_final: 0.8632 (t80) REVERT: B 409 MET cc_start: 0.8527 (ppp) cc_final: 0.8317 (ppp) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1647 time to fit residues: 28.4078 Evaluate side-chains 91 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 103 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 43 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 ASN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9050 Z= 0.151 Angle : 0.679 8.620 12278 Z= 0.343 Chirality : 0.042 0.187 1498 Planarity : 0.003 0.037 1522 Dihedral : 6.588 86.571 1280 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.81 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.25), residues: 1122 helix: 0.69 (0.21), residues: 668 sheet: 0.91 (1.19), residues: 24 loop : -1.35 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 408 HIS 0.005 0.001 HIS A 490 PHE 0.028 0.001 PHE B 309 TYR 0.014 0.001 TYR A 559 ARG 0.004 0.000 ARG A 557 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.4033 (ttt) cc_final: 0.2763 (ptm) REVERT: A 357 ILE cc_start: 0.9695 (mp) cc_final: 0.9231 (tp) REVERT: A 607 MET cc_start: 0.7956 (tmm) cc_final: 0.7645 (tmm) REVERT: B 196 TYR cc_start: 0.8069 (m-80) cc_final: 0.7760 (m-80) REVERT: B 308 PHE cc_start: 0.8791 (t80) cc_final: 0.8582 (t80) REVERT: B 310 MET cc_start: 0.4783 (ptp) cc_final: 0.4567 (ptm) REVERT: B 357 ILE cc_start: 0.9761 (mm) cc_final: 0.9456 (tp) REVERT: B 367 TYR cc_start: 0.9175 (t80) cc_final: 0.8912 (t80) REVERT: B 384 TYR cc_start: 0.9035 (t80) cc_final: 0.8612 (t80) REVERT: B 409 MET cc_start: 0.8478 (ppp) cc_final: 0.8266 (ppp) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1613 time to fit residues: 27.7756 Evaluate side-chains 89 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 73 optimal weight: 0.5980 chunk 111 optimal weight: 7.9990 chunk 102 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 54 optimal weight: 20.0000 chunk 70 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 ASN ** B 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9050 Z= 0.189 Angle : 0.714 10.122 12278 Z= 0.365 Chirality : 0.043 0.179 1498 Planarity : 0.004 0.037 1522 Dihedral : 6.702 86.227 1280 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.70 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: -0.14 (0.25), residues: 1122 helix: 0.65 (0.20), residues: 672 sheet: 0.89 (1.18), residues: 24 loop : -1.31 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 408 HIS 0.008 0.001 HIS A 490 PHE 0.028 0.002 PHE B 309 TYR 0.025 0.001 TYR A 559 ARG 0.003 0.000 ARG B 457 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 ILE cc_start: 0.9710 (mp) cc_final: 0.9270 (tp) REVERT: A 404 VAL cc_start: 0.8851 (m) cc_final: 0.8613 (p) REVERT: A 607 MET cc_start: 0.7992 (tmm) cc_final: 0.7677 (tmm) REVERT: B 201 MET cc_start: 0.3310 (mpp) cc_final: 0.2918 (mpp) REVERT: B 310 MET cc_start: 0.5344 (ptp) cc_final: 0.5070 (ptm) REVERT: B 357 ILE cc_start: 0.9774 (mm) cc_final: 0.9480 (tp) REVERT: B 367 TYR cc_start: 0.9204 (t80) cc_final: 0.8628 (t80) REVERT: B 384 TYR cc_start: 0.9091 (t80) cc_final: 0.8890 (t80) REVERT: B 409 MET cc_start: 0.8512 (ppp) cc_final: 0.8278 (ppp) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1638 time to fit residues: 27.9081 Evaluate side-chains 90 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 88 optimal weight: 0.0570 chunk 37 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 overall best weight: 2.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.056713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.045658 restraints weight = 68285.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.046809 restraints weight = 51124.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.047677 restraints weight = 40734.802| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9050 Z= 0.157 Angle : 0.696 9.901 12278 Z= 0.352 Chirality : 0.043 0.175 1498 Planarity : 0.003 0.038 1522 Dihedral : 6.623 87.158 1280 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.55 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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 (0.25), residues: 1122 helix: 0.73 (0.20), residues: 672 sheet: 0.97 (1.18), residues: 24 loop : -1.32 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 408 HIS 0.008 0.001 HIS A 490 PHE 0.029 0.001 PHE B 309 TYR 0.012 0.001 TYR A 559 ARG 0.004 0.000 ARG A 457 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1663.02 seconds wall clock time: 30 minutes 44.45 seconds (1844.45 seconds total)