Starting phenix.real_space_refine on Wed Feb 14 08:07:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k7a_36936/02_2024/8k7a_36936_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k7a_36936/02_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_36936/02_2024/8k7a_36936.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k7a_36936/02_2024/8k7a_36936.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k7a_36936/02_2024/8k7a_36936_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k7a_36936/02_2024/8k7a_36936_updated.pdb" } 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-5238/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: 5.15, per 1000 atoms: 0.58 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: 3.45 Conformation dependent library (CDL) restraints added in 1.9 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... running ksdssp... Secondary structure from input PDB file: 42 helices and 4 sheets defined 60.2% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 169 through 172 No H-bonds generated for 'chain 'A' and resid 169 through 172' Processing helix chain 'A' and resid 175 through 189 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) removed outlier: 4.856A pdb=" N LEU A 189 " --> pdb=" O GLY A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 250 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) Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 263 through 303 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) removed outlier: 4.905A pdb=" N ASN A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N SER A 274 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ILE A 275 " --> pdb=" O ASP A 271 " (cutoff:3.500A) 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) removed outlier: 4.618A pdb=" N VAL A 293 " --> pdb=" O ASP A 289 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) 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 306 through 324 removed outlier: 4.659A pdb=" N LEU A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ALA A 314 " --> pdb=" O MET A 310 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) Proline residue: A 316 - end of helix Processing helix chain 'A' and resid 327 through 351 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 354 through 360 Processing helix chain 'A' and resid 363 through 415 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 421 through 443 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 445 through 462 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 524 through 530 Processing helix chain 'A' and resid 553 through 559 Processing helix chain 'A' and resid 575 through 578 No H-bonds generated for 'chain 'A' and resid 575 through 578' Processing helix chain 'A' and resid 589 through 597 Processing helix chain 'A' and resid 624 through 637 Processing helix chain 'A' and resid 654 through 664 Processing helix chain 'A' and resid 678 through 682 removed outlier: 3.565A pdb=" N GLU A 682 " --> pdb=" O LEU A 678 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 678 through 682' Processing helix chain 'A' and resid 701 through 706 Processing helix chain 'A' and resid 710 through 716 Processing helix chain 'B' and resid 158 through 163 removed outlier: 3.910A pdb=" N LYS B 163 " --> pdb=" O PRO B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 189 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) Processing helix chain 'B' and resid 191 through 194 No H-bonds generated for 'chain 'B' and resid 191 through 194' Processing helix chain 'B' and resid 202 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 254 through 259 Processing helix chain 'B' and resid 263 through 271 removed outlier: 3.944A pdb=" N ARG B 268 " --> pdb=" O GLU B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 303 removed outlier: 5.005A pdb=" N SER B 291 " --> pdb=" O PHE B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 325 removed outlier: 5.368A pdb=" N LEU B 313 " --> pdb=" O PHE B 309 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA B 314 " --> pdb=" O MET B 310 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 328 through 352 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) Processing helix chain 'B' and resid 354 through 360 Processing helix chain 'B' and resid 363 through 416 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 421 through 443 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 445 through 462 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) removed outlier: 4.713A pdb=" N VAL B 461 " --> pdb=" O ARG B 457 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 531 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 553 through 559 Processing helix chain 'B' and resid 574 through 578 Processing helix chain 'B' and resid 589 through 597 Processing helix chain 'B' and resid 624 through 637 Processing helix chain 'B' and resid 654 through 666 removed outlier: 3.758A pdb=" N ILE B 665 " --> pdb=" O VAL B 661 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ALA B 666 " --> pdb=" O ASP B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 683 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) No H-bonds generated for 'chain 'B' and resid 678 through 683' Processing helix chain 'B' and resid 701 through 707 Processing helix chain 'B' and resid 710 through 715 Processing sheet with id= A, first strand: chain 'A' and resid 485 through 487 removed outlier: 3.758A pdb=" N SER A 542 " --> pdb=" O THR A 485 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS A 487 " --> pdb=" O GLU A 540 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU A 540 " --> pdb=" O LYS A 487 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 695 through 699 removed outlier: 6.582A pdb=" N VAL A 689 " --> pdb=" O VAL A 696 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU A 698 " --> pdb=" O VAL A 687 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL A 687 " --> pdb=" O GLU A 698 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS A 686 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU A 671 " --> pdb=" O VAL A 513 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N PHE A 515 " --> pdb=" O LEU A 671 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N PHE A 673 " --> pdb=" O PHE A 515 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N GLY A 517 " --> pdb=" O PHE A 673 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 672 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 484 through 487 removed outlier: 3.832A pdb=" N SER B 542 " --> pdb=" O THR B 485 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 695 through 699 removed outlier: 3.534A pdb=" N VAL B 696 " --> pdb=" O VAL B 689 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N VAL B 689 " --> pdb=" O VAL B 696 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLU B 698 " --> pdb=" O VAL B 687 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL B 687 " --> pdb=" O GLU B 698 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS B 686 " --> pdb=" O LYS B 512 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU B 671 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N PHE B 515 " --> pdb=" O LEU B 671 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE B 673 " --> pdb=" O PHE B 515 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N GLY B 517 " --> pdb=" O PHE B 673 " (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) 422 hydrogen bonds defined for protein. 1260 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: 2.39 Time building geometry restraints manager: 3.71 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: 3721 2.94 - 3.60: 13927 3.60 - 4.25: 20055 4.25 - 4.90: 32795 Nonbonded interactions: 70505 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 70500 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' 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: 0.890 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: 4.010 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 27.480 Find NCS groups from input model: 0.490 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: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.140 ------------------------------------------------------------------------------- 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= 0.446 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 : 1.139 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: 0.1846 time to fit residues: 37.3366 Evaluate side-chains 94 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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: 8.9990 chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 101 optimal weight: 0.0170 overall best weight: 1.2024 ------------------------------------------------------------------------------- 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** A 676 HIS ** B 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 ASN ** 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: 0.7670 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9050 Z= 0.134 Angle : 0.649 7.334 12278 Z= 0.327 Chirality : 0.040 0.204 1498 Planarity : 0.004 0.046 1522 Dihedral : 8.509 85.067 1280 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.37 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % 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: -1.84 (0.23), residues: 1122 helix: -0.62 (0.20), residues: 666 sheet: 0.03 (1.21), residues: 24 loop : -2.16 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 408 HIS 0.003 0.001 HIS A 490 PHE 0.026 0.001 PHE B 309 TYR 0.011 0.001 TYR A 559 ARG 0.005 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 126 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 607 MET cc_start: 0.7741 (tmm) cc_final: 0.7431 (tmm) REVERT: B 371 ASP cc_start: 0.9506 (t0) cc_final: 0.9238 (m-30) REVERT: B 409 MET cc_start: 0.8776 (ppp) cc_final: 0.8309 (ppp) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1763 time to fit residues: 32.8322 Evaluate side-chains 94 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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: 7.9990 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 110 optimal weight: 20.0000 chunk 90 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 81 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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** B 459 ASN ** B 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2024 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= 0.141 Angle : 0.621 7.292 12278 Z= 0.313 Chirality : 0.040 0.157 1498 Planarity : 0.003 0.039 1522 Dihedral : 8.018 84.443 1280 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.08 % Favored : 94.65 % Rotamer: Outliers : 0.20 % Allowed : 4.34 % Favored : 95.45 % 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: -1.02 (0.24), residues: 1122 helix: 0.07 (0.21), residues: 662 sheet: 0.15 (1.27), residues: 24 loop : -1.86 (0.26), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 408 HIS 0.005 0.001 HIS A 490 PHE 0.020 0.001 PHE B 309 TYR 0.013 0.001 TYR A 493 ARG 0.003 0.000 ARG B 627 *********************** 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 121 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 ILE cc_start: 0.9639 (pt) cc_final: 0.9294 (mm) REVERT: A 409 MET cc_start: 0.9137 (tmm) cc_final: 0.8861 (tmm) REVERT: A 607 MET cc_start: 0.7744 (tmm) cc_final: 0.7359 (tmm) REVERT: B 310 MET cc_start: 0.4681 (ptp) cc_final: 0.4474 (ptm) REVERT: B 409 MET cc_start: 0.8689 (ppp) cc_final: 0.8357 (ppp) outliers start: 2 outliers final: 0 residues processed: 121 average time/residue: 0.1608 time to fit residues: 29.5770 Evaluate side-chains 93 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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: 10.0000 chunk 52 optimal weight: 0.0070 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 chunk 108 optimal weight: 0.4980 chunk 53 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 90 optimal weight: 20.0000 overall best weight: 2.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 628 GLN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 ASN ** 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: 0.7764 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9050 Z= 0.153 Angle : 0.610 7.452 12278 Z= 0.310 Chirality : 0.040 0.161 1498 Planarity : 0.003 0.034 1522 Dihedral : 7.354 79.249 1280 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.61 % Favored : 94.12 % Rotamer: Outliers : 0.10 % Allowed : 5.35 % Favored : 94.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.25), residues: 1122 helix: 0.43 (0.21), residues: 662 sheet: 0.21 (1.26), residues: 24 loop : -1.69 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 408 HIS 0.005 0.001 HIS A 490 PHE 0.019 0.001 PHE B 309 TYR 0.020 0.001 TYR A 559 ARG 0.002 0.000 ARG B 457 *********************** 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 118 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ILE cc_start: 0.9625 (pt) cc_final: 0.9291 (mm) REVERT: A 310 MET cc_start: 0.1606 (tpt) cc_final: 0.1380 (tpt) REVERT: A 409 MET cc_start: 0.9186 (tmm) cc_final: 0.8665 (ppp) REVERT: A 607 MET cc_start: 0.7829 (tmm) cc_final: 0.7176 (tmm) REVERT: B 196 TYR cc_start: 0.8091 (m-80) cc_final: 0.7577 (m-80) REVERT: B 229 LEU cc_start: 0.9686 (mm) cc_final: 0.9422 (pp) REVERT: B 310 MET cc_start: 0.4802 (ptp) cc_final: 0.4596 (ptm) REVERT: B 409 MET cc_start: 0.8627 (ppp) cc_final: 0.8337 (ppp) outliers start: 1 outliers final: 0 residues processed: 118 average time/residue: 0.1665 time to fit residues: 29.5641 Evaluate side-chains 94 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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: 8.9990 chunk 80 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 7.9990 chunk 97 optimal weight: 0.0060 chunk 27 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 overall best weight: 3.4004 ------------------------------------------------------------------------------- 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** A 628 GLN ** B 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9050 Z= 0.185 Angle : 0.649 7.943 12278 Z= 0.330 Chirality : 0.040 0.173 1498 Planarity : 0.004 0.040 1522 Dihedral : 6.925 82.578 1280 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.15 % Favored : 93.58 % 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: -0.36 (0.25), residues: 1122 helix: 0.61 (0.21), residues: 660 sheet: 0.32 (1.23), residues: 24 loop : -1.57 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 408 HIS 0.006 0.001 HIS A 490 PHE 0.019 0.001 PHE B 309 TYR 0.011 0.001 TYR A 493 ARG 0.003 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 117 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 115 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.2082 (tpt) cc_final: 0.1783 (tpt) REVERT: A 409 MET cc_start: 0.9221 (tmm) cc_final: 0.8701 (ppp) REVERT: A 607 MET cc_start: 0.8020 (tmm) cc_final: 0.7307 (tmm) REVERT: B 196 TYR cc_start: 0.8138 (m-80) cc_final: 0.7783 (m-80) REVERT: B 409 MET cc_start: 0.8579 (ppp) cc_final: 0.8309 (ppp) REVERT: B 484 MET cc_start: 0.8904 (tpt) cc_final: 0.8365 (tpp) outliers start: 2 outliers final: 1 residues processed: 117 average time/residue: 0.1661 time to fit residues: 28.9856 Evaluate side-chains 87 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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: 0.7980 chunk 21 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 108 optimal weight: 0.1980 chunk 89 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 35 optimal weight: 0.0020 chunk 56 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- 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 ** B 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2986 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= 0.133 Angle : 0.641 8.921 12278 Z= 0.316 Chirality : 0.041 0.199 1498 Planarity : 0.003 0.033 1522 Dihedral : 6.398 87.532 1280 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.90 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.25), residues: 1122 helix: 0.78 (0.21), residues: 656 sheet: 0.41 (1.22), residues: 24 loop : -1.60 (0.27), residues: 442 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 0.019 0.001 PHE B 309 TYR 0.011 0.001 TYR A 559 ARG 0.002 0.000 ARG B 260 *********************** 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 118 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.1607 (tpt) cc_final: 0.1349 (tpt) REVERT: A 409 MET cc_start: 0.9192 (tmm) cc_final: 0.8675 (ppp) REVERT: A 607 MET cc_start: 0.7801 (tmm) cc_final: 0.7039 (tmm) REVERT: B 196 TYR cc_start: 0.8023 (m-80) cc_final: 0.7689 (m-80) REVERT: B 310 MET cc_start: 0.4853 (ptm) cc_final: 0.4107 (ptm) REVERT: B 409 MET cc_start: 0.8517 (ppp) cc_final: 0.8267 (ppp) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1789 time to fit residues: 31.4029 Evaluate side-chains 94 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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: 7.9990 chunk 61 optimal weight: 20.0000 chunk 79 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 ASN B 628 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 9050 Z= 0.224 Angle : 0.708 8.334 12278 Z= 0.363 Chirality : 0.043 0.181 1498 Planarity : 0.004 0.044 1522 Dihedral : 6.740 82.734 1280 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.60 % Favored : 93.14 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.25), residues: 1122 helix: 0.68 (0.21), residues: 656 sheet: 0.41 (1.20), residues: 24 loop : -1.42 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 408 HIS 0.007 0.001 HIS A 490 PHE 0.021 0.002 PHE A 308 TYR 0.025 0.002 TYR A 559 ARG 0.003 0.000 ARG B 457 *********************** 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 112 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 MET cc_start: 0.9311 (tmm) cc_final: 0.8813 (ppp) REVERT: A 607 MET cc_start: 0.8138 (tmm) cc_final: 0.7367 (tmm) REVERT: B 196 TYR cc_start: 0.8131 (m-80) cc_final: 0.7786 (m-80) REVERT: B 310 MET cc_start: 0.5561 (ptm) cc_final: 0.4794 (ptm) REVERT: B 332 MET cc_start: 0.8356 (ptp) cc_final: 0.8148 (ptp) REVERT: B 367 TYR cc_start: 0.9312 (t80) cc_final: 0.8952 (t80) REVERT: B 384 TYR cc_start: 0.8912 (t80) cc_final: 0.8645 (t80) REVERT: B 409 MET cc_start: 0.8462 (ppp) cc_final: 0.8230 (ppp) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1716 time to fit residues: 28.4936 Evaluate side-chains 90 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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: 5.9990 chunk 32 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 0.0670 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 overall best weight: 1.7924 ------------------------------------------------------------------------------- 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 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9050 Z= 0.146 Angle : 0.660 9.684 12278 Z= 0.332 Chirality : 0.041 0.189 1498 Planarity : 0.003 0.034 1522 Dihedral : 6.580 86.874 1280 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.61 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.25), residues: 1122 helix: 0.89 (0.21), residues: 656 sheet: 0.69 (1.22), residues: 24 loop : -1.54 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 408 HIS 0.005 0.001 HIS A 490 PHE 0.019 0.001 PHE B 309 TYR 0.011 0.001 TYR A 559 ARG 0.002 0.000 ARG A 557 *********************** 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 112 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.1991 (tpt) cc_final: 0.1397 (mtt) REVERT: A 409 MET cc_start: 0.9286 (tmm) cc_final: 0.8952 (ppp) REVERT: A 607 MET cc_start: 0.8029 (tmm) cc_final: 0.7269 (tmm) REVERT: B 196 TYR cc_start: 0.8057 (m-80) cc_final: 0.7732 (m-80) REVERT: B 310 MET cc_start: 0.5335 (ptm) cc_final: 0.4569 (ptm) REVERT: B 367 TYR cc_start: 0.9280 (t80) cc_final: 0.8871 (t80) REVERT: B 384 TYR cc_start: 0.8816 (t80) cc_final: 0.8356 (t80) REVERT: B 409 MET cc_start: 0.8423 (ppp) cc_final: 0.8198 (ppp) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1753 time to fit residues: 29.4179 Evaluate side-chains 90 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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: 0.0980 chunk 100 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 60 optimal weight: 0.0030 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 90 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 overall best weight: 2.0196 ------------------------------------------------------------------------------- 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 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9050 Z= 0.149 Angle : 0.665 10.230 12278 Z= 0.334 Chirality : 0.041 0.170 1498 Planarity : 0.003 0.034 1522 Dihedral : 6.467 85.235 1280 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.88 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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: 0.01 (0.25), residues: 1122 helix: 0.98 (0.21), residues: 648 sheet: 0.79 (1.21), residues: 24 loop : -1.50 (0.27), residues: 450 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 0.018 0.001 PHE B 309 TYR 0.025 0.001 TYR A 559 ARG 0.002 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 : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.1933 (tpt) cc_final: 0.1296 (mtt) REVERT: A 409 MET cc_start: 0.9282 (tmm) cc_final: 0.8938 (ppp) REVERT: A 607 MET cc_start: 0.8007 (tmm) cc_final: 0.7177 (tmm) REVERT: B 196 TYR cc_start: 0.8102 (m-80) cc_final: 0.7771 (m-80) REVERT: B 310 MET cc_start: 0.5360 (ptm) cc_final: 0.4625 (ptm) REVERT: B 367 TYR cc_start: 0.9289 (t80) cc_final: 0.8684 (t80) REVERT: B 409 MET cc_start: 0.8353 (ppp) cc_final: 0.8104 (ppp) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1738 time to fit residues: 29.4295 Evaluate side-chains 90 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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: 5.9990 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 0.4980 chunk 111 optimal weight: 7.9990 chunk 102 optimal weight: 20.0000 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 overall best weight: 3.2988 ------------------------------------------------------------------------------- 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 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9050 Z= 0.184 Angle : 0.680 9.178 12278 Z= 0.347 Chirality : 0.042 0.189 1498 Planarity : 0.004 0.039 1522 Dihedral : 6.666 84.679 1280 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.79 % Favored : 93.94 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.25), residues: 1122 helix: 0.83 (0.21), residues: 662 sheet: 0.79 (1.20), residues: 24 loop : -1.54 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 408 HIS 0.006 0.001 HIS A 490 PHE 0.018 0.001 PHE B 309 TYR 0.016 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 115 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.1790 (tpt) cc_final: 0.1282 (mtt) REVERT: A 357 ILE cc_start: 0.9798 (mp) cc_final: 0.9424 (tp) REVERT: A 404 VAL cc_start: 0.8881 (m) cc_final: 0.8644 (p) REVERT: A 409 MET cc_start: 0.9288 (tmm) cc_final: 0.9039 (tmm) REVERT: A 607 MET cc_start: 0.8017 (tmm) cc_final: 0.7180 (tmm) REVERT: B 196 TYR cc_start: 0.8182 (m-80) cc_final: 0.7851 (m-80) REVERT: B 310 MET cc_start: 0.5459 (ptm) cc_final: 0.4735 (ptm) REVERT: B 357 ILE cc_start: 0.9815 (mp) cc_final: 0.9508 (tt) REVERT: B 367 TYR cc_start: 0.9298 (t80) cc_final: 0.8722 (t80) REVERT: B 384 TYR cc_start: 0.8877 (t80) cc_final: 0.8596 (t80) REVERT: B 409 MET cc_start: 0.8396 (ppp) cc_final: 0.8148 (ppp) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1734 time to fit residues: 29.8004 Evaluate side-chains 93 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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: 4.9990 chunk 81 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.081122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.069789 restraints weight = 71614.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.071274 restraints weight = 42273.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.072284 restraints weight = 28411.461| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9050 Z= 0.199 Angle : 0.697 11.012 12278 Z= 0.357 Chirality : 0.042 0.193 1498 Planarity : 0.004 0.045 1522 Dihedral : 6.900 86.253 1280 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.42 % Favored : 93.32 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.25), residues: 1122 helix: 0.81 (0.21), residues: 662 sheet: 0.90 (1.20), residues: 24 loop : -1.47 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 408 HIS 0.006 0.001 HIS A 490 PHE 0.020 0.002 PHE A 308 TYR 0.016 0.001 TYR A 493 ARG 0.003 0.000 ARG B 457 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1670.79 seconds wall clock time: 31 minutes 32.18 seconds (1892.18 seconds total)