Starting phenix.real_space_refine on Thu Mar 13 17:54:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zdu_14670/03_2025/7zdu_14670_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zdu_14670/03_2025/7zdu_14670.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zdu_14670/03_2025/7zdu_14670.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zdu_14670/03_2025/7zdu_14670.map" model { file = "/net/cci-nas-00/data/ceres_data/7zdu_14670/03_2025/7zdu_14670_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zdu_14670/03_2025/7zdu_14670_neut.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 29 5.16 5 C 5729 2.51 5 N 1580 2.21 5 O 1629 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8975 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 4344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4344 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 18, 'TRANS': 544} Chain: "D" Number of atoms: 4567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4567 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 27, 'TRANS': 557} Chain: "C" 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: "D" 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: 5.76, per 1000 atoms: 0.64 Number of scatterers: 8975 At special positions: 0 Unit cell: (100.44, 73.656, 138.105, 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 29 16.00 P 6 15.00 Mg 2 11.99 O 1629 8.00 N 1580 7.00 C 5729 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 1.0 seconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 5 sheets defined 68.6% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'C' and resid 1 through 3 No H-bonds generated for 'chain 'C' and resid 1 through 3' Processing helix chain 'C' and resid 4 through 9 removed outlier: 3.518A pdb=" N ALA C 9 " --> pdb=" O LEU C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 13 Processing helix chain 'C' and resid 14 through 50 removed outlier: 3.598A pdb=" N ILE C 22 " --> pdb=" O LEU C 18 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER C 44 " --> pdb=" O GLY C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 55 removed outlier: 4.609A pdb=" N TYR C 55 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 101 removed outlier: 3.537A pdb=" N ARG C 67 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG C 90 " --> pdb=" O ASP C 86 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN C 93 " --> pdb=" O PHE C 89 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS C 94 " --> pdb=" O ARG C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 114 Processing helix chain 'C' and resid 115 through 131 removed outlier: 4.311A pdb=" N VAL C 127 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP C 128 " --> pdb=" O VAL C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 137 removed outlier: 4.544A pdb=" N LEU C 135 " --> pdb=" O ASP C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 157 removed outlier: 3.783A pdb=" N PHE C 157 " --> pdb=" O ILE C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 209 Proline residue: C 178 - end of helix removed outlier: 4.875A pdb=" N SER C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N THR C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 216 removed outlier: 3.552A pdb=" N ILE C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 269 removed outlier: 3.719A pdb=" N GLN C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL C 259 " --> pdb=" O GLY C 255 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY C 268 " --> pdb=" O TRP C 264 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY C 269 " --> pdb=" O MET C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 290 removed outlier: 3.609A pdb=" N LEU C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE C 283 " --> pdb=" O LEU C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 294 Processing helix chain 'C' and resid 299 through 319 removed outlier: 3.674A pdb=" N GLY C 305 " --> pdb=" O PHE C 301 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN C 306 " --> pdb=" O GLN C 302 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA C 309 " --> pdb=" O GLY C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 386 removed outlier: 3.568A pdb=" N GLN C 384 " --> pdb=" O SER C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 408 through 415 removed outlier: 3.920A pdb=" N GLN C 414 " --> pdb=" O ALA C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 435 Processing helix chain 'C' and resid 442 through 454 Processing helix chain 'C' and resid 455 through 459 Processing helix chain 'C' and resid 462 through 466 removed outlier: 3.535A pdb=" N ASN C 465 " --> pdb=" O ALA C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 492 Processing helix chain 'C' and resid 506 through 521 Processing helix chain 'C' and resid 555 through 563 removed outlier: 3.510A pdb=" N ALA C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 16 Processing helix chain 'D' and resid 17 through 19 No H-bonds generated for 'chain 'D' and resid 17 through 19' Processing helix chain 'D' and resid 20 through 54 Processing helix chain 'D' and resid 63 through 110 removed outlier: 3.560A pdb=" N ARG D 85 " --> pdb=" O TRP D 81 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 115 Processing helix chain 'D' and resid 118 through 127 removed outlier: 3.618A pdb=" N THR D 124 " --> pdb=" O GLY D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 132 Processing helix chain 'D' and resid 133 through 139 Processing helix chain 'D' and resid 139 through 157 removed outlier: 3.577A pdb=" N GLN D 143 " --> pdb=" O ARG D 139 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ALA D 145 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU D 146 " --> pdb=" O PRO D 142 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL D 148 " --> pdb=" O MET D 144 " (cutoff:3.500A) Proline residue: D 151 - end of helix Processing helix chain 'D' and resid 162 through 173 removed outlier: 3.641A pdb=" N ALA D 166 " --> pdb=" O ASN D 162 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU D 169 " --> pdb=" O ALA D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 184 removed outlier: 3.807A pdb=" N LEU D 178 " --> pdb=" O PRO D 174 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA D 181 " --> pdb=" O PRO D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 211 Processing helix chain 'D' and resid 211 through 218 Processing helix chain 'D' and resid 220 through 272 removed outlier: 3.517A pdb=" N ILE D 225 " --> pdb=" O GLY D 221 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU D 226 " --> pdb=" O GLU D 222 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU D 245 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA D 246 " --> pdb=" O VAL D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 330 removed outlier: 3.545A pdb=" N GLY D 290 " --> pdb=" O THR D 286 " (cutoff:3.500A) Proline residue: D 298 - end of helix removed outlier: 3.773A pdb=" N PHE D 301 " --> pdb=" O ALA D 297 " (cutoff:3.500A) Proline residue: D 303 - end of helix removed outlier: 3.655A pdb=" N HIS D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA D 313 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N SER D 323 " --> pdb=" O GLY D 319 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU D 324 " --> pdb=" O ALA D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 397 removed outlier: 3.521A pdb=" N LEU D 392 " --> pdb=" O GLY D 388 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU D 393 " --> pdb=" O LYS D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 423 removed outlier: 3.579A pdb=" N LYS D 423 " --> pdb=" O GLU D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 444 Processing helix chain 'D' and resid 451 through 462 Processing helix chain 'D' and resid 463 through 467 removed outlier: 3.809A pdb=" N GLU D 466 " --> pdb=" O TRP D 463 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE D 467 " --> pdb=" O VAL D 464 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 463 through 467' Processing helix chain 'D' and resid 473 through 477 removed outlier: 3.558A pdb=" N THR D 477 " --> pdb=" O GLY D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 502 removed outlier: 3.599A pdb=" N ALA D 499 " --> pdb=" O ALA D 495 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN D 502 " --> pdb=" O ARG D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 532 removed outlier: 3.843A pdb=" N GLN D 522 " --> pdb=" O ALA D 518 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA D 527 " --> pdb=" O ARG D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 573 removed outlier: 3.883A pdb=" N VAL D 572 " --> pdb=" O ALA D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 584 removed outlier: 3.847A pdb=" N ALA D 578 " --> pdb=" O GLY D 574 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG D 584 " --> pdb=" O LEU D 580 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 356 through 363 removed outlier: 6.872A pdb=" N LYS C 357 " --> pdb=" O GLN C 345 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLN C 345 " --> pdb=" O LYS C 357 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ILE C 359 " --> pdb=" O ASP C 343 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU C 396 " --> pdb=" O ARG C 342 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 416 through 419 removed outlier: 6.270A pdb=" N SER C 417 " --> pdb=" O LEU C 497 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ASP C 499 " --> pdb=" O SER C 417 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL C 419 " --> pdb=" O ASP C 499 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN C 541 " --> pdb=" O HIS C 368 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE C 542 " --> pdb=" O GLN C 553 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN C 553 " --> pdb=" O ILE C 542 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL C 544 " --> pdb=" O ILE C 551 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 364 through 373 removed outlier: 6.784A pdb=" N ILE D 357 " --> pdb=" O LEU D 365 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLY D 367 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU D 355 " --> pdb=" O GLY D 367 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU D 369 " --> pdb=" O GLU D 353 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU D 353 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N PHE D 371 " --> pdb=" O GLU D 351 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N GLU D 351 " --> pdb=" O PHE D 371 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER D 401 " --> pdb=" O THR D 358 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 364 through 373 removed outlier: 6.784A pdb=" N ILE D 357 " --> pdb=" O LEU D 365 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLY D 367 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU D 355 " --> pdb=" O GLY D 367 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU D 369 " --> pdb=" O GLU D 353 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU D 353 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N PHE D 371 " --> pdb=" O GLU D 351 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N GLU D 351 " --> pdb=" O PHE D 371 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 425 through 428 removed outlier: 6.650A pdb=" N SER D 426 " --> pdb=" O LEU D 508 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N ASP D 510 " --> pdb=" O SER D 426 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL D 428 " --> pdb=" O ASP D 510 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU D 507 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N VAL D 540 " --> pdb=" O LEU D 507 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU D 509 " --> pdb=" O VAL D 540 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ARG D 378 " --> pdb=" O VAL D 552 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N TRP D 554 " --> pdb=" O ARG D 378 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL D 380 " --> pdb=" O TRP D 554 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N MET D 556 " --> pdb=" O VAL D 380 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL D 382 " --> pdb=" O MET D 556 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU D 563 " --> pdb=" O VAL D 555 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLN D 557 " --> pdb=" O ILE D 561 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ILE D 561 " --> pdb=" O GLN D 557 " (cutoff:3.500A) 551 hydrogen bonds defined for protein. 1614 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: 2.65 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2254 1.33 - 1.45: 1668 1.45 - 1.57: 5165 1.57 - 1.69: 10 1.69 - 1.81: 55 Bond restraints: 9152 Sorted by residual: bond pdb=" C4 ATP C 602 " pdb=" C5 ATP C 602 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.13e+01 bond pdb=" C4 ATP D 602 " pdb=" C5 ATP D 602 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.08e+01 bond pdb=" C5 ATP C 602 " pdb=" C6 ATP C 602 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.92e+01 bond pdb=" C5 ATP D 602 " pdb=" C6 ATP D 602 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.87e+01 bond pdb=" C8 ATP D 602 " pdb=" N7 ATP D 602 " ideal model delta sigma weight residual 1.310 1.358 -0.048 1.00e-02 1.00e+04 2.26e+01 ... (remaining 9147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.06: 12393 4.06 - 8.12: 48 8.12 - 12.18: 4 12.18 - 16.24: 1 16.24 - 20.31: 3 Bond angle restraints: 12449 Sorted by residual: angle pdb=" PB ATP C 602 " pdb=" O3B ATP C 602 " pdb=" PG ATP C 602 " ideal model delta sigma weight residual 139.87 119.56 20.31 1.00e+00 1.00e+00 4.12e+02 angle pdb=" PB ATP D 602 " pdb=" O3B ATP D 602 " pdb=" PG ATP D 602 " ideal model delta sigma weight residual 139.87 120.06 19.81 1.00e+00 1.00e+00 3.92e+02 angle pdb=" PA ATP C 602 " pdb=" O3A ATP C 602 " pdb=" PB ATP C 602 " ideal model delta sigma weight residual 136.83 120.08 16.75 1.00e+00 1.00e+00 2.81e+02 angle pdb=" PA ATP D 602 " pdb=" O3A ATP D 602 " pdb=" PB ATP D 602 " ideal model delta sigma weight residual 136.83 120.80 16.03 1.00e+00 1.00e+00 2.57e+02 angle pdb=" C5 ATP C 602 " pdb=" C4 ATP C 602 " pdb=" N3 ATP C 602 " ideal model delta sigma weight residual 126.80 118.40 8.40 1.00e+00 1.00e+00 7.06e+01 ... (remaining 12444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 4953 17.62 - 35.23: 433 35.23 - 52.85: 78 52.85 - 70.47: 26 70.47 - 88.08: 10 Dihedral angle restraints: 5500 sinusoidal: 2206 harmonic: 3294 Sorted by residual: dihedral pdb=" C PHE C 291 " pdb=" N PHE C 291 " pdb=" CA PHE C 291 " pdb=" CB PHE C 291 " ideal model delta harmonic sigma weight residual -122.60 -132.82 10.22 0 2.50e+00 1.60e-01 1.67e+01 dihedral pdb=" CA ASP D 277 " pdb=" CB ASP D 277 " pdb=" CG ASP D 277 " pdb=" OD1 ASP D 277 " ideal model delta sinusoidal sigma weight residual -30.00 -88.65 58.65 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASN D 162 " pdb=" CB ASN D 162 " pdb=" CG ASN D 162 " pdb=" OD1 ASN D 162 " ideal model delta sinusoidal sigma weight residual 120.00 -171.11 -68.89 2 2.00e+01 2.50e-03 1.04e+01 ... (remaining 5497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1272 0.060 - 0.120: 154 0.120 - 0.180: 20 0.180 - 0.241: 1 0.241 - 0.301: 1 Chirality restraints: 1448 Sorted by residual: chirality pdb=" CA PHE C 291 " pdb=" N PHE C 291 " pdb=" C PHE C 291 " pdb=" CB PHE C 291 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CG LEU D 547 " pdb=" CB LEU D 547 " pdb=" CD1 LEU D 547 " pdb=" CD2 LEU D 547 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ARG C 522 " pdb=" N ARG C 522 " pdb=" C ARG C 522 " pdb=" CB ARG C 522 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.56e-01 ... (remaining 1445 not shown) Planarity restraints: 1584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 555 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.55e+00 pdb=" C THR C 555 " 0.041 2.00e-02 2.50e+03 pdb=" O THR C 555 " -0.015 2.00e-02 2.50e+03 pdb=" N HIS C 556 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 104 " 0.028 5.00e-02 4.00e+02 4.18e-02 2.80e+00 pdb=" N PRO C 105 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 105 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 105 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET C 177 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO C 178 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 178 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 178 " 0.022 5.00e-02 4.00e+02 ... (remaining 1581 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 71 2.55 - 3.14: 6959 3.14 - 3.73: 14296 3.73 - 4.31: 20405 4.31 - 4.90: 34392 Nonbonded interactions: 76123 Sorted by model distance: nonbonded pdb=" OG SER D 390 " pdb="MG MG D 601 " model vdw 1.966 2.170 nonbonded pdb=" OE1 GLN D 430 " pdb="MG MG D 601 " model vdw 2.011 2.170 nonbonded pdb="MG MG D 601 " pdb=" O3G ATP D 602 " model vdw 2.014 2.170 nonbonded pdb=" OE1 GLN C 421 " pdb="MG MG C 601 " model vdw 2.036 2.170 nonbonded pdb=" OG SER C 380 " pdb="MG MG C 601 " model vdw 2.083 2.170 ... (remaining 76118 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.030 Find NCS groups from input model: 0.150 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: 0.000 Load rotamer database and sin/cos tables:12.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 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 : 0.005 0.078 9152 Z= 0.307 Angle : 0.753 20.306 12449 Z= 0.533 Chirality : 0.042 0.301 1448 Planarity : 0.004 0.042 1584 Dihedral : 14.467 88.083 3374 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.09 % 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: -0.78 (0.24), residues: 1144 helix: -0.54 (0.19), residues: 694 sheet: 0.16 (0.65), residues: 64 loop : -0.24 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 427 HIS 0.004 0.001 HIS C 94 PHE 0.018 0.001 PHE D 467 TYR 0.012 0.001 TYR C 59 ARG 0.011 0.000 ARG D 523 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: C 59 TYR cc_start: 0.8155 (p90) cc_final: 0.7929 (p90) REVERT: C 134 TYR cc_start: 0.8465 (t80) cc_final: 0.6621 (m-80) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 1.4802 time to fit residues: 183.7783 Evaluate side-chains 96 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 191 ASN D 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.114459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.089552 restraints weight = 12232.683| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.77 r_work: 0.2874 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9152 Z= 0.228 Angle : 0.571 8.397 12449 Z= 0.296 Chirality : 0.041 0.155 1448 Planarity : 0.005 0.042 1584 Dihedral : 7.797 82.701 1317 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.25 % Allowed : 7.73 % Favored : 90.02 % 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: 0.91 (0.25), residues: 1144 helix: 1.19 (0.20), residues: 691 sheet: 0.06 (0.63), residues: 64 loop : -0.23 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 12 HIS 0.008 0.001 HIS D 280 PHE 0.013 0.001 PHE D 205 TYR 0.013 0.001 TYR D 88 ARG 0.009 0.001 ARG D 523 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 1.073 Fit side-chains revert: symmetry clash REVERT: C 134 TYR cc_start: 0.8642 (t80) cc_final: 0.6397 (m-80) REVERT: D 88 TYR cc_start: 0.8606 (t80) cc_final: 0.8075 (t80) REVERT: D 336 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8009 (pp30) outliers start: 21 outliers final: 6 residues processed: 117 average time/residue: 1.4419 time to fit residues: 179.2003 Evaluate side-chains 103 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 353 GLN Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain D residue 372 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 88 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 98 optimal weight: 0.0970 chunk 81 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 GLN ** D 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 583 HIS D 585 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.115868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.091104 restraints weight = 12238.050| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.77 r_work: 0.2894 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9152 Z= 0.180 Angle : 0.508 6.266 12449 Z= 0.261 Chirality : 0.039 0.143 1448 Planarity : 0.004 0.041 1584 Dihedral : 7.749 82.912 1317 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.15 % Allowed : 9.76 % Favored : 88.09 % 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: 1.59 (0.25), residues: 1144 helix: 1.83 (0.20), residues: 693 sheet: 0.12 (0.65), residues: 61 loop : -0.13 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 12 HIS 0.008 0.001 HIS D 280 PHE 0.012 0.001 PHE D 205 TYR 0.014 0.001 TYR D 88 ARG 0.006 0.000 ARG D 523 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 1.090 Fit side-chains revert: symmetry clash REVERT: C 134 TYR cc_start: 0.8679 (t80) cc_final: 0.6384 (m-80) REVERT: C 414 GLN cc_start: 0.8032 (mt0) cc_final: 0.7735 (mm-40) REVERT: D 88 TYR cc_start: 0.8558 (t80) cc_final: 0.7970 (t80) REVERT: D 336 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.7976 (pp30) REVERT: D 337 ARG cc_start: 0.8592 (tpt-90) cc_final: 0.8167 (ttt90) outliers start: 20 outliers final: 3 residues processed: 112 average time/residue: 1.3218 time to fit residues: 158.8477 Evaluate side-chains 98 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain D residue 372 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 81 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 112 optimal weight: 0.0770 chunk 70 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 583 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.116535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.091883 restraints weight = 12160.903| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.76 r_work: 0.2906 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9152 Z= 0.175 Angle : 0.497 6.292 12449 Z= 0.254 Chirality : 0.039 0.160 1448 Planarity : 0.004 0.040 1584 Dihedral : 7.644 85.093 1317 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.04 % Allowed : 11.70 % Favored : 86.27 % 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: 1.99 (0.25), residues: 1144 helix: 2.18 (0.20), residues: 697 sheet: 0.17 (0.64), residues: 61 loop : -0.03 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 12 HIS 0.003 0.001 HIS D 280 PHE 0.011 0.001 PHE D 205 TYR 0.020 0.001 TYR C 59 ARG 0.008 0.000 ARG D 523 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: C 134 TYR cc_start: 0.8662 (t80) cc_final: 0.6349 (m-80) REVERT: C 414 GLN cc_start: 0.8052 (mt0) cc_final: 0.7717 (mm-40) REVERT: C 521 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8127 (mtm) REVERT: D 88 TYR cc_start: 0.8582 (t80) cc_final: 0.7998 (t80) REVERT: D 180 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.7016 (ttm) REVERT: D 566 ARG cc_start: 0.7544 (mtp-110) cc_final: 0.7264 (mtp85) outliers start: 19 outliers final: 8 residues processed: 115 average time/residue: 1.2770 time to fit residues: 156.8358 Evaluate side-chains 106 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 372 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 9 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 113 optimal weight: 0.0670 chunk 49 optimal weight: 0.0970 chunk 39 optimal weight: 0.0050 chunk 15 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 88 optimal weight: 0.4980 chunk 67 optimal weight: 0.0870 chunk 60 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 overall best weight: 0.1508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 GLN ** D 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 583 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.119490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.095175 restraints weight = 12134.532| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.75 r_work: 0.2956 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9152 Z= 0.137 Angle : 0.482 5.992 12449 Z= 0.244 Chirality : 0.037 0.147 1448 Planarity : 0.004 0.039 1584 Dihedral : 7.390 87.953 1317 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.25 % Allowed : 12.98 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.26), residues: 1144 helix: 2.46 (0.20), residues: 703 sheet: 0.31 (0.64), residues: 61 loop : 0.11 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 12 HIS 0.003 0.001 HIS C 85 PHE 0.009 0.001 PHE D 205 TYR 0.015 0.001 TYR D 88 ARG 0.008 0.000 ARG D 523 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 1.094 Fit side-chains REVERT: C 36 LEU cc_start: 0.8345 (mm) cc_final: 0.8034 (mm) REVERT: C 134 TYR cc_start: 0.8604 (t80) cc_final: 0.6243 (m-80) REVERT: C 414 GLN cc_start: 0.7967 (mt0) cc_final: 0.7593 (mm-40) REVERT: C 521 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8096 (mtm) REVERT: D 88 TYR cc_start: 0.8449 (t80) cc_final: 0.7919 (t80) REVERT: D 180 MET cc_start: 0.7292 (OUTLIER) cc_final: 0.6924 (ttm) REVERT: D 482 GLN cc_start: 0.8669 (mp-120) cc_final: 0.8457 (mm-40) REVERT: D 566 ARG cc_start: 0.7511 (mtp-110) cc_final: 0.7270 (mtp85) outliers start: 21 outliers final: 6 residues processed: 124 average time/residue: 1.1999 time to fit residues: 159.5497 Evaluate side-chains 109 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 372 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 53 optimal weight: 0.0870 chunk 96 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 583 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.117739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.093093 restraints weight = 12118.452| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.75 r_work: 0.2928 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9152 Z= 0.192 Angle : 0.496 5.966 12449 Z= 0.250 Chirality : 0.039 0.144 1448 Planarity : 0.004 0.048 1584 Dihedral : 7.377 86.822 1317 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.79 % Allowed : 13.95 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.26), residues: 1144 helix: 2.49 (0.20), residues: 703 sheet: 0.41 (0.65), residues: 61 loop : 0.09 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 12 HIS 0.003 0.001 HIS C 85 PHE 0.011 0.001 PHE C 181 TYR 0.016 0.001 TYR D 88 ARG 0.011 0.000 ARG D 560 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: C 134 TYR cc_start: 0.8631 (t80) cc_final: 0.6275 (m-80) REVERT: C 414 GLN cc_start: 0.7975 (mt0) cc_final: 0.7702 (mm-40) REVERT: D 88 TYR cc_start: 0.8556 (t80) cc_final: 0.8038 (t80) REVERT: D 104 ASP cc_start: 0.8812 (m-30) cc_final: 0.8611 (m-30) REVERT: D 159 PHE cc_start: 0.8574 (OUTLIER) cc_final: 0.8021 (m-10) REVERT: D 180 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.7009 (ttm) REVERT: D 336 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7962 (pp30) REVERT: D 482 GLN cc_start: 0.8713 (mp-120) cc_final: 0.8499 (mm-40) outliers start: 26 outliers final: 10 residues processed: 115 average time/residue: 1.3354 time to fit residues: 163.9229 Evaluate side-chains 110 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 159 PHE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 564 GLN Chi-restraints excluded: chain D residue 570 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 68 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 chunk 35 optimal weight: 0.0370 chunk 11 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.117503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.092853 restraints weight = 12334.610| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.77 r_work: 0.2920 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9152 Z= 0.178 Angle : 0.496 6.557 12449 Z= 0.251 Chirality : 0.039 0.142 1448 Planarity : 0.004 0.049 1584 Dihedral : 7.379 87.587 1317 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.93 % Allowed : 14.81 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.26), residues: 1144 helix: 2.48 (0.19), residues: 709 sheet: 0.48 (0.66), residues: 61 loop : 0.11 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 12 HIS 0.003 0.001 HIS C 85 PHE 0.011 0.001 PHE D 205 TYR 0.016 0.001 TYR D 88 ARG 0.010 0.000 ARG D 560 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: C 134 TYR cc_start: 0.8634 (t80) cc_final: 0.6229 (m-80) REVERT: C 414 GLN cc_start: 0.7911 (mt0) cc_final: 0.7632 (mm-40) REVERT: D 88 TYR cc_start: 0.8566 (t80) cc_final: 0.8042 (t80) REVERT: D 104 ASP cc_start: 0.8781 (m-30) cc_final: 0.8561 (m-30) REVERT: D 180 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.7004 (ttm) REVERT: D 336 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.7960 (pp30) REVERT: D 482 GLN cc_start: 0.8710 (mp-120) cc_final: 0.8507 (mm-40) outliers start: 18 outliers final: 12 residues processed: 111 average time/residue: 1.3022 time to fit residues: 154.3415 Evaluate side-chains 112 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 520 MET Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 564 GLN Chi-restraints excluded: chain D residue 570 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 0 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 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 = 0.3400 r_free = 0.3400 target = 0.117088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.092303 restraints weight = 12420.043| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.78 r_work: 0.2911 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9152 Z= 0.195 Angle : 0.504 6.641 12449 Z= 0.255 Chirality : 0.039 0.139 1448 Planarity : 0.004 0.053 1584 Dihedral : 7.398 87.769 1317 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.72 % Allowed : 15.67 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.25), residues: 1144 helix: 2.48 (0.19), residues: 709 sheet: 0.50 (0.65), residues: 61 loop : 0.11 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 12 HIS 0.003 0.001 HIS C 85 PHE 0.017 0.001 PHE C 164 TYR 0.016 0.001 TYR D 88 ARG 0.013 0.000 ARG D 560 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.986 Fit side-chains REVERT: C 124 VAL cc_start: 0.8271 (t) cc_final: 0.7823 (p) REVERT: C 134 TYR cc_start: 0.8647 (t80) cc_final: 0.6234 (m-80) REVERT: C 414 GLN cc_start: 0.7922 (mt0) cc_final: 0.7668 (mm-40) REVERT: D 104 ASP cc_start: 0.8811 (m-30) cc_final: 0.8593 (m-30) REVERT: D 180 MET cc_start: 0.7303 (OUTLIER) cc_final: 0.6967 (ttm) REVERT: D 336 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7963 (pp30) REVERT: D 482 GLN cc_start: 0.8709 (mp-120) cc_final: 0.8505 (mm-40) outliers start: 16 outliers final: 12 residues processed: 113 average time/residue: 1.2889 time to fit residues: 155.2006 Evaluate side-chains 113 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 564 GLN Chi-restraints excluded: chain D residue 570 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 67 optimal weight: 0.2980 chunk 18 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 208 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 = 0.3403 r_free = 0.3403 target = 0.117297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.092653 restraints weight = 12177.678| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.76 r_work: 0.2918 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9152 Z= 0.188 Angle : 0.515 6.966 12449 Z= 0.262 Chirality : 0.039 0.139 1448 Planarity : 0.004 0.058 1584 Dihedral : 7.390 88.597 1317 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.04 % Allowed : 15.77 % Favored : 82.19 % 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: 2.45 (0.25), residues: 1144 helix: 2.50 (0.19), residues: 709 sheet: 0.51 (0.65), residues: 61 loop : 0.12 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 12 HIS 0.003 0.001 HIS C 85 PHE 0.012 0.001 PHE D 205 TYR 0.016 0.001 TYR D 88 ARG 0.014 0.000 ARG D 560 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 1.076 Fit side-chains REVERT: C 134 TYR cc_start: 0.8642 (t80) cc_final: 0.6228 (m-80) REVERT: C 414 GLN cc_start: 0.7891 (mt0) cc_final: 0.7664 (mm-40) REVERT: D 104 ASP cc_start: 0.8814 (m-30) cc_final: 0.8597 (m-30) REVERT: D 180 MET cc_start: 0.7263 (OUTLIER) cc_final: 0.6925 (ttm) REVERT: D 336 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.7954 (pp30) REVERT: D 482 GLN cc_start: 0.8696 (mp-120) cc_final: 0.8493 (mm-40) outliers start: 19 outliers final: 13 residues processed: 111 average time/residue: 1.4739 time to fit residues: 174.8197 Evaluate side-chains 114 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 520 MET Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 564 GLN Chi-restraints excluded: chain D residue 570 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 14 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 93 optimal weight: 0.0970 chunk 76 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 GLN C 302 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.117463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.092768 restraints weight = 12207.838| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.76 r_work: 0.2920 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9152 Z= 0.188 Angle : 0.521 8.993 12449 Z= 0.264 Chirality : 0.039 0.142 1448 Planarity : 0.004 0.061 1584 Dihedral : 7.350 89.282 1317 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.82 % Allowed : 16.09 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.26), residues: 1144 helix: 2.51 (0.19), residues: 709 sheet: 0.45 (0.65), residues: 62 loop : 0.14 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 12 HIS 0.003 0.001 HIS C 85 PHE 0.017 0.001 PHE C 164 TYR 0.016 0.001 TYR D 88 ARG 0.014 0.000 ARG D 560 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 1.196 Fit side-chains REVERT: C 59 TYR cc_start: 0.8437 (p90) cc_final: 0.8027 (p90) REVERT: C 124 VAL cc_start: 0.8098 (t) cc_final: 0.7874 (p) REVERT: C 134 TYR cc_start: 0.8641 (t80) cc_final: 0.6223 (m-80) REVERT: C 414 GLN cc_start: 0.7820 (mt0) cc_final: 0.7591 (mm-40) REVERT: D 88 TYR cc_start: 0.8561 (t80) cc_final: 0.8024 (t80) REVERT: D 104 ASP cc_start: 0.8813 (m-30) cc_final: 0.8592 (m-30) REVERT: D 159 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.8157 (m-80) REVERT: D 180 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.6937 (ttm) REVERT: D 336 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8052 (pp30) REVERT: D 482 GLN cc_start: 0.8694 (mp-120) cc_final: 0.8489 (mm-40) outliers start: 17 outliers final: 13 residues processed: 112 average time/residue: 1.9775 time to fit residues: 236.7143 Evaluate side-chains 113 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 520 MET Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 159 PHE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 564 GLN Chi-restraints excluded: chain D residue 570 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 208 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 = 0.3400 r_free = 0.3400 target = 0.117080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.092397 restraints weight = 12345.317| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.77 r_work: 0.2916 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9152 Z= 0.201 Angle : 0.539 11.123 12449 Z= 0.269 Chirality : 0.041 0.429 1448 Planarity : 0.004 0.062 1584 Dihedral : 7.366 89.374 1317 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.82 % Allowed : 16.31 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.25), residues: 1144 helix: 2.49 (0.19), residues: 709 sheet: 0.46 (0.65), residues: 62 loop : 0.14 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 12 HIS 0.003 0.001 HIS C 85 PHE 0.012 0.001 PHE D 205 TYR 0.017 0.001 TYR D 88 ARG 0.014 0.000 ARG D 560 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6203.27 seconds wall clock time: 110 minutes 12.29 seconds (6612.29 seconds total)