Starting phenix.real_space_refine on Tue Mar 3 22:47:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zdu_14670/03_2026/7zdu_14670_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zdu_14670/03_2026/7zdu_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 { model { file = "/net/cci-nas-00/data/ceres_data/7zdu_14670/03_2026/7zdu_14670_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zdu_14670/03_2026/7zdu_14670_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zdu_14670/03_2026/7zdu_14670.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zdu_14670/03_2026/7zdu_14670.map" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.21, per 1000 atoms: 0.25 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: 0.71 Conformation dependent library (CDL) restraints added in 351.8 milliseconds 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: 0.28 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: 1.32 Time building geometry restraints manager: 0.97 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.620 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:6.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.060 ------------------------------------------------------------------------------- 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= 0.304 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.011 0.000 ARG D 523 TYR 0.012 0.001 TYR C 59 PHE 0.018 0.001 PHE D 467 TRP 0.019 0.001 TRP D 427 HIS 0.004 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 9152) covalent geometry : angle 0.75345 (12449) hydrogen bonds : bond 0.24432 ( 550) hydrogen bonds : angle 8.21624 ( 1614) *********************** 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 : 0.372 Fit side-chains 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: 0.6635 time to fit residues: 82.2173 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 : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 191 ASN C 362 GLN D 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.115227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.090602 restraints weight = 12304.739| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.75 r_work: 0.2876 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9152 Z= 0.158 Angle : 0.576 8.425 12449 Z= 0.299 Chirality : 0.041 0.155 1448 Planarity : 0.005 0.042 1584 Dihedral : 7.777 84.478 1317 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.36 % Allowed : 7.83 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.25), residues: 1144 helix: 1.22 (0.20), residues: 689 sheet: 0.14 (0.67), residues: 58 loop : -0.30 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 523 TYR 0.013 0.001 TYR D 88 PHE 0.014 0.001 PHE D 205 TRP 0.013 0.001 TRP D 12 HIS 0.008 0.001 HIS D 280 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9152) covalent geometry : angle 0.57599 (12449) hydrogen bonds : bond 0.05609 ( 550) hydrogen bonds : angle 4.67028 ( 1614) *********************** 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 128 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.326 Fit side-chains REVERT: C 134 TYR cc_start: 0.8638 (t80) cc_final: 0.6392 (m-80) REVERT: D 336 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8029 (pp30) outliers start: 22 outliers final: 7 residues processed: 118 average time/residue: 0.6850 time to fit residues: 85.5459 Evaluate side-chains 104 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 556 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 101 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 302 GLN ** D 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.114145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.089361 restraints weight = 12245.272| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.75 r_work: 0.2873 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9152 Z= 0.157 Angle : 0.532 6.331 12449 Z= 0.273 Chirality : 0.040 0.142 1448 Planarity : 0.004 0.044 1584 Dihedral : 7.863 82.280 1317 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.36 % Allowed : 10.52 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.25), residues: 1144 helix: 1.74 (0.20), residues: 695 sheet: 0.12 (0.67), residues: 55 loop : -0.23 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 523 TYR 0.016 0.001 TYR D 88 PHE 0.012 0.001 PHE D 205 TRP 0.012 0.001 TRP D 12 HIS 0.008 0.001 HIS D 280 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 9152) covalent geometry : angle 0.53184 (12449) hydrogen bonds : bond 0.04839 ( 550) hydrogen bonds : angle 4.24074 ( 1614) *********************** 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 123 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.349 Fit side-chains REVERT: C 134 TYR cc_start: 0.8711 (t80) cc_final: 0.6420 (m-80) REVERT: C 414 GLN cc_start: 0.8072 (mt0) cc_final: 0.7828 (mm-40) REVERT: D 336 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8014 (pp30) REVERT: D 337 ARG cc_start: 0.8565 (tpt-90) cc_final: 0.8141 (ttt90) REVERT: D 557 GLN cc_start: 0.8157 (tt0) cc_final: 0.7939 (tt0) outliers start: 22 outliers final: 5 residues processed: 112 average time/residue: 0.6310 time to fit residues: 75.2555 Evaluate side-chains 98 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 175 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 16 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3380 r_free = 0.3380 target = 0.115453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.090756 restraints weight = 12365.435| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.76 r_work: 0.2890 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9152 Z= 0.127 Angle : 0.507 6.507 12449 Z= 0.260 Chirality : 0.039 0.160 1448 Planarity : 0.004 0.042 1584 Dihedral : 7.749 82.604 1317 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.15 % Allowed : 12.02 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.25), residues: 1144 helix: 2.09 (0.20), residues: 696 sheet: 0.10 (0.66), residues: 55 loop : -0.14 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 566 TYR 0.016 0.001 TYR D 88 PHE 0.012 0.001 PHE D 205 TRP 0.010 0.001 TRP D 12 HIS 0.007 0.001 HIS D 280 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9152) covalent geometry : angle 0.50710 (12449) hydrogen bonds : bond 0.04312 ( 550) hydrogen bonds : angle 4.06139 ( 1614) *********************** 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 120 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.392 Fit side-chains REVERT: C 134 TYR cc_start: 0.8686 (t80) cc_final: 0.6368 (m-80) REVERT: C 414 GLN cc_start: 0.8041 (mt0) cc_final: 0.7777 (mm-40) REVERT: C 521 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8139 (mtm) REVERT: D 180 MET cc_start: 0.7393 (OUTLIER) cc_final: 0.7100 (ttm) REVERT: D 336 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8016 (pp30) REVERT: D 560 ARG cc_start: 0.7400 (ttp-110) cc_final: 0.7115 (ttm110) REVERT: D 566 ARG cc_start: 0.7578 (mtp-110) cc_final: 0.7265 (mtp85) outliers start: 20 outliers final: 8 residues processed: 110 average time/residue: 0.6353 time to fit residues: 74.2076 Evaluate side-chains 104 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 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 336 GLN Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 556 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 72 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 353 GLN ** D 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.115089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.090330 restraints weight = 12302.900| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.77 r_work: 0.2880 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9152 Z= 0.141 Angle : 0.509 6.389 12449 Z= 0.260 Chirality : 0.040 0.150 1448 Planarity : 0.004 0.042 1584 Dihedral : 7.691 82.647 1317 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.36 % Allowed : 12.77 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.25), residues: 1144 helix: 2.22 (0.20), residues: 697 sheet: 0.11 (0.66), residues: 55 loop : -0.12 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 522 TYR 0.017 0.001 TYR D 88 PHE 0.012 0.001 PHE D 205 TRP 0.009 0.001 TRP D 12 HIS 0.003 0.001 HIS D 312 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9152) covalent geometry : angle 0.50912 (12449) hydrogen bonds : bond 0.04267 ( 550) hydrogen bonds : angle 3.97579 ( 1614) *********************** 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 119 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.227 Fit side-chains REVERT: C 134 TYR cc_start: 0.8703 (t80) cc_final: 0.6349 (m-80) REVERT: C 414 GLN cc_start: 0.8052 (mt0) cc_final: 0.7768 (mm-40) REVERT: C 521 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8140 (mtm) REVERT: D 159 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.8148 (m-10) REVERT: D 180 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.7049 (ttm) REVERT: D 336 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8012 (pp30) REVERT: D 566 ARG cc_start: 0.7543 (mtp-110) cc_final: 0.7321 (mtp85) outliers start: 22 outliers final: 13 residues processed: 109 average time/residue: 0.6055 time to fit residues: 70.2913 Evaluate side-chains 107 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 340 THR Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 520 MET 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 159 PHE 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 336 GLN Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 570 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 70 optimal weight: 0.0980 chunk 99 optimal weight: 0.0770 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.116472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.091889 restraints weight = 12244.125| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.76 r_work: 0.2906 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2079 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= 0.113 Angle : 0.493 6.308 12449 Z= 0.252 Chirality : 0.038 0.146 1448 Planarity : 0.004 0.041 1584 Dihedral : 7.561 84.399 1317 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.47 % Allowed : 13.73 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.26), residues: 1144 helix: 2.37 (0.20), residues: 704 sheet: 0.14 (0.66), residues: 55 loop : -0.00 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 560 TYR 0.017 0.001 TYR D 88 PHE 0.011 0.001 PHE D 205 TRP 0.009 0.001 TRP D 12 HIS 0.003 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 9152) covalent geometry : angle 0.49273 (12449) hydrogen bonds : bond 0.03962 ( 550) hydrogen bonds : angle 3.87119 ( 1614) *********************** 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 124 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.232 Fit side-chains REVERT: C 134 TYR cc_start: 0.8641 (t80) cc_final: 0.6238 (m-80) REVERT: C 414 GLN cc_start: 0.8033 (mt0) cc_final: 0.7728 (mm-40) REVERT: C 521 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8130 (mtm) REVERT: D 88 TYR cc_start: 0.8559 (t80) cc_final: 0.8038 (t80) REVERT: D 104 ASP cc_start: 0.8794 (m-30) cc_final: 0.8585 (m-30) REVERT: D 159 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.8112 (m-10) REVERT: D 180 MET cc_start: 0.7300 (OUTLIER) cc_final: 0.6974 (ttm) REVERT: D 556 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8701 (ttm) REVERT: D 560 ARG cc_start: 0.7390 (ttp-110) cc_final: 0.7152 (ttp-110) REVERT: D 566 ARG cc_start: 0.7574 (mtp-110) cc_final: 0.7344 (mtp85) outliers start: 23 outliers final: 11 residues processed: 112 average time/residue: 0.5706 time to fit residues: 68.2211 Evaluate side-chains 111 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 464 LEU 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 144 MET 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 21 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 5 optimal weight: 6.9990 chunk 14 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 43 optimal weight: 0.0870 chunk 75 optimal weight: 0.5980 chunk 93 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 433 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 = 0.3401 r_free = 0.3401 target = 0.117145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.092483 restraints weight = 12288.291| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.78 r_work: 0.2912 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9152 Z= 0.112 Angle : 0.490 6.075 12449 Z= 0.250 Chirality : 0.038 0.146 1448 Planarity : 0.004 0.045 1584 Dihedral : 7.428 84.885 1317 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.25 % Allowed : 14.59 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.26), residues: 1144 helix: 2.48 (0.20), residues: 703 sheet: 0.20 (0.66), residues: 55 loop : 0.04 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 523 TYR 0.017 0.001 TYR D 88 PHE 0.010 0.001 PHE D 205 TRP 0.008 0.001 TRP D 12 HIS 0.003 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9152) covalent geometry : angle 0.48973 (12449) hydrogen bonds : bond 0.03833 ( 550) hydrogen bonds : angle 3.82143 ( 1614) *********************** 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 123 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.340 Fit side-chains REVERT: C 134 TYR cc_start: 0.8644 (t80) cc_final: 0.6241 (m-80) REVERT: C 521 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8178 (mtm) REVERT: D 88 TYR cc_start: 0.8564 (t80) cc_final: 0.8052 (t80) REVERT: D 104 ASP cc_start: 0.8813 (m-30) cc_final: 0.8609 (m-30) REVERT: D 336 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8001 (pp30) REVERT: D 556 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8700 (ttm) REVERT: D 560 ARG cc_start: 0.7403 (ttp-110) cc_final: 0.7174 (ttp-110) REVERT: D 566 ARG cc_start: 0.7592 (mtp-110) cc_final: 0.7378 (mtp85) outliers start: 21 outliers final: 9 residues processed: 113 average time/residue: 0.6314 time to fit residues: 75.9040 Evaluate side-chains 105 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 340 THR Chi-restraints excluded: chain C residue 497 LEU 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 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 570 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 67 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 98 optimal weight: 0.3980 chunk 94 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ** D 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.117070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.092324 restraints weight = 12239.924| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.78 r_work: 0.2913 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2250 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= 0.117 Angle : 0.501 6.338 12449 Z= 0.254 Chirality : 0.039 0.158 1448 Planarity : 0.004 0.040 1584 Dihedral : 7.388 85.643 1317 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.04 % Allowed : 15.45 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.26), residues: 1144 helix: 2.53 (0.20), residues: 703 sheet: 0.25 (0.66), residues: 55 loop : 0.04 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 523 TYR 0.017 0.001 TYR D 88 PHE 0.018 0.001 PHE C 164 TRP 0.007 0.001 TRP D 12 HIS 0.003 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9152) covalent geometry : angle 0.50138 (12449) hydrogen bonds : bond 0.03808 ( 550) hydrogen bonds : angle 3.78309 ( 1614) *********************** 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 115 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.289 Fit side-chains REVERT: C 134 TYR cc_start: 0.8659 (t80) cc_final: 0.6243 (m-80) REVERT: C 414 GLN cc_start: 0.7906 (mt0) cc_final: 0.7661 (mm-40) REVERT: C 521 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8221 (mtm) REVERT: D 104 ASP cc_start: 0.8836 (m-30) cc_final: 0.8628 (m-30) REVERT: D 180 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.7011 (ttm) REVERT: D 336 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.7964 (pp30) REVERT: D 482 GLN cc_start: 0.8694 (mp-120) cc_final: 0.8493 (mm-40) REVERT: D 556 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8699 (ttm) REVERT: D 560 ARG cc_start: 0.7430 (ttp-110) cc_final: 0.7208 (ttp-110) REVERT: D 566 ARG cc_start: 0.7583 (mtp-110) cc_final: 0.7302 (mtp85) outliers start: 19 outliers final: 10 residues processed: 108 average time/residue: 0.5257 time to fit residues: 60.4883 Evaluate side-chains 110 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 340 THR Chi-restraints excluded: chain C residue 497 LEU 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 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 570 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 11 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 99 optimal weight: 0.0060 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 ** D 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.117047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.092346 restraints weight = 12228.725| |-----------------------------------------------------------------------------| 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: 0.2772 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2313 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= 0.120 Angle : 0.506 7.484 12449 Z= 0.256 Chirality : 0.039 0.169 1448 Planarity : 0.004 0.042 1584 Dihedral : 7.352 86.152 1317 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.93 % Allowed : 15.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.26), residues: 1144 helix: 2.55 (0.20), residues: 702 sheet: 0.31 (0.67), residues: 55 loop : 0.03 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 523 TYR 0.017 0.001 TYR D 88 PHE 0.011 0.001 PHE D 205 TRP 0.007 0.001 TRP D 12 HIS 0.003 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9152) covalent geometry : angle 0.50622 (12449) hydrogen bonds : bond 0.03802 ( 550) hydrogen bonds : angle 3.77033 ( 1614) *********************** 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 117 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.274 Fit side-chains REVERT: C 124 VAL cc_start: 0.8105 (t) cc_final: 0.7903 (p) REVERT: C 134 TYR cc_start: 0.8659 (t80) cc_final: 0.6243 (m-80) REVERT: C 414 GLN cc_start: 0.7902 (mt0) cc_final: 0.7636 (mm-40) REVERT: C 521 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8248 (mtm) REVERT: D 71 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8249 (mm) REVERT: D 104 ASP cc_start: 0.8843 (m-30) cc_final: 0.8630 (m-30) REVERT: D 336 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8060 (pp30) REVERT: D 482 GLN cc_start: 0.8691 (mp-120) cc_final: 0.8491 (mm-40) REVERT: D 556 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8705 (ttm) REVERT: D 560 ARG cc_start: 0.7421 (ttp-110) cc_final: 0.7215 (ttp-110) REVERT: D 566 ARG cc_start: 0.7609 (mtp-110) cc_final: 0.7324 (mtp85) outliers start: 18 outliers final: 12 residues processed: 110 average time/residue: 0.5581 time to fit residues: 65.4272 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 : 0.308 ------------------------------------------------------------------------------- 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 340 THR Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 497 LEU 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 71 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 86 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 100 optimal weight: 0.0050 chunk 42 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.117194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.092507 restraints weight = 12253.563| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.76 r_work: 0.2915 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2326 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= 0.121 Angle : 0.516 7.620 12449 Z= 0.261 Chirality : 0.039 0.160 1448 Planarity : 0.004 0.041 1584 Dihedral : 7.345 86.885 1317 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.15 % Allowed : 15.34 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.26), residues: 1144 helix: 2.52 (0.20), residues: 708 sheet: 0.04 (0.63), residues: 60 loop : 0.05 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 523 TYR 0.017 0.001 TYR D 88 PHE 0.019 0.001 PHE C 164 TRP 0.007 0.001 TRP D 12 HIS 0.003 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9152) covalent geometry : angle 0.51612 (12449) hydrogen bonds : bond 0.03780 ( 550) hydrogen bonds : angle 3.75422 ( 1614) ********************** 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 124 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.344 Fit side-chains REVERT: C 134 TYR cc_start: 0.8663 (t80) cc_final: 0.6233 (m-80) REVERT: C 414 GLN cc_start: 0.7895 (mt0) cc_final: 0.7643 (mm-40) REVERT: C 521 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8268 (mtm) REVERT: D 71 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8247 (mm) REVERT: D 104 ASP cc_start: 0.8842 (m-30) cc_final: 0.8630 (m-30) REVERT: D 180 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.7025 (ttm) REVERT: D 336 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8083 (pp30) REVERT: D 556 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8701 (ttm) REVERT: D 560 ARG cc_start: 0.7420 (ttp-110) cc_final: 0.7220 (ttp-110) REVERT: D 566 ARG cc_start: 0.7657 (mtp-110) cc_final: 0.7322 (mtp85) outliers start: 20 outliers final: 10 residues processed: 115 average time/residue: 0.6317 time to fit residues: 77.2598 Evaluate side-chains 112 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 340 THR Chi-restraints excluded: chain C residue 497 LEU 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 71 LEU 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 570 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 7 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.116535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.091897 restraints weight = 12083.044| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.74 r_work: 0.2906 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2330 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= 0.136 Angle : 0.531 8.024 12449 Z= 0.269 Chirality : 0.039 0.169 1448 Planarity : 0.004 0.042 1584 Dihedral : 7.384 86.370 1317 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.72 % Allowed : 16.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.25), residues: 1144 helix: 2.47 (0.19), residues: 708 sheet: -0.00 (0.63), residues: 60 loop : 0.03 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 523 TYR 0.017 0.001 TYR D 88 PHE 0.012 0.001 PHE D 205 TRP 0.007 0.001 TRP D 12 HIS 0.003 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9152) covalent geometry : angle 0.53100 (12449) hydrogen bonds : bond 0.03882 ( 550) hydrogen bonds : angle 3.76936 ( 1614) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2878.49 seconds wall clock time: 49 minutes 41.22 seconds (2981.22 seconds total)