Starting phenix.real_space_refine on Thu Mar 13 17:56:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zdt_14669/03_2025/7zdt_14669_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zdt_14669/03_2025/7zdt_14669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zdt_14669/03_2025/7zdt_14669.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zdt_14669/03_2025/7zdt_14669.map" model { file = "/net/cci-nas-00/data/ceres_data/7zdt_14669/03_2025/7zdt_14669_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zdt_14669/03_2025/7zdt_14669_neut.cif" } resolution = 2.71 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= 0.006 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 3 5.49 5 Mg 1 5.21 5 S 30 5.16 5 C 5761 2.51 5 N 1584 2.21 5 O 1624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9003 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 4425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4425 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 18, 'TRANS': 553} Chain: "D" Number of atoms: 4546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4546 Classifications: {'peptide': 583} Link IDs: {'PTRANS': 27, 'TRANS': 555} 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} Time building chain proxies: 5.49, per 1000 atoms: 0.61 Number of scatterers: 9003 At special positions: 0 Unit cell: (137.268, 77.841, 100.44, 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 30 16.00 P 3 15.00 Mg 1 11.99 O 1624 8.00 N 1584 7.00 C 5761 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: 2.18 Conformation dependent library (CDL) restraints added in 1.0 seconds 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2136 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 5 sheets defined 69.3% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 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 Processing helix chain 'C' and resid 10 through 12 No H-bonds generated for 'chain 'C' and resid 10 through 12' Processing helix chain 'C' and resid 14 through 50 removed outlier: 3.654A pdb=" N LEU C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 101 removed outlier: 3.585A pdb=" N ILE C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 107 Proline residue: C 105 - end of helix No H-bonds generated for 'chain 'C' and resid 102 through 107' Processing helix chain 'C' and resid 110 through 114 Processing helix chain 'C' and resid 115 through 130 removed outlier: 4.687A pdb=" N VAL C 127 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP C 128 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C 130 " --> pdb=" O ASP C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 136 removed outlier: 3.721A pdb=" N TYR C 134 " --> pdb=" O LEU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 159 removed outlier: 3.768A pdb=" N PHE C 157 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU C 158 " --> pdb=" O GLY C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 209 Proline residue: C 178 - end of helix removed outlier: 4.649A pdb=" N SER C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N THR C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 216 removed outlier: 3.782A pdb=" N ILE C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 269 removed outlier: 3.596A pdb=" N SER C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY C 268 " --> pdb=" O TRP C 264 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY C 269 " --> pdb=" O MET C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 291 removed outlier: 4.450A pdb=" N ALA C 281 " --> pdb=" O GLY C 277 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE C 291 " --> pdb=" O ALA C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 removed outlier: 4.094A pdb=" N THR C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLY C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE C 301 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS C 303 " --> pdb=" O GLY C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 319 Processing helix chain 'C' and resid 378 through 386 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 414 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 460 removed outlier: 3.547A pdb=" N GLU C 460 " --> pdb=" O LYS C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 466 Processing helix chain 'C' and resid 476 through 492 removed outlier: 3.519A pdb=" N ASP C 492 " --> pdb=" O ALA C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 521 Processing helix chain 'C' and resid 555 through 563 Processing helix chain 'C' and resid 564 through 571 removed outlier: 3.585A pdb=" N GLN C 568 " --> pdb=" O GLY C 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 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 55 Processing helix chain 'D' and resid 63 through 115 removed outlier: 3.702A pdb=" N GLY D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) Proline residue: D 111 - end of helix Processing helix chain 'D' and resid 118 through 127 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: 4.767A pdb=" N ALA D 145 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU D 146 " --> pdb=" O PRO D 142 " (cutoff:3.500A) removed outlier: 3.837A 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: 3.534A pdb=" N ALA D 166 " --> pdb=" O ASN D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 184 removed outlier: 4.305A pdb=" N LEU D 178 " --> pdb=" O PRO D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 211 Processing helix chain 'D' and resid 211 through 219 Processing helix chain 'D' and resid 220 through 274 removed outlier: 3.652A pdb=" N LEU D 245 " --> pdb=" O GLU D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 328 removed outlier: 3.522A pdb=" N GLY D 290 " --> pdb=" O THR D 286 " (cutoff:3.500A) Proline residue: D 298 - end of helix removed outlier: 3.625A pdb=" N PHE D 301 " --> pdb=" O ALA D 297 " (cutoff:3.500A) Proline residue: D 303 - end of helix removed outlier: 3.703A pdb=" N HIS D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA D 313 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N SER D 323 " --> pdb=" O GLY D 319 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU D 324 " --> pdb=" O ALA D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 397 removed outlier: 3.570A pdb=" N LEU D 392 " --> pdb=" O GLY D 388 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU D 393 " --> pdb=" O LYS D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 416 No H-bonds generated for 'chain 'D' and resid 414 through 416' Processing helix chain 'D' and resid 417 through 423 removed outlier: 3.625A 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 473 through 477 Processing helix chain 'D' and resid 487 through 500 Processing helix chain 'D' and resid 517 through 533 removed outlier: 3.546A pdb=" N GLN D 522 " --> pdb=" O ALA D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 573 removed outlier: 3.997A pdb=" N VAL D 572 " --> pdb=" O ALA D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 583 removed outlier: 3.885A pdb=" N HIS D 583 " --> pdb=" O THR D 579 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 356 through 363 removed outlier: 5.662A pdb=" N LYS C 357 " --> pdb=" O PHE C 346 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N PHE C 346 " --> pdb=" O LYS C 357 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N LEU C 361 " --> pdb=" O ARG C 342 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ARG C 342 " --> pdb=" O LEU C 361 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL C 363 " --> pdb=" O THR C 340 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N THR C 340 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 3.656A 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: 6.261A pdb=" N SER C 417 " --> pdb=" O LEU C 497 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ASP C 499 " --> pdb=" O SER C 417 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL C 419 " --> pdb=" O ASP C 499 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL C 496 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N VAL C 529 " --> pdb=" O VAL C 496 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU C 498 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE C 369 " --> pdb=" O MET C 528 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN C 541 " --> pdb=" O HIS C 368 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU C 552 " --> pdb=" O VAL C 544 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 364 through 373 removed outlier: 6.630A pdb=" N ILE D 357 " --> pdb=" O LEU D 365 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLY D 367 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LEU D 355 " --> pdb=" O GLY D 367 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU D 369 " --> pdb=" O GLU D 353 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU D 353 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N PHE D 371 " --> pdb=" O GLU D 351 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLU D 351 " --> pdb=" O PHE D 371 " (cutoff:3.500A) removed outlier: 3.996A 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: 6.630A pdb=" N ILE D 357 " --> pdb=" O LEU D 365 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLY D 367 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LEU D 355 " --> pdb=" O GLY D 367 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU D 369 " --> pdb=" O GLU D 353 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU D 353 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N PHE D 371 " --> pdb=" O GLU D 351 " (cutoff:3.500A) removed outlier: 4.688A 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: 6.429A pdb=" N SER D 426 " --> pdb=" O LEU D 508 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU D 507 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N VAL D 540 " --> pdb=" O LEU D 507 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU D 509 " --> pdb=" O VAL D 540 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG D 378 " --> pdb=" O VAL D 552 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N TRP D 554 " --> pdb=" O ARG D 378 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL D 380 " --> pdb=" O TRP D 554 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N MET D 556 " --> pdb=" O VAL D 380 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL D 382 " --> pdb=" O MET D 556 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL D 555 " --> pdb=" O ILE D 562 " (cutoff:3.500A) 575 hydrogen bonds defined for protein. 1689 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: 2.73 Time building geometry restraints manager: 2.59 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: 1923 1.33 - 1.45: 1980 1.45 - 1.57: 5217 1.57 - 1.69: 5 1.69 - 1.81: 57 Bond restraints: 9182 Sorted by residual: bond pdb=" N GLN C 500 " pdb=" CA GLN C 500 " ideal model delta sigma weight residual 1.457 1.488 -0.031 9.10e-03 1.21e+04 1.17e+01 bond pdb=" N GLN D 302 " pdb=" CA GLN D 302 " ideal model delta sigma weight residual 1.462 1.486 -0.024 7.70e-03 1.69e+04 9.48e+00 bond pdb=" N PHE D 159 " pdb=" CA PHE D 159 " ideal model delta sigma weight residual 1.461 1.488 -0.026 9.20e-03 1.18e+04 8.26e+00 bond pdb=" N GLU C 460 " pdb=" CA GLU C 460 " ideal model delta sigma weight residual 1.454 1.490 -0.037 1.34e-02 5.57e+03 7.62e+00 bond pdb=" N GLN C 351 " pdb=" CA GLN C 351 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.29e-02 6.01e+03 6.96e+00 ... (remaining 9177 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 11956 1.51 - 3.02: 437 3.02 - 4.54: 69 4.54 - 6.05: 14 6.05 - 7.56: 4 Bond angle restraints: 12480 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 139.87 133.93 5.94 1.00e+00 1.00e+00 3.53e+01 angle pdb=" PA ATP C 602 " pdb=" O3A ATP C 602 " pdb=" PB ATP C 602 " ideal model delta sigma weight residual 136.83 132.97 3.86 1.00e+00 1.00e+00 1.49e+01 angle pdb=" CA GLN C 500 " pdb=" C GLN C 500 " pdb=" O GLN C 500 " ideal model delta sigma weight residual 120.47 117.97 2.50 6.90e-01 2.10e+00 1.31e+01 angle pdb=" CA THR C 502 " pdb=" C THR C 502 " pdb=" O THR C 502 " ideal model delta sigma weight residual 122.63 117.97 4.66 1.29e+00 6.01e-01 1.31e+01 angle pdb=" CA ASP C 461 " pdb=" C ASP C 461 " pdb=" N ALA C 462 " ideal model delta sigma weight residual 119.98 117.02 2.96 8.50e-01 1.38e+00 1.21e+01 ... (remaining 12475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.15: 4892 16.15 - 32.29: 461 32.29 - 48.43: 114 48.43 - 64.58: 22 64.58 - 80.72: 9 Dihedral angle restraints: 5498 sinusoidal: 2185 harmonic: 3313 Sorted by residual: dihedral pdb=" CA ARG C 473 " pdb=" C ARG C 473 " pdb=" N GLN C 474 " pdb=" CA GLN C 474 " ideal model delta harmonic sigma weight residual 180.00 159.60 20.40 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA LEU C 106 " pdb=" C LEU C 106 " pdb=" N SER C 107 " pdb=" CA SER C 107 " ideal model delta harmonic sigma weight residual -180.00 -161.23 -18.77 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA ARG C 136 " pdb=" C ARG C 136 " pdb=" N VAL C 137 " pdb=" CA VAL C 137 " ideal model delta harmonic sigma weight residual 180.00 162.40 17.60 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 5495 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1098 0.044 - 0.087: 255 0.087 - 0.131: 76 0.131 - 0.175: 17 0.175 - 0.218: 3 Chirality restraints: 1449 Sorted by residual: chirality pdb=" CA PHE C 181 " pdb=" N PHE C 181 " pdb=" C PHE C 181 " pdb=" CB PHE C 181 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ARG C 534 " pdb=" N ARG C 534 " pdb=" C ARG C 534 " pdb=" CB ARG C 534 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ARG C 538 " pdb=" N ARG C 538 " pdb=" C ARG C 538 " pdb=" CB ARG C 538 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.19 2.00e-01 2.50e+01 9.48e-01 ... (remaining 1446 not shown) Planarity restraints: 1593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 61 " 0.034 5.00e-02 4.00e+02 5.18e-02 4.30e+00 pdb=" N PRO C 62 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 62 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 62 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 158 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.44e+00 pdb=" C ILE D 158 " 0.032 2.00e-02 2.50e+03 pdb=" O ILE D 158 " -0.012 2.00e-02 2.50e+03 pdb=" N PHE D 159 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 159 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C PHE D 159 " -0.031 2.00e-02 2.50e+03 pdb=" O PHE D 159 " 0.011 2.00e-02 2.50e+03 pdb=" N PRO D 160 " 0.011 2.00e-02 2.50e+03 ... (remaining 1590 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 48 2.54 - 3.13: 6728 3.13 - 3.72: 14401 3.72 - 4.31: 20830 4.31 - 4.90: 34918 Nonbonded interactions: 76925 Sorted by model distance: nonbonded pdb=" OE1 GLN C 421 " pdb="MG MG C 601 " model vdw 1.945 2.170 nonbonded pdb=" N GLU D 545 " pdb=" OE1 GLU D 545 " model vdw 2.204 3.120 nonbonded pdb="MG MG C 601 " pdb=" O1B ATP C 602 " model vdw 2.215 2.170 nonbonded pdb=" OG SER C 380 " pdb="MG MG C 601 " model vdw 2.228 2.170 nonbonded pdb=" NH2 ARG D 337 " pdb=" OE1 GLU D 419 " model vdw 2.257 3.120 ... (remaining 76920 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: 1.850 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.760 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:11.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 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 0.047 9182 Z= 0.312 Angle : 0.662 7.561 12480 Z= 0.416 Chirality : 0.044 0.218 1449 Planarity : 0.004 0.052 1593 Dihedral : 13.922 80.724 3362 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % 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: -0.81 (0.23), residues: 1151 helix: -0.62 (0.18), residues: 712 sheet: 0.22 (0.67), residues: 63 loop : -0.10 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 390 HIS 0.005 0.001 HIS C 132 PHE 0.015 0.001 PHE D 467 TYR 0.015 0.002 TYR D 88 ARG 0.007 0.000 ARG D 337 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.965 Fit side-chains REVERT: D 11 ARG cc_start: 0.7955 (ttm110) cc_final: 0.7743 (ttp-170) REVERT: D 523 ARG cc_start: 0.7832 (mmm-85) cc_final: 0.7601 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 1.6172 time to fit residues: 214.8266 Evaluate side-chains 97 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 104 optimal weight: 0.3980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 210 GLN C 474 GLN D 115 GLN D 557 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.122726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.096183 restraints weight = 11032.415| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.70 r_work: 0.2892 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9182 Z= 0.208 Angle : 0.545 6.175 12480 Z= 0.288 Chirality : 0.040 0.173 1449 Planarity : 0.005 0.050 1593 Dihedral : 7.110 85.452 1292 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.39 % Allowed : 7.26 % Favored : 91.36 % 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: 1.35 (0.24), residues: 1151 helix: 1.41 (0.19), residues: 715 sheet: 0.13 (0.65), residues: 63 loop : 0.20 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 427 HIS 0.006 0.001 HIS D 312 PHE 0.016 0.002 PHE C 89 TYR 0.014 0.001 TYR D 88 ARG 0.005 0.000 ARG D 337 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: C 275 GLN cc_start: 0.8324 (mt0) cc_final: 0.8077 (mm-40) REVERT: D 11 ARG cc_start: 0.8535 (ttm110) cc_final: 0.8283 (ttp-110) REVERT: D 384 ARG cc_start: 0.8179 (mmm-85) cc_final: 0.7955 (mmt90) outliers start: 13 outliers final: 1 residues processed: 113 average time/residue: 2.2035 time to fit residues: 263.7598 Evaluate side-chains 97 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 172 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 115 GLN D 557 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.123480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.098282 restraints weight = 11210.156| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.49 r_work: 0.2946 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9182 Z= 0.224 Angle : 0.520 8.119 12480 Z= 0.271 Chirality : 0.040 0.170 1449 Planarity : 0.004 0.048 1593 Dihedral : 7.026 81.415 1292 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.81 % Allowed : 9.61 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.25), residues: 1151 helix: 2.04 (0.19), residues: 714 sheet: 0.13 (0.67), residues: 62 loop : 0.28 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 81 HIS 0.006 0.001 HIS D 312 PHE 0.017 0.002 PHE C 89 TYR 0.016 0.001 TYR D 88 ARG 0.006 0.000 ARG D 337 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 1.015 Fit side-chains REVERT: C 60 MET cc_start: 0.7637 (mmm) cc_final: 0.7412 (mmm) REVERT: C 474 GLN cc_start: 0.8205 (tp40) cc_final: 0.7926 (mp10) REVERT: D 11 ARG cc_start: 0.8602 (ttm110) cc_final: 0.8349 (ttp-110) REVERT: D 384 ARG cc_start: 0.8229 (mmm-85) cc_final: 0.8019 (mmm-85) REVERT: D 419 GLU cc_start: 0.8060 (mp0) cc_final: 0.7713 (mp0) outliers start: 17 outliers final: 8 residues processed: 104 average time/residue: 1.5670 time to fit residues: 172.2329 Evaluate side-chains 103 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 342 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 30 optimal weight: 0.0030 chunk 5 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 557 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.124210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.098808 restraints weight = 11117.236| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.52 r_work: 0.2959 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9182 Z= 0.180 Angle : 0.482 6.150 12480 Z= 0.254 Chirality : 0.038 0.164 1449 Planarity : 0.004 0.045 1593 Dihedral : 6.817 79.635 1292 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.92 % Allowed : 10.03 % Favored : 88.05 % 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 (0.25), residues: 1151 helix: 2.40 (0.19), residues: 714 sheet: 0.10 (0.68), residues: 62 loop : 0.32 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 81 HIS 0.005 0.001 HIS D 312 PHE 0.013 0.001 PHE C 89 TYR 0.014 0.001 TYR D 88 ARG 0.008 0.000 ARG C 374 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 1.036 Fit side-chains REVERT: C 60 MET cc_start: 0.7486 (mmm) cc_final: 0.7261 (mmm) REVERT: C 267 SER cc_start: 0.9048 (OUTLIER) cc_final: 0.8718 (m) REVERT: C 297 VAL cc_start: 0.9098 (OUTLIER) cc_final: 0.8786 (m) REVERT: D 11 ARG cc_start: 0.8585 (ttm110) cc_final: 0.8306 (ttp-110) outliers start: 18 outliers final: 6 residues processed: 113 average time/residue: 1.4485 time to fit residues: 173.5186 Evaluate side-chains 105 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 276 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 4 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 74 optimal weight: 0.1980 chunk 25 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 408 ASN D 543 GLN D 557 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.124366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.098990 restraints weight = 11100.238| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.52 r_work: 0.2992 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9182 Z= 0.177 Angle : 0.484 6.454 12480 Z= 0.250 Chirality : 0.038 0.159 1449 Planarity : 0.004 0.043 1593 Dihedral : 6.772 80.782 1292 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.03 % Allowed : 11.31 % Favored : 86.66 % 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: 2.61 (0.25), residues: 1151 helix: 2.60 (0.19), residues: 713 sheet: 0.06 (0.69), residues: 62 loop : 0.37 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 81 HIS 0.005 0.001 HIS D 312 PHE 0.015 0.001 PHE C 89 TYR 0.015 0.001 TYR D 88 ARG 0.007 0.000 ARG D 337 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.992 Fit side-chains REVERT: C 267 SER cc_start: 0.9055 (OUTLIER) cc_final: 0.8723 (m) outliers start: 19 outliers final: 10 residues processed: 102 average time/residue: 1.5670 time to fit residues: 168.9520 Evaluate side-chains 102 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 427 TRP Chi-restraints excluded: chain D residue 544 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 98 optimal weight: 3.9990 chunk 30 optimal weight: 0.0570 chunk 28 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 557 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.123060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.096620 restraints weight = 11068.392| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.69 r_work: 0.2924 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9182 Z= 0.224 Angle : 0.502 6.194 12480 Z= 0.260 Chirality : 0.039 0.160 1449 Planarity : 0.004 0.041 1593 Dihedral : 6.830 82.058 1292 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.03 % Allowed : 12.17 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.25), residues: 1151 helix: 2.52 (0.19), residues: 713 sheet: 0.10 (0.69), residues: 62 loop : 0.31 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 427 HIS 0.006 0.001 HIS D 312 PHE 0.016 0.001 PHE C 89 TYR 0.016 0.001 TYR D 88 ARG 0.008 0.000 ARG D 337 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 1.449 Fit side-chains REVERT: C 267 SER cc_start: 0.9033 (OUTLIER) cc_final: 0.8636 (m) REVERT: C 297 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8764 (m) REVERT: C 521 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.7711 (mtm) outliers start: 19 outliers final: 12 residues processed: 99 average time/residue: 1.7832 time to fit residues: 187.6157 Evaluate side-chains 105 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 427 TRP Chi-restraints excluded: chain D residue 544 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 49 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 32 optimal weight: 0.0980 chunk 86 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 557 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.122039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.096347 restraints weight = 11200.542| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.54 r_work: 0.2948 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9182 Z= 0.257 Angle : 0.515 6.244 12480 Z= 0.268 Chirality : 0.040 0.161 1449 Planarity : 0.004 0.040 1593 Dihedral : 6.918 82.436 1292 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.35 % Allowed : 12.27 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.25), residues: 1151 helix: 2.45 (0.19), residues: 718 sheet: 0.13 (0.69), residues: 62 loop : 0.27 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 81 HIS 0.006 0.001 HIS D 312 PHE 0.017 0.002 PHE D 467 TYR 0.016 0.001 TYR D 88 ARG 0.008 0.000 ARG D 337 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 1.049 Fit side-chains REVERT: C 267 SER cc_start: 0.9054 (OUTLIER) cc_final: 0.8692 (m) REVERT: C 297 VAL cc_start: 0.9106 (OUTLIER) cc_final: 0.8863 (m) REVERT: C 521 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.7810 (mtm) REVERT: D 407 ARG cc_start: 0.8488 (mtm110) cc_final: 0.8255 (mtm180) outliers start: 22 outliers final: 14 residues processed: 103 average time/residue: 1.5484 time to fit residues: 168.4563 Evaluate side-chains 110 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 427 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 482 GLN D 557 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.123066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.097448 restraints weight = 11247.817| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.54 r_work: 0.2965 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9182 Z= 0.210 Angle : 0.497 6.307 12480 Z= 0.259 Chirality : 0.039 0.151 1449 Planarity : 0.004 0.039 1593 Dihedral : 6.861 83.424 1292 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.13 % Allowed : 12.70 % Favored : 85.17 % 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: 2.54 (0.25), residues: 1151 helix: 2.55 (0.19), residues: 713 sheet: 0.14 (0.69), residues: 62 loop : 0.31 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 81 HIS 0.005 0.001 HIS D 312 PHE 0.015 0.001 PHE C 89 TYR 0.015 0.001 TYR D 88 ARG 0.009 0.000 ARG D 337 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 1.048 Fit side-chains REVERT: C 267 SER cc_start: 0.9045 (OUTLIER) cc_final: 0.8697 (m) REVERT: C 521 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.7820 (mtm) REVERT: D 407 ARG cc_start: 0.8492 (mtm110) cc_final: 0.8257 (mtm180) REVERT: D 523 ARG cc_start: 0.8086 (mmm-85) cc_final: 0.7704 (mmp80) outliers start: 20 outliers final: 14 residues processed: 102 average time/residue: 1.6206 time to fit residues: 174.4430 Evaluate side-chains 107 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 427 TRP Chi-restraints excluded: chain D residue 544 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 48 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 41 optimal weight: 0.0980 chunk 83 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 96 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 482 GLN D 557 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.124545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.099080 restraints weight = 11166.730| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.53 r_work: 0.2991 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9182 Z= 0.167 Angle : 0.472 6.262 12480 Z= 0.247 Chirality : 0.038 0.148 1449 Planarity : 0.004 0.039 1593 Dihedral : 6.714 86.046 1292 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.13 % Allowed : 12.81 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.25), residues: 1151 helix: 2.67 (0.19), residues: 715 sheet: 0.18 (0.70), residues: 62 loop : 0.37 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 81 HIS 0.004 0.001 HIS D 312 PHE 0.015 0.001 PHE C 89 TYR 0.013 0.001 TYR D 88 ARG 0.010 0.000 ARG D 337 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 2.248 Fit side-chains REVERT: C 176 LEU cc_start: 0.8807 (tt) cc_final: 0.8551 (mt) REVERT: C 267 SER cc_start: 0.9030 (OUTLIER) cc_final: 0.8698 (m) REVERT: D 222 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7898 (mp0) REVERT: D 407 ARG cc_start: 0.8491 (mtm110) cc_final: 0.8262 (mtm180) REVERT: D 523 ARG cc_start: 0.8016 (mmm-85) cc_final: 0.7619 (mmp80) outliers start: 20 outliers final: 14 residues processed: 102 average time/residue: 2.2026 time to fit residues: 237.5687 Evaluate side-chains 110 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 427 TRP Chi-restraints excluded: chain D residue 544 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 83 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 30 optimal weight: 0.4980 chunk 57 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 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 408 ASN D 107 GLN D 482 GLN D 557 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.124066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.098502 restraints weight = 11151.046| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.53 r_work: 0.2981 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9182 Z= 0.192 Angle : 0.493 7.267 12480 Z= 0.255 Chirality : 0.039 0.151 1449 Planarity : 0.004 0.039 1593 Dihedral : 6.692 88.134 1292 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.81 % Allowed : 13.13 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.25), residues: 1151 helix: 2.64 (0.19), residues: 715 sheet: 0.22 (0.70), residues: 62 loop : 0.35 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 81 HIS 0.005 0.001 HIS D 312 PHE 0.016 0.001 PHE C 89 TYR 0.015 0.001 TYR D 88 ARG 0.006 0.000 ARG D 337 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.948 Fit side-chains REVERT: C 176 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8571 (mt) REVERT: C 267 SER cc_start: 0.9024 (OUTLIER) cc_final: 0.8700 (m) REVERT: D 407 ARG cc_start: 0.8498 (mtm110) cc_final: 0.8267 (mtm180) REVERT: D 523 ARG cc_start: 0.8049 (mmm-85) cc_final: 0.7648 (mmp80) outliers start: 17 outliers final: 14 residues processed: 98 average time/residue: 1.6562 time to fit residues: 171.4685 Evaluate side-chains 105 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 427 TRP Chi-restraints excluded: chain D residue 544 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 105 optimal weight: 0.3980 chunk 104 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 482 GLN D 557 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.123644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.096849 restraints weight = 11090.114| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.69 r_work: 0.2953 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9182 Z= 0.185 Angle : 0.484 8.422 12480 Z= 0.251 Chirality : 0.038 0.152 1449 Planarity : 0.004 0.040 1593 Dihedral : 6.626 89.708 1292 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.13 % Allowed : 13.23 % Favored : 84.63 % 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: 2.66 (0.25), residues: 1151 helix: 2.63 (0.19), residues: 721 sheet: 0.25 (0.71), residues: 62 loop : 0.33 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 81 HIS 0.005 0.001 HIS D 312 PHE 0.015 0.001 PHE C 89 TYR 0.015 0.001 TYR D 88 ARG 0.006 0.000 ARG C 374 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6738.79 seconds wall clock time: 119 minutes 13.05 seconds (7153.05 seconds total)