Starting phenix.real_space_refine on Thu Feb 13 15:14:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zdt_14669/02_2025/7zdt_14669_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zdt_14669/02_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_14669/02_2025/7zdt_14669.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zdt_14669/02_2025/7zdt_14669.map" model { file = "/net/cci-nas-00/data/ceres_data/7zdt_14669/02_2025/7zdt_14669_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zdt_14669/02_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-5592/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: 5.12, per 1000 atoms: 0.57 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: 2.19 Conformation dependent library (CDL) restraints added in 1.1 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: 0.91 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: 2.81 Time building geometry restraints manager: 2.53 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: 1.480 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.550 Find NCS groups from input model: 0.150 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:11.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.680 ------------------------------------------------------------------------------- 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 : 1.000 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: 1.6138 time to fit residues: 214.6492 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 : 1.023 ------------------------------------------------------------------------------- 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 = 38)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.096179 restraints weight = 11032.415| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.70 r_work: 0.2891 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- 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 : 1.031 Fit side-chains revert: symmetry clash REVERT: C 275 GLN cc_start: 0.8323 (mt0) cc_final: 0.8075 (mm-40) REVERT: D 11 ARG cc_start: 0.8535 (ttm110) cc_final: 0.8283 (ttp-110) REVERT: D 384 ARG cc_start: 0.8178 (mmm-85) cc_final: 0.7953 (mmt90) outliers start: 13 outliers final: 1 residues processed: 113 average time/residue: 1.6611 time to fit residues: 198.7056 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 : 1.031 ------------------------------------------------------------------------------- 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: 0.9980 chunk 73 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3424 r_free = 0.3424 target = 0.122694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.097453 restraints weight = 11220.018| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.49 r_work: 0.2934 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 9182 Z= 0.257 Angle : 0.535 8.144 12480 Z= 0.278 Chirality : 0.040 0.172 1449 Planarity : 0.004 0.048 1593 Dihedral : 7.074 80.622 1292 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.92 % Allowed : 9.50 % 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: 1.93 (0.24), residues: 1151 helix: 1.96 (0.19), residues: 714 sheet: 0.13 (0.67), residues: 62 loop : 0.25 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 427 HIS 0.007 0.001 HIS D 312 PHE 0.018 0.002 PHE C 89 TYR 0.017 0.002 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 115 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 1.063 Fit side-chains REVERT: C 60 MET cc_start: 0.7634 (mmm) cc_final: 0.7405 (mmm) REVERT: C 267 SER cc_start: 0.9051 (OUTLIER) cc_final: 0.8699 (m) REVERT: C 474 GLN cc_start: 0.8214 (tp40) cc_final: 0.7916 (mp10) REVERT: D 11 ARG cc_start: 0.8602 (ttm110) cc_final: 0.8350 (ttp-110) outliers start: 18 outliers final: 8 residues processed: 103 average time/residue: 1.5828 time to fit residues: 172.2819 Evaluate side-chains 103 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 70 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 30 optimal weight: 0.0570 chunk 5 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 543 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 = 0.3443 r_free = 0.3443 target = 0.124322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.097968 restraints weight = 11125.069| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.70 r_work: 0.2937 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1922 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= 0.173 Angle : 0.480 6.166 12480 Z= 0.253 Chirality : 0.038 0.163 1449 Planarity : 0.004 0.045 1593 Dihedral : 6.816 79.447 1292 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.81 % Allowed : 10.03 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.40 (0.25), residues: 1151 helix: 2.40 (0.19), residues: 714 sheet: 0.11 (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 0.004 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 121 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 1.011 Fit side-chains REVERT: C 60 MET cc_start: 0.7412 (mmm) cc_final: 0.7172 (mmm) REVERT: C 267 SER cc_start: 0.9021 (OUTLIER) cc_final: 0.8640 (m) REVERT: C 297 VAL cc_start: 0.9032 (OUTLIER) cc_final: 0.8705 (m) REVERT: D 11 ARG cc_start: 0.8542 (ttm110) cc_final: 0.8249 (ttp-110) REVERT: D 384 ARG cc_start: 0.8224 (mmm-85) cc_final: 0.8016 (mmm-85) outliers start: 17 outliers final: 6 residues processed: 112 average time/residue: 1.4912 time to fit residues: 176.9976 Evaluate side-chains 104 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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: 0.9990 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 chunk 74 optimal weight: 0.0670 chunk 25 optimal weight: 4.9990 chunk 78 optimal weight: 0.5980 chunk 45 optimal weight: 0.2980 chunk 72 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.4920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 408 ASN D 557 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.125572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.100298 restraints weight = 11060.723| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.51 r_work: 0.3011 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9182 Z= 0.157 Angle : 0.474 6.593 12480 Z= 0.246 Chirality : 0.038 0.158 1449 Planarity : 0.004 0.043 1593 Dihedral : 6.699 81.331 1292 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.13 % Allowed : 10.57 % Favored : 87.30 % 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: 2.71 (0.25), residues: 1151 helix: 2.68 (0.19), residues: 713 sheet: 0.11 (0.70), residues: 62 loop : 0.41 (0.32), residues: 376 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 0.016 0.001 PHE C 89 TYR 0.014 0.001 TYR D 88 ARG 0.008 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 122 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.963 Fit side-chains REVERT: C 267 SER cc_start: 0.9039 (OUTLIER) cc_final: 0.8710 (m) REVERT: D 419 GLU cc_start: 0.7975 (mp0) cc_final: 0.7624 (mp0) outliers start: 20 outliers final: 12 residues processed: 108 average time/residue: 1.5852 time to fit residues: 180.9109 Evaluate side-chains 105 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 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 544 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 98 optimal weight: 0.9980 chunk 30 optimal weight: 0.0770 chunk 28 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 = 0.3445 r_free = 0.3445 target = 0.124674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.099355 restraints weight = 11018.191| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.52 r_work: 0.2995 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2114 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= 0.182 Angle : 0.477 6.165 12480 Z= 0.248 Chirality : 0.038 0.157 1449 Planarity : 0.004 0.041 1593 Dihedral : 6.716 84.651 1292 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.13 % Allowed : 11.74 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.25), residues: 1151 helix: 2.66 (0.19), residues: 713 sheet: 0.16 (0.70), residues: 62 loop : 0.39 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 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 D 560 *********************** 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 114 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 1.206 Fit side-chains REVERT: C 267 SER cc_start: 0.9037 (OUTLIER) cc_final: 0.8710 (m) REVERT: D 523 ARG cc_start: 0.8069 (mmm-85) cc_final: 0.7694 (mmp80) outliers start: 20 outliers final: 13 residues processed: 103 average time/residue: 1.5860 time to fit residues: 173.1782 Evaluate side-chains 104 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 46 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3436 r_free = 0.3436 target = 0.123865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.098458 restraints weight = 11153.126| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.52 r_work: 0.2981 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2137 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= 0.206 Angle : 0.489 6.255 12480 Z= 0.254 Chirality : 0.039 0.158 1449 Planarity : 0.004 0.040 1593 Dihedral : 6.742 87.018 1292 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.92 % Allowed : 12.59 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.25), residues: 1151 helix: 2.61 (0.19), residues: 715 sheet: 0.18 (0.70), residues: 62 loop : 0.41 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 81 HIS 0.006 0.001 HIS D 312 PHE 0.015 0.001 PHE C 89 TYR 0.016 0.001 TYR D 88 ARG 0.007 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 110 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 1.037 Fit side-chains REVERT: C 267 SER cc_start: 0.9033 (OUTLIER) cc_final: 0.8707 (m) REVERT: C 521 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.7670 (mtm) REVERT: D 523 ARG cc_start: 0.8083 (mmm-85) cc_final: 0.7710 (mmp80) outliers start: 18 outliers final: 14 residues processed: 98 average time/residue: 1.6351 time to fit residues: 169.3279 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 : 1.054 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 2 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 104 optimal weight: 0.0870 chunk 76 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 = 0.124618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.099174 restraints weight = 11200.022| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.53 r_work: 0.2990 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9182 Z= 0.177 Angle : 0.474 6.313 12480 Z= 0.247 Chirality : 0.038 0.154 1449 Planarity : 0.004 0.039 1593 Dihedral : 6.617 89.743 1292 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.45 % Allowed : 12.59 % Favored : 84.95 % 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: 2.74 (0.25), residues: 1151 helix: 2.68 (0.19), residues: 715 sheet: 0.25 (0.70), residues: 62 loop : 0.43 (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 0.015 0.001 PHE C 89 TYR 0.014 0.001 TYR D 88 ARG 0.007 0.000 ARG D 560 *********************** 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 116 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.954 Fit side-chains REVERT: C 176 LEU cc_start: 0.8768 (tt) cc_final: 0.8539 (mt) REVERT: C 521 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.7697 (mtm) REVERT: D 222 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7890 (mp0) REVERT: D 407 ARG cc_start: 0.8484 (mtm110) cc_final: 0.8257 (mtm180) REVERT: D 523 ARG cc_start: 0.8055 (mmm-85) cc_final: 0.7647 (mmp80) outliers start: 23 outliers final: 15 residues processed: 102 average time/residue: 1.7103 time to fit residues: 183.5958 Evaluate side-chains 106 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 48 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 96 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 107 GLN D 482 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 = 0.124376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.098868 restraints weight = 11122.192| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.52 r_work: 0.2988 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9182 Z= 0.186 Angle : 0.479 6.373 12480 Z= 0.249 Chirality : 0.038 0.155 1449 Planarity : 0.004 0.039 1593 Dihedral : 6.512 87.411 1292 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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: 2.74 (0.25), residues: 1151 helix: 2.68 (0.19), residues: 715 sheet: 0.33 (0.71), residues: 62 loop : 0.42 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 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 560 *********************** 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 114 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.974 Fit side-chains REVERT: C 176 LEU cc_start: 0.8764 (tt) cc_final: 0.8549 (mt) REVERT: C 177 MET cc_start: 0.8888 (mtp) cc_final: 0.8675 (ttt) REVERT: C 521 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.7726 (mtm) REVERT: D 222 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7891 (mp0) REVERT: D 523 ARG cc_start: 0.8048 (mmm-85) cc_final: 0.7621 (mmp80) outliers start: 20 outliers final: 14 residues processed: 101 average time/residue: 1.8426 time to fit residues: 195.6456 Evaluate side-chains 109 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 83 optimal weight: 0.7980 chunk 53 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 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 C 541 GLN C 553 GLN D 482 GLN D 557 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.124314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.097797 restraints weight = 11171.060| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.70 r_work: 0.2942 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9182 Z= 0.191 Angle : 0.484 6.320 12480 Z= 0.251 Chirality : 0.038 0.150 1449 Planarity : 0.004 0.039 1593 Dihedral : 6.475 85.969 1292 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.81 % Allowed : 13.66 % Favored : 84.53 % 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: 2.74 (0.25), residues: 1151 helix: 2.68 (0.19), residues: 715 sheet: 0.32 (0.71), residues: 62 loop : 0.41 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 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 0.008 0.000 ARG D 560 ********************** 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 106 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 1.228 Fit side-chains REVERT: C 176 LEU cc_start: 0.8725 (tt) cc_final: 0.8504 (mt) REVERT: C 521 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.7784 (mtm) REVERT: D 222 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7849 (mp0) REVERT: D 523 ARG cc_start: 0.7981 (mmm-85) cc_final: 0.7464 (mmp80) outliers start: 17 outliers final: 14 residues processed: 97 average time/residue: 1.7004 time to fit residues: 174.3563 Evaluate side-chains 104 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 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 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 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: 2.9990 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 0.0470 chunk 19 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 541 GLN D 482 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 = 0.3450 r_free = 0.3450 target = 0.125050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.099594 restraints weight = 11050.301| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.52 r_work: 0.3000 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2283 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= 0.173 Angle : 0.472 6.334 12480 Z= 0.246 Chirality : 0.038 0.147 1449 Planarity : 0.004 0.039 1593 Dihedral : 6.338 83.593 1292 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.71 % Allowed : 13.77 % Favored : 84.53 % 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: 2.75 (0.25), residues: 1151 helix: 2.69 (0.19), residues: 721 sheet: 0.30 (0.71), residues: 62 loop : 0.38 (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 0.014 0.001 TYR D 88 ARG 0.008 0.000 ARG D 560 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5915.18 seconds wall clock time: 105 minutes 1.47 seconds (6301.47 seconds total)