Starting phenix.real_space_refine on Fri Sep 11 11:44:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6d7w_7826/09_2026/6d7w_7826.cif Found real_map, /net/cci-nas-00/data/ceres_data/6d7w_7826/09_2026/6d7w_7826.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6d7w_7826/09_2026/6d7w_7826.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6d7w_7826/09_2026/6d7w_7826.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6d7w_7826/09_2026/6d7w_7826.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6d7w_7826/09_2026/6d7w_7826.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6d7w_7826/09_2026/6d7w_7826.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6d7w_7826/09_2026/6d7w_7826.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 464 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 20 5.16 5 C 5749 2.51 5 N 1560 2.21 5 O 1616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8946 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2264 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 11, 'TRANS': 263} Chain breaks: 2 Chain: "C" Number of atoms: 2213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2213 Classifications: {'peptide': 269} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 256} Chain breaks: 2 Chain: "B" Number of atoms: 2255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2255 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 11, 'TRANS': 262} Chain breaks: 2 Chain: "D" Number of atoms: 2213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2213 Classifications: {'peptide': 269} Link IDs: {'CIS': 2, 'PTRANS': 11, 'TRANS': 255} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.78, per 1000 atoms: 0.20 Number of scatterers: 8946 At special positions: 0 Unit cell: (86.52, 84.84, 148.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 20 16.00 O 1616 8.00 N 1560 7.00 C 5749 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 313.6 milliseconds 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2062 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 4 sheets defined 55.8% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 164 through 175 removed outlier: 3.694A pdb=" N LEU A 168 " --> pdb=" O PRO A 164 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 280 removed outlier: 3.756A pdb=" N PHE A 272 " --> pdb=" O GLU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 363 removed outlier: 4.029A pdb=" N PHE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU A 310 " --> pdb=" O ARG A 306 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ARG A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU A 363 " --> pdb=" O LYS A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 370 removed outlier: 3.676A pdb=" N THR A 370 " --> pdb=" O GLY A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 370' Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'A' and resid 413 through 418 removed outlier: 3.640A pdb=" N LYS A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 446 removed outlier: 3.924A pdb=" N ALA A 434 " --> pdb=" O ASP A 430 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ILE A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG A 437 " --> pdb=" O ASN A 433 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 459 removed outlier: 4.450A pdb=" N GLN A 457 " --> pdb=" O LYS A 454 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP A 459 " --> pdb=" O GLU A 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 175 removed outlier: 3.989A pdb=" N LEU C 168 " --> pdb=" O PRO C 164 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU C 175 " --> pdb=" O LEU C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 280 Processing helix chain 'C' and resid 302 through 307 Processing helix chain 'C' and resid 307 through 362 removed outlier: 5.012A pdb=" N ARG C 313 " --> pdb=" O PHE C 309 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS C 336 " --> pdb=" O ASP C 332 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY C 338 " --> pdb=" O LEU C 334 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL C 357 " --> pdb=" O TRP C 353 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR C 361 " --> pdb=" O VAL C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 370 Processing helix chain 'C' and resid 371 through 392 removed outlier: 3.692A pdb=" N GLY C 385 " --> pdb=" O SER C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 419 removed outlier: 3.704A pdb=" N GLN C 411 " --> pdb=" O ILE C 407 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN C 416 " --> pdb=" O LYS C 412 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N MET C 417 " --> pdb=" O LYS C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 447 removed outlier: 3.688A pdb=" N TRP C 425 " --> pdb=" O ASP C 421 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU C 438 " --> pdb=" O ALA C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 457 removed outlier: 3.905A pdb=" N GLU C 456 " --> pdb=" O GLU C 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 175 removed outlier: 3.582A pdb=" N LEU B 168 " --> pdb=" O PRO B 164 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU B 175 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 280 removed outlier: 3.688A pdb=" N PHE B 272 " --> pdb=" O GLU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 363 removed outlier: 4.514A pdb=" N LEU B 324 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL B 342 " --> pdb=" O GLY B 338 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU B 363 " --> pdb=" O LYS B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 389 removed outlier: 3.812A pdb=" N MET B 371 " --> pdb=" O GLY B 367 " (cutoff:3.500A) Proline residue: B 373 - end of helix removed outlier: 3.788A pdb=" N TRP B 389 " --> pdb=" O GLY B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'B' and resid 422 through 447 removed outlier: 4.031A pdb=" N ALA B 434 " --> pdb=" O ASP B 430 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG B 437 " --> pdb=" O ASN B 433 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 459 removed outlier: 3.531A pdb=" N ASP B 459 " --> pdb=" O GLU B 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 174 Processing helix chain 'D' and resid 268 through 280 Processing helix chain 'D' and resid 302 through 364 removed outlier: 3.580A pdb=" N PHE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU D 310 " --> pdb=" O ARG D 306 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG D 313 " --> pdb=" O PHE D 309 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU D 324 " --> pdb=" O ARG D 320 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR D 364 " --> pdb=" O LEU D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 386 Processing helix chain 'D' and resid 387 through 391 Processing helix chain 'D' and resid 406 through 415 removed outlier: 3.764A pdb=" N GLN D 411 " --> pdb=" O ILE D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 446 removed outlier: 3.799A pdb=" N TRP D 425 " --> pdb=" O ASP D 421 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU D 438 " --> pdb=" O ALA D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 457 removed outlier: 3.951A pdb=" N GLU D 456 " --> pdb=" O GLU D 452 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 129 through 132 removed outlier: 3.572A pdb=" N LYS A 129 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 139 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A 142 " --> pdb=" O ILE A 155 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 153 " --> pdb=" O LEU A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 194 through 196 removed outlier: 3.518A pdb=" N ILE A 261 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N PHE A 260 " --> pdb=" O GLN C 154 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N ALA C 156 " --> pdb=" O PHE A 260 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ARG A 262 " --> pdb=" O ALA C 156 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N LEU C 158 " --> pdb=" O ARG A 262 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE C 142 " --> pdb=" O ILE C 155 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 283 through 284 Processing sheet with id=AA4, first strand: chain 'B' and resid 153 through 159 removed outlier: 3.855A pdb=" N GLU B 153 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU B 144 " --> pdb=" O GLU B 153 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LYS B 139 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS B 129 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ALA B 127 " --> pdb=" O PRO B 143 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLY B 128 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE B 282 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N PHE B 193 " --> pdb=" O TRP B 263 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ARG B 262 " --> pdb=" O ALA D 156 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N LEU D 158 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ALA D 127 " --> pdb=" O PRO D 143 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU D 130 " --> pdb=" O ALA D 299 " (cutoff:3.500A) 477 hydrogen bonds defined for protein. 1380 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.14 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1577 1.32 - 1.44: 2376 1.44 - 1.56: 5152 1.56 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 9141 Sorted by residual: bond pdb=" C PHE D 303 " pdb=" O PHE D 303 " ideal model delta sigma weight residual 1.237 1.201 0.036 1.17e-02 7.31e+03 9.51e+00 bond pdb=" CA ASN D 183 " pdb=" C ASN D 183 " ideal model delta sigma weight residual 1.529 1.556 -0.027 1.26e-02 6.30e+03 4.75e+00 bond pdb=" CG LEU B 140 " pdb=" CD2 LEU B 140 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.47e+00 bond pdb=" CA PHE D 303 " pdb=" C PHE D 303 " ideal model delta sigma weight residual 1.523 1.496 0.027 1.30e-02 5.92e+03 4.26e+00 bond pdb=" N LEU A 293 " pdb=" CA LEU A 293 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.88e+00 ... (remaining 9136 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 11843 2.67 - 5.35: 432 5.35 - 8.02: 68 8.02 - 10.69: 20 10.69 - 13.37: 3 Bond angle restraints: 12366 Sorted by residual: angle pdb=" C ALA D 289 " pdb=" N PRO D 290 " pdb=" CA PRO D 290 " ideal model delta sigma weight residual 119.05 132.42 -13.37 1.11e+00 8.12e-01 1.45e+02 angle pdb=" N ASP B 365 " pdb=" CA ASP B 365 " pdb=" C ASP B 365 " ideal model delta sigma weight residual 111.28 100.85 10.43 1.09e+00 8.42e-01 9.16e+01 angle pdb=" N ASN D 183 " pdb=" CA ASN D 183 " pdb=" C ASN D 183 " ideal model delta sigma weight residual 111.24 124.20 -12.96 1.38e+00 5.25e-01 8.82e+01 angle pdb=" N ASN B 148 " pdb=" CA ASN B 148 " pdb=" C ASN B 148 " ideal model delta sigma weight residual 112.34 122.75 -10.41 1.30e+00 5.92e-01 6.41e+01 angle pdb=" C ARG D 187 " pdb=" N PRO D 188 " pdb=" CA PRO D 188 " ideal model delta sigma weight residual 120.38 127.65 -7.27 1.03e+00 9.43e-01 4.98e+01 ... (remaining 12361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.82: 5091 15.82 - 31.65: 304 31.65 - 47.47: 77 47.47 - 63.30: 12 63.30 - 79.12: 6 Dihedral angle restraints: 5490 sinusoidal: 2319 harmonic: 3171 Sorted by residual: dihedral pdb=" N GLU D 182 " pdb=" C GLU D 182 " pdb=" CA GLU D 182 " pdb=" CB GLU D 182 " ideal model delta harmonic sigma weight residual 122.80 139.46 -16.66 0 2.50e+00 1.60e-01 4.44e+01 dihedral pdb=" C GLU D 182 " pdb=" N GLU D 182 " pdb=" CA GLU D 182 " pdb=" CB GLU D 182 " ideal model delta harmonic sigma weight residual -122.60 -138.85 16.25 0 2.50e+00 1.60e-01 4.23e+01 dihedral pdb=" CA TYR D 415 " pdb=" C TYR D 415 " pdb=" N GLN D 416 " pdb=" CA GLN D 416 " ideal model delta harmonic sigma weight residual 180.00 153.13 26.87 0 5.00e+00 4.00e-02 2.89e+01 ... (remaining 5487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 1263 0.130 - 0.260: 83 0.260 - 0.390: 9 0.390 - 0.520: 3 0.520 - 0.650: 1 Chirality restraints: 1359 Sorted by residual: chirality pdb=" CA GLU D 182 " pdb=" N GLU D 182 " pdb=" C GLU D 182 " pdb=" CB GLU D 182 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" CA GLU D 294 " pdb=" N GLU D 294 " pdb=" C GLU D 294 " pdb=" CB GLU D 294 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.86e+00 chirality pdb=" CA LEU A 293 " pdb=" N LEU A 293 " pdb=" C LEU A 293 " pdb=" CB LEU A 293 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.04e+00 ... (remaining 1356 not shown) Planarity restraints: 1580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 147 " -0.026 2.00e-02 2.50e+03 5.19e-02 2.70e+01 pdb=" C ILE B 147 " 0.090 2.00e-02 2.50e+03 pdb=" O ILE B 147 " -0.033 2.00e-02 2.50e+03 pdb=" N ASN B 148 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 394 " 0.020 2.00e-02 2.50e+03 4.01e-02 1.61e+01 pdb=" C ASN C 394 " -0.069 2.00e-02 2.50e+03 pdb=" O ASN C 394 " 0.027 2.00e-02 2.50e+03 pdb=" N ARG C 395 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 381 " -0.015 2.00e-02 2.50e+03 3.07e-02 9.41e+00 pdb=" C SER C 381 " 0.053 2.00e-02 2.50e+03 pdb=" O SER C 381 " -0.020 2.00e-02 2.50e+03 pdb=" N THR C 382 " -0.018 2.00e-02 2.50e+03 ... (remaining 1577 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1040 2.75 - 3.29: 8399 3.29 - 3.82: 13688 3.82 - 4.36: 15192 4.36 - 4.90: 25607 Nonbonded interactions: 63926 Sorted by model distance: nonbonded pdb=" O PHE C 303 " pdb=" OG1 THR C 307 " model vdw 2.210 3.040 nonbonded pdb=" O PHE B 303 " pdb=" OG1 THR B 307 " model vdw 2.267 3.040 nonbonded pdb=" OG1 THR B 133 " pdb=" O LEU B 137 " model vdw 2.270 3.040 nonbonded pdb=" O VAL A 357 " pdb=" OG1 THR A 361 " model vdw 2.275 3.040 nonbonded pdb=" O LYS C 359 " pdb=" OG1 THR C 364 " model vdw 2.281 3.040 ... (remaining 63921 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 124 through 196 or resid 259 through 396 or resid 406 thro \ ugh 461)) selection = (chain 'B' and (resid 124 through 196 or resid 259 through 396 or resid 406 thro \ ugh 461)) selection = (chain 'C' and (resid 124 through 396 or resid 406 through 461)) selection = (chain 'D' and (resid 124 through 396 or resid 406 through 461)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.690 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 9141 Z= 0.345 Angle : 1.205 13.366 12366 Z= 0.703 Chirality : 0.074 0.650 1359 Planarity : 0.009 0.120 1580 Dihedral : 11.663 79.123 3428 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.73 % Allowed : 6.62 % Favored : 90.64 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.65 (0.22), residues: 1063 helix: -1.70 (0.19), residues: 554 sheet: -3.18 (0.31), residues: 163 loop : -2.91 (0.29), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 278 TYR 0.031 0.003 TYR C 308 PHE 0.036 0.004 PHE D 272 TRP 0.027 0.003 TRP B 368 HIS 0.017 0.002 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00746 / 0.34 ( 9141) covalent geometry : angle 1.20516 / 0.70 (12366) hydrogen bonds : bond 0.18062 / 11.57 ( 477) hydrogen bonds : angle 8.78638 / 6.06 ( 1380) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 235 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8847 (tt) REVERT: A 198 LEU cc_start: 0.8256 (tp) cc_final: 0.7968 (tp) REVERT: A 361 THR cc_start: 0.7709 (m) cc_final: 0.7492 (m) REVERT: A 415 TYR cc_start: 0.7810 (p90) cc_final: 0.7435 (p90) REVERT: A 453 ARG cc_start: 0.8310 (mtt180) cc_final: 0.7759 (mmp-170) REVERT: C 352 PHE cc_start: 0.7591 (t80) cc_final: 0.7326 (t80) REVERT: B 328 LYS cc_start: 0.8045 (tppt) cc_final: 0.7844 (tttt) REVERT: B 361 THR cc_start: 0.7513 (m) cc_final: 0.6197 (m) REVERT: B 372 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6766 (tp30) REVERT: B 453 ARG cc_start: 0.8263 (mtt180) cc_final: 0.7925 (mmp-170) REVERT: D 147 ILE cc_start: 0.8107 (mm) cc_final: 0.7897 (mt) REVERT: D 307 THR cc_start: 0.6756 (m) cc_final: 0.6463 (p) REVERT: D 311 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.6470 (mpp-170) REVERT: D 352 PHE cc_start: 0.7459 (t80) cc_final: 0.7243 (t80) outliers start: 26 outliers final: 9 residues processed: 261 average time/residue: 0.1321 time to fit residues: 43.7121 Evaluate side-chains 129 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 308 TYR Chi-restraints excluded: chain D residue 311 ARG Chi-restraints excluded: chain D residue 383 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 30.0000 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 HIS A 295 GLN ** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 GLN A 408 ASN A 411 GLN ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN B 167 HIS ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 GLN ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 GLN D 167 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.137781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.113638 restraints weight = 20884.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.114908 restraints weight = 14768.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.115666 restraints weight = 11454.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.116959 restraints weight = 10106.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.116902 restraints weight = 9821.879| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9141 Z= 0.192 Angle : 0.780 12.635 12366 Z= 0.411 Chirality : 0.048 0.253 1359 Planarity : 0.006 0.054 1580 Dihedral : 7.343 62.281 1222 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 5.05 % Allowed : 12.41 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.25), residues: 1063 helix: 0.20 (0.22), residues: 543 sheet: -2.71 (0.33), residues: 165 loop : -2.38 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 278 TYR 0.043 0.003 TYR C 308 PHE 0.027 0.002 PHE A 282 TRP 0.011 0.001 TRP B 354 HIS 0.010 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.19 ( 9141) covalent geometry : angle 0.77981 / 0.41 (12366) hydrogen bonds : bond 0.07550 / 5.04 ( 477) hydrogen bonds : angle 5.77753 / 3.97 ( 1380) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 117 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 VAL cc_start: 0.8207 (t) cc_final: 0.8000 (p) REVERT: A 415 TYR cc_start: 0.7786 (p90) cc_final: 0.7356 (p90) REVERT: A 453 ARG cc_start: 0.8187 (mtt180) cc_final: 0.7986 (mmp-170) REVERT: A 454 LYS cc_start: 0.7424 (mttt) cc_final: 0.7030 (pttt) REVERT: C 142 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8420 (pp) REVERT: C 175 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7220 (mt-10) REVERT: D 147 ILE cc_start: 0.7927 (mm) cc_final: 0.7711 (mt) outliers start: 48 outliers final: 29 residues processed: 158 average time/residue: 0.1102 time to fit residues: 23.3712 Evaluate side-chains 115 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 260 PHE Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 308 TYR Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 336 HIS Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain D residue 451 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 47 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 ASN B 148 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.135480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.112399 restraints weight = 21207.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.112482 restraints weight = 16119.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.113357 restraints weight = 13405.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.113569 restraints weight = 11608.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.113815 restraints weight = 11183.269| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9141 Z= 0.177 Angle : 0.723 10.410 12366 Z= 0.376 Chirality : 0.046 0.177 1359 Planarity : 0.005 0.049 1580 Dihedral : 6.335 54.990 1210 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 5.57 % Allowed : 12.93 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.25), residues: 1063 helix: 0.83 (0.22), residues: 545 sheet: -2.46 (0.36), residues: 159 loop : -2.11 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 278 TYR 0.031 0.002 TYR C 308 PHE 0.025 0.002 PHE A 282 TRP 0.013 0.002 TRP B 354 HIS 0.008 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 ( 9141) covalent geometry : angle 0.72286 / 0.38 (12366) hydrogen bonds : bond 0.06937 / 4.62 ( 477) hydrogen bonds : angle 5.26982 / 3.62 ( 1380) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 101 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 142 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8102 (tt) REVERT: C 271 ASP cc_start: 0.7449 (OUTLIER) cc_final: 0.7124 (t70) outliers start: 53 outliers final: 36 residues processed: 144 average time/residue: 0.1047 time to fit residues: 20.4137 Evaluate side-chains 116 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 78 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 336 HIS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 260 PHE Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 308 TYR Chi-restraints excluded: chain D residue 336 HIS Chi-restraints excluded: chain D residue 382 THR Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 388 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 76 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 HIS B 148 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.135485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.111532 restraints weight = 21666.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.112553 restraints weight = 13657.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.113507 restraints weight = 10975.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.113736 restraints weight = 9713.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.113830 restraints weight = 9314.594| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9141 Z= 0.171 Angle : 0.696 11.442 12366 Z= 0.358 Chirality : 0.045 0.167 1359 Planarity : 0.005 0.044 1580 Dihedral : 6.081 56.667 1210 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 5.36 % Allowed : 14.41 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.26), residues: 1063 helix: 1.04 (0.22), residues: 553 sheet: -2.22 (0.39), residues: 150 loop : -1.89 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 278 TYR 0.027 0.002 TYR C 308 PHE 0.023 0.002 PHE A 282 TRP 0.011 0.001 TRP A 354 HIS 0.008 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 ( 9141) covalent geometry : angle 0.69565 / 0.36 (12366) hydrogen bonds : bond 0.06626 / 4.39 ( 477) hydrogen bonds : angle 5.04718 / 3.46 ( 1380) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 92 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 ARG cc_start: 0.8078 (mmp-170) cc_final: 0.7438 (mtt90) REVERT: C 152 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.7186 (tt) REVERT: C 271 ASP cc_start: 0.7584 (OUTLIER) cc_final: 0.7248 (t70) REVERT: C 387 TYR cc_start: 0.6640 (OUTLIER) cc_final: 0.6135 (t80) REVERT: D 260 PHE cc_start: 0.7240 (OUTLIER) cc_final: 0.6623 (p90) outliers start: 51 outliers final: 39 residues processed: 139 average time/residue: 0.1003 time to fit residues: 18.9898 Evaluate side-chains 124 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 81 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 336 HIS Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 260 PHE Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 336 HIS Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 382 THR Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 388 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 98 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 6 optimal weight: 8.9990 chunk 73 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN B 148 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.134233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.110890 restraints weight = 21719.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.111285 restraints weight = 16238.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.112087 restraints weight = 13187.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.112303 restraints weight = 11657.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.112489 restraints weight = 11143.188| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9141 Z= 0.183 Angle : 0.687 9.680 12366 Z= 0.357 Chirality : 0.046 0.205 1359 Planarity : 0.005 0.048 1580 Dihedral : 5.932 57.108 1208 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 5.57 % Allowed : 15.46 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.26), residues: 1063 helix: 1.16 (0.22), residues: 554 sheet: -2.29 (0.38), residues: 150 loop : -1.81 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 453 TYR 0.027 0.002 TYR C 308 PHE 0.025 0.002 PHE A 282 TRP 0.011 0.001 TRP D 389 HIS 0.009 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 ( 9141) covalent geometry : angle 0.68672 / 0.36 (12366) hydrogen bonds : bond 0.06598 / 4.37 ( 477) hydrogen bonds : angle 4.99046 / 3.41 ( 1380) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 89 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 ARG cc_start: 0.8051 (mmp-170) cc_final: 0.7444 (mtt90) REVERT: C 152 ILE cc_start: 0.7557 (OUTLIER) cc_final: 0.7223 (tt) REVERT: C 271 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.7051 (t70) REVERT: C 387 TYR cc_start: 0.6600 (OUTLIER) cc_final: 0.6088 (t80) outliers start: 53 outliers final: 41 residues processed: 137 average time/residue: 0.0982 time to fit residues: 18.5372 Evaluate side-chains 122 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 78 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 336 HIS Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 260 PHE Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 336 HIS Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 382 THR Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain D residue 407 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 29 optimal weight: 1.9990 chunk 101 optimal weight: 20.0000 chunk 37 optimal weight: 0.0370 chunk 102 optimal weight: 0.0020 chunk 83 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 overall best weight: 2.0072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 HIS ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.135754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.112915 restraints weight = 21688.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.113300 restraints weight = 16188.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.113909 restraints weight = 12980.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.114194 restraints weight = 12328.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.114387 restraints weight = 11265.498| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9141 Z= 0.146 Angle : 0.654 11.989 12366 Z= 0.333 Chirality : 0.045 0.197 1359 Planarity : 0.004 0.042 1580 Dihedral : 5.787 59.855 1208 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 5.15 % Allowed : 15.35 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.26), residues: 1063 helix: 1.29 (0.22), residues: 560 sheet: -2.20 (0.38), residues: 150 loop : -1.76 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 278 TYR 0.022 0.002 TYR C 376 PHE 0.019 0.001 PHE B 352 TRP 0.009 0.001 TRP D 389 HIS 0.007 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 ( 9141) covalent geometry : angle 0.65396 / 0.33 (12366) hydrogen bonds : bond 0.06202 / 4.10 ( 477) hydrogen bonds : angle 4.76810 / 3.28 ( 1380) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 94 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 ARG cc_start: 0.7968 (mmp-170) cc_final: 0.7464 (mtt90) REVERT: C 152 ILE cc_start: 0.7510 (OUTLIER) cc_final: 0.7195 (tt) REVERT: C 271 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.7063 (t70) REVERT: C 387 TYR cc_start: 0.6578 (OUTLIER) cc_final: 0.5950 (t80) outliers start: 49 outliers final: 38 residues processed: 138 average time/residue: 0.0917 time to fit residues: 17.7108 Evaluate side-chains 120 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 79 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 336 HIS Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 382 THR Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain D residue 407 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 22 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 2 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 83 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 148 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.135593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.111790 restraints weight = 21864.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.112789 restraints weight = 16189.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.113213 restraints weight = 13322.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.113760 restraints weight = 12037.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.113851 restraints weight = 11471.983| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9141 Z= 0.165 Angle : 0.667 11.547 12366 Z= 0.342 Chirality : 0.045 0.193 1359 Planarity : 0.004 0.044 1580 Dihedral : 5.725 59.811 1208 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 5.78 % Allowed : 15.56 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.26), residues: 1063 helix: 1.37 (0.22), residues: 560 sheet: -2.19 (0.38), residues: 150 loop : -1.73 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 278 TYR 0.024 0.002 TYR C 376 PHE 0.021 0.002 PHE B 282 TRP 0.010 0.001 TRP A 425 HIS 0.007 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 9141) covalent geometry : angle 0.66708 / 0.34 (12366) hydrogen bonds : bond 0.06265 / 4.15 ( 477) hydrogen bonds : angle 4.74172 / 3.25 ( 1380) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 84 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 ARG cc_start: 0.8009 (mmp-170) cc_final: 0.7505 (mtt90) REVERT: C 152 ILE cc_start: 0.7530 (OUTLIER) cc_final: 0.7214 (tt) REVERT: C 271 ASP cc_start: 0.7426 (OUTLIER) cc_final: 0.7088 (t70) REVERT: C 387 TYR cc_start: 0.6633 (OUTLIER) cc_final: 0.6218 (t80) outliers start: 55 outliers final: 41 residues processed: 132 average time/residue: 0.0964 time to fit residues: 17.5373 Evaluate side-chains 126 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 82 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 336 HIS Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 260 PHE Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 336 HIS Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 382 THR Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain D residue 407 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 68 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 58 optimal weight: 0.3980 chunk 48 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 overall best weight: 4.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 GLN C 167 HIS B 148 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN B 340 GLN D 167 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.129358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.105540 restraints weight = 20314.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.107507 restraints weight = 13061.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.108741 restraints weight = 9973.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.109528 restraints weight = 8430.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.109815 restraints weight = 7608.768| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9141 Z= 0.225 Angle : 0.739 10.378 12366 Z= 0.382 Chirality : 0.047 0.202 1359 Planarity : 0.005 0.046 1580 Dihedral : 5.966 59.430 1208 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 6.10 % Allowed : 15.25 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.26), residues: 1063 helix: 1.33 (0.22), residues: 554 sheet: -2.35 (0.38), residues: 150 loop : -1.67 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 313 TYR 0.031 0.003 TYR C 376 PHE 0.030 0.002 PHE A 282 TRP 0.017 0.002 TRP B 389 HIS 0.010 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.23 ( 9141) covalent geometry : angle 0.73911 / 0.38 (12366) hydrogen bonds : bond 0.06893 / 4.58 ( 477) hydrogen bonds : angle 4.94640 / 3.39 ( 1380) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 82 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 ASP cc_start: 0.7792 (p0) cc_final: 0.7265 (t0) REVERT: A 453 ARG cc_start: 0.7917 (mmp-170) cc_final: 0.7468 (mtt90) REVERT: C 152 ILE cc_start: 0.7688 (OUTLIER) cc_final: 0.7255 (tt) REVERT: C 271 ASP cc_start: 0.7687 (OUTLIER) cc_final: 0.7358 (t70) REVERT: D 350 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7253 (tp) outliers start: 58 outliers final: 48 residues processed: 134 average time/residue: 0.0898 time to fit residues: 17.0314 Evaluate side-chains 127 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 76 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 336 HIS Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 336 HIS Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 382 THR Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain D residue 407 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 12 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 20.0000 chunk 4 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 32 optimal weight: 0.0770 chunk 85 optimal weight: 0.0020 chunk 28 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.2152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 HIS B 148 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.132960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.109695 restraints weight = 19948.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.111741 restraints weight = 12663.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.113027 restraints weight = 9533.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.113864 restraints weight = 7987.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.114303 restraints weight = 7163.357| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9141 Z= 0.144 Angle : 0.666 10.308 12366 Z= 0.340 Chirality : 0.045 0.194 1359 Planarity : 0.004 0.040 1580 Dihedral : 5.690 56.438 1208 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 5.15 % Allowed : 16.51 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.26), residues: 1063 helix: 1.48 (0.22), residues: 560 sheet: -2.24 (0.38), residues: 150 loop : -1.64 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 278 TYR 0.024 0.002 TYR C 376 PHE 0.024 0.001 PHE B 352 TRP 0.011 0.001 TRP A 425 HIS 0.009 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 ( 9141) covalent geometry : angle 0.66628 / 0.34 (12366) hydrogen bonds : bond 0.06199 / 4.11 ( 477) hydrogen bonds : angle 4.67015 / 3.21 ( 1380) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 90 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 ASP cc_start: 0.7745 (p0) cc_final: 0.7262 (t0) REVERT: A 453 ARG cc_start: 0.7822 (mmp-170) cc_final: 0.7513 (mtt90) REVERT: C 152 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7114 (tt) REVERT: C 271 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7357 (t70) REVERT: C 387 TYR cc_start: 0.6766 (OUTLIER) cc_final: 0.5991 (t80) REVERT: B 384 MET cc_start: 0.3545 (mtt) cc_final: 0.2927 (mtm) REVERT: D 350 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7283 (tp) outliers start: 49 outliers final: 40 residues processed: 132 average time/residue: 0.0988 time to fit residues: 18.0147 Evaluate side-chains 121 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 77 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 336 HIS Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 260 PHE Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 382 THR Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain D residue 407 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 78 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 4 optimal weight: 0.0050 chunk 30 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 overall best weight: 2.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 148 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.131808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.108272 restraints weight = 20229.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.110380 restraints weight = 12611.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.111675 restraints weight = 9391.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.112567 restraints weight = 7846.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.113012 restraints weight = 7004.004| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.5276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9141 Z= 0.164 Angle : 0.681 11.460 12366 Z= 0.350 Chirality : 0.045 0.224 1359 Planarity : 0.005 0.052 1580 Dihedral : 5.685 56.399 1208 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 4.84 % Allowed : 16.82 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.26), residues: 1063 helix: 1.43 (0.22), residues: 561 sheet: -2.24 (0.39), residues: 150 loop : -1.62 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 453 TYR 0.027 0.002 TYR C 376 PHE 0.025 0.002 PHE B 352 TRP 0.037 0.002 TRP A 425 HIS 0.006 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 9141) covalent geometry : angle 0.68120 / 0.35 (12366) hydrogen bonds : bond 0.06253 / 4.14 ( 477) hydrogen bonds : angle 4.66707 / 3.21 ( 1380) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 80 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 304 ASP cc_start: 0.7779 (p0) cc_final: 0.7285 (t0) REVERT: A 453 ARG cc_start: 0.7795 (mmp-170) cc_final: 0.7510 (mtt90) REVERT: C 152 ILE cc_start: 0.7584 (OUTLIER) cc_final: 0.7083 (tt) REVERT: C 271 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7307 (t70) REVERT: C 387 TYR cc_start: 0.6719 (OUTLIER) cc_final: 0.5943 (t80) REVERT: B 384 MET cc_start: 0.3578 (mtt) cc_final: 0.2970 (mtm) REVERT: D 309 PHE cc_start: 0.7251 (OUTLIER) cc_final: 0.6937 (t80) REVERT: D 350 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7224 (tt) outliers start: 46 outliers final: 40 residues processed: 119 average time/residue: 0.0864 time to fit residues: 14.6651 Evaluate side-chains 121 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 76 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 336 HIS Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 260 PHE Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 309 PHE Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 382 THR Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain D residue 407 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 2 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 71 optimal weight: 0.6980 chunk 22 optimal weight: 20.0000 chunk 100 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.133610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.110118 restraints weight = 19689.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.112230 restraints weight = 12317.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.113584 restraints weight = 9186.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.114447 restraints weight = 7655.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.114938 restraints weight = 6835.427| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.5467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9141 Z= 0.141 Angle : 0.659 11.079 12366 Z= 0.334 Chirality : 0.044 0.197 1359 Planarity : 0.004 0.046 1580 Dihedral : 5.502 53.252 1208 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 4.73 % Allowed : 16.93 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.27), residues: 1063 helix: 1.59 (0.22), residues: 561 sheet: -2.12 (0.39), residues: 150 loop : -1.58 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 453 TYR 0.024 0.002 TYR C 376 PHE 0.024 0.001 PHE B 352 TRP 0.022 0.001 TRP A 425 HIS 0.010 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 9141) covalent geometry : angle 0.65899 / 0.33 (12366) hydrogen bonds : bond 0.05845 / 3.87 ( 477) hydrogen bonds : angle 4.47699 / 3.08 ( 1380) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1408.80 seconds wall clock time: 25 minutes 44.42 seconds (1544.42 seconds total)