Starting phenix.real_space_refine on Thu Feb 13 17:08:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6d7w_7826/02_2025/6d7w_7826.cif Found real_map, /net/cci-nas-00/data/ceres_data/6d7w_7826/02_2025/6d7w_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6d7w_7826/02_2025/6d7w_7826.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6d7w_7826/02_2025/6d7w_7826.map" model { file = "/net/cci-nas-00/data/ceres_data/6d7w_7826/02_2025/6d7w_7826.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6d7w_7826/02_2025/6d7w_7826.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.42, per 1000 atoms: 0.61 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: 2.18 Conformation dependent library (CDL) restraints added in 900.4 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: 0.76 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: 1.93 Time building geometry restraints manager: 2.54 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: 0.010 Normalize map: mean=0, sd=1: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 21.330 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 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= 0.480 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.027 0.003 TRP B 368 HIS 0.017 0.002 HIS A 336 PHE 0.036 0.004 PHE D 272 TYR 0.031 0.003 TYR C 308 ARG 0.014 0.001 ARG A 278 *********************** 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 : 0.976 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: 0.7969 (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: 0.6765 (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: 0.7242 (t80) outliers start: 26 outliers final: 9 residues processed: 261 average time/residue: 0.3241 time to fit residues: 105.0818 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 : 1.005 ------------------------------------------------------------------------------- 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 89 optimal weight: 0.0870 chunk 80 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 32 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 overall best weight: 3.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4074 r_free = 0.4074 target = 0.137452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.113570 restraints weight = 20713.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.114686 restraints weight = 15073.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.115208 restraints weight = 11901.799| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9141 Z= 0.283 Angle : 0.783 12.298 12366 Z= 0.412 Chirality : 0.048 0.258 1359 Planarity : 0.006 0.055 1580 Dihedral : 7.344 63.710 1222 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 5.15 % Allowed : 12.20 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.25), residues: 1063 helix: 0.21 (0.22), residues: 543 sheet: -2.74 (0.33), residues: 165 loop : -2.34 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 354 HIS 0.010 0.001 HIS A 336 PHE 0.029 0.002 PHE A 282 TYR 0.043 0.003 TYR C 308 ARG 0.007 0.001 ARG A 278 *********************** 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 168 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 119 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 VAL cc_start: 0.8202 (t) cc_final: 0.7991 (p) REVERT: A 415 TYR cc_start: 0.7738 (p90) cc_final: 0.7335 (p90) REVERT: A 453 ARG cc_start: 0.8250 (mtt180) cc_final: 0.8001 (mmp-170) REVERT: A 454 LYS cc_start: 0.7442 (mttt) cc_final: 0.7014 (pttt) REVERT: C 142 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8413 (pp) REVERT: C 175 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7242 (mt-10) REVERT: B 304 ASP cc_start: 0.7091 (t0) cc_final: 0.6883 (t0) REVERT: D 147 ILE cc_start: 0.7942 (mm) cc_final: 0.7735 (mt) outliers start: 49 outliers final: 30 residues processed: 161 average time/residue: 0.2402 time to fit residues: 51.2573 Evaluate side-chains 115 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 84 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 141 LEU 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 83 optimal weight: 0.8980 chunk 70 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.135688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.112312 restraints weight = 21099.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.112705 restraints weight = 15264.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.113496 restraints weight = 12583.425| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9141 Z= 0.267 Angle : 0.732 10.369 12366 Z= 0.382 Chirality : 0.046 0.176 1359 Planarity : 0.005 0.049 1580 Dihedral : 6.356 55.424 1210 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 5.36 % Allowed : 13.35 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.26), residues: 1063 helix: 0.83 (0.22), residues: 547 sheet: -2.44 (0.37), residues: 155 loop : -2.09 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 425 HIS 0.008 0.001 HIS A 336 PHE 0.027 0.002 PHE A 282 TYR 0.032 0.002 TYR C 308 ARG 0.007 0.001 ARG A 278 *********************** 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 152 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 101 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 LYS cc_start: 0.7541 (mttt) cc_final: 0.7040 (pttt) REVERT: C 142 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8127 (tt) REVERT: C 271 ASP cc_start: 0.7493 (OUTLIER) cc_final: 0.7165 (t70) REVERT: D 147 ILE cc_start: 0.7958 (mm) cc_final: 0.7736 (mt) outliers start: 51 outliers final: 37 residues processed: 142 average time/residue: 0.2420 time to fit residues: 45.8488 Evaluate side-chains 116 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 77 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 342 VAL 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 260 PHE Chi-restraints excluded: chain D residue 298 VAL 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 33 optimal weight: 9.9990 chunk 55 optimal weight: 0.0060 chunk 53 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 24 optimal weight: 20.0000 chunk 76 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 3 optimal weight: 0.0980 overall best weight: 2.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN ** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4045 r_free = 0.4045 target = 0.135751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.112116 restraints weight = 20925.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.113474 restraints weight = 14901.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.114026 restraints weight = 11966.481| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9141 Z= 0.233 Angle : 0.693 11.228 12366 Z= 0.357 Chirality : 0.045 0.174 1359 Planarity : 0.004 0.044 1580 Dihedral : 6.001 57.274 1208 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 5.26 % Allowed : 14.20 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.26), residues: 1063 helix: 1.07 (0.22), residues: 550 sheet: -2.25 (0.39), residues: 150 loop : -1.82 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 263 HIS 0.008 0.001 HIS A 336 PHE 0.022 0.002 PHE A 282 TYR 0.026 0.002 TYR D 308 ARG 0.007 0.000 ARG A 278 *********************** 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 142 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 92 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 ARG cc_start: 0.8052 (mmp-170) cc_final: 0.7435 (mtt90) REVERT: C 152 ILE cc_start: 0.7495 (OUTLIER) cc_final: 0.7174 (tt) REVERT: C 271 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.7131 (t70) REVERT: C 387 TYR cc_start: 0.6564 (OUTLIER) cc_final: 0.6131 (t80) REVERT: D 260 PHE cc_start: 0.7212 (OUTLIER) cc_final: 0.6668 (p90) outliers start: 50 outliers final: 34 residues processed: 138 average time/residue: 0.2512 time to fit residues: 46.1831 Evaluate side-chains 118 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 80 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 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 304 ASP 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 342 VAL 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 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 75 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 4 optimal weight: 0.0060 chunk 5 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 90 optimal weight: 0.3980 chunk 34 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 overall best weight: 2.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN ** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4057 r_free = 0.4057 target = 0.136421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.113125 restraints weight = 21487.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.114144 restraints weight = 15415.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.114706 restraints weight = 12776.278| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9141 Z= 0.197 Angle : 0.657 11.062 12366 Z= 0.337 Chirality : 0.045 0.199 1359 Planarity : 0.004 0.046 1580 Dihedral : 5.816 58.760 1208 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 6.10 % Allowed : 14.30 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.26), residues: 1063 helix: 1.20 (0.22), residues: 561 sheet: -2.24 (0.39), residues: 150 loop : -1.81 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 389 HIS 0.008 0.001 HIS A 336 PHE 0.024 0.001 PHE B 352 TYR 0.021 0.002 TYR C 308 ARG 0.006 0.000 ARG A 278 *********************** 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 151 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 93 time to evaluate : 1.102 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: 0.8010 (mmp-170) cc_final: 0.7396 (mtt90) REVERT: C 152 ILE cc_start: 0.7480 (OUTLIER) cc_final: 0.7183 (tt) REVERT: C 271 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.7077 (t70) REVERT: C 387 TYR cc_start: 0.6529 (OUTLIER) cc_final: 0.6175 (t80) outliers start: 58 outliers final: 42 residues processed: 145 average time/residue: 0.2209 time to fit residues: 43.2521 Evaluate side-chains 125 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 80 time to evaluate : 1.110 ------------------------------------------------------------------------------- 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 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 342 VAL 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 95 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4036 r_free = 0.4036 target = 0.134632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.111727 restraints weight = 21407.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.112297 restraints weight = 15921.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.112826 restraints weight = 12658.673| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9141 Z= 0.250 Angle : 0.686 11.942 12366 Z= 0.351 Chirality : 0.046 0.197 1359 Planarity : 0.004 0.044 1580 Dihedral : 5.825 58.490 1208 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 5.99 % Allowed : 14.72 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.26), residues: 1063 helix: 1.26 (0.22), residues: 561 sheet: -2.27 (0.38), residues: 150 loop : -1.73 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 389 HIS 0.008 0.001 HIS A 336 PHE 0.024 0.002 PHE A 282 TYR 0.025 0.002 TYR C 308 ARG 0.006 0.001 ARG A 278 *********************** 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 138 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 81 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 ARG cc_start: 0.7979 (mmp-170) cc_final: 0.7434 (mtt90) REVERT: C 152 ILE cc_start: 0.7559 (OUTLIER) cc_final: 0.7233 (tt) REVERT: C 271 ASP cc_start: 0.7349 (OUTLIER) cc_final: 0.7007 (t70) REVERT: C 387 TYR cc_start: 0.6621 (OUTLIER) cc_final: 0.6158 (t80) outliers start: 57 outliers final: 48 residues processed: 131 average time/residue: 0.2246 time to fit residues: 40.0889 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 : 1.088 ------------------------------------------------------------------------------- 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 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 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 310 LEU Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 342 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 13 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 48 optimal weight: 30.0000 chunk 54 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 74 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3969 r_free = 0.3969 target = 0.131868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.109092 restraints weight = 19822.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.111060 restraints weight = 12808.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.112328 restraints weight = 9699.558| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9141 Z= 0.242 Angle : 0.677 10.599 12366 Z= 0.347 Chirality : 0.045 0.195 1359 Planarity : 0.004 0.044 1580 Dihedral : 5.755 59.197 1208 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 6.62 % Allowed : 14.83 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.27), residues: 1063 helix: 1.40 (0.22), residues: 553 sheet: -2.28 (0.38), residues: 150 loop : -1.55 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 389 HIS 0.013 0.001 HIS A 336 PHE 0.022 0.002 PHE A 282 TYR 0.024 0.002 TYR C 308 ARG 0.005 0.000 ARG A 278 *********************** 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 152 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 89 time to evaluate : 1.024 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: 0.7893 (mmp-170) cc_final: 0.7455 (mtt90) REVERT: C 152 ILE cc_start: 0.7563 (OUTLIER) cc_final: 0.7329 (tt) REVERT: C 271 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7326 (t70) REVERT: C 387 TYR cc_start: 0.6719 (OUTLIER) cc_final: 0.6179 (t80) REVERT: D 169 GLU cc_start: 0.7567 (tt0) cc_final: 0.7323 (tt0) REVERT: D 350 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7293 (tp) outliers start: 63 outliers final: 47 residues processed: 145 average time/residue: 0.2305 time to fit residues: 45.4871 Evaluate side-chains 132 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 81 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 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 342 VAL 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 54 optimal weight: 2.9990 chunk 90 optimal weight: 0.0670 chunk 57 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 26 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 3 optimal weight: 0.0970 chunk 79 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.9518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 GLN ** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4084 r_free = 0.4084 target = 0.138094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.115506 restraints weight = 21835.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.115888 restraints weight = 16369.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.116488 restraints weight = 13080.970| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9141 Z= 0.180 Angle : 0.658 10.174 12366 Z= 0.334 Chirality : 0.044 0.199 1359 Planarity : 0.004 0.039 1580 Dihedral : 5.542 56.849 1208 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.52 % Allowed : 17.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.27), residues: 1063 helix: 1.55 (0.22), residues: 553 sheet: -2.11 (0.39), residues: 150 loop : -1.44 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 368 HIS 0.008 0.001 HIS A 336 PHE 0.025 0.001 PHE B 352 TYR 0.024 0.002 TYR C 376 ARG 0.006 0.000 ARG D 136 *********************** 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 141 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 98 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 ASP cc_start: 0.7553 (p0) cc_final: 0.7017 (t0) REVERT: A 453 ARG cc_start: 0.7874 (mmp-170) cc_final: 0.7489 (mtt90) REVERT: C 152 ILE cc_start: 0.7504 (OUTLIER) cc_final: 0.7139 (tt) REVERT: C 271 ASP cc_start: 0.7363 (OUTLIER) cc_final: 0.7006 (t70) REVERT: C 387 TYR cc_start: 0.6644 (OUTLIER) cc_final: 0.6079 (t80) REVERT: B 384 MET cc_start: 0.3136 (mtt) cc_final: 0.2751 (mtm) outliers start: 43 outliers final: 33 residues processed: 135 average time/residue: 0.2299 time to fit residues: 42.2334 Evaluate side-chains 117 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 81 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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 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 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 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 383 LEU 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 298 VAL Chi-restraints excluded: chain D residue 317 ILE 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 3 optimal weight: 0.5980 chunk 88 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 57 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 98 optimal weight: 0.3980 chunk 99 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 HIS ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 GLN ** D 162 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 = 0.4073 r_free = 0.4073 target = 0.137489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.112733 restraints weight = 21568.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.114860 restraints weight = 14178.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.116218 restraints weight = 10912.139| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.5338 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= 0.185 Angle : 0.663 11.276 12366 Z= 0.337 Chirality : 0.045 0.190 1359 Planarity : 0.004 0.044 1580 Dihedral : 5.442 55.917 1208 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 4.42 % Allowed : 17.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.27), residues: 1063 helix: 1.58 (0.22), residues: 555 sheet: -2.00 (0.40), residues: 151 loop : -1.46 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 425 HIS 0.008 0.001 HIS A 336 PHE 0.022 0.001 PHE B 352 TYR 0.022 0.002 TYR C 376 ARG 0.006 0.000 ARG D 136 *********************** 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 129 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 87 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 ASP cc_start: 0.7569 (p0) cc_final: 0.7013 (t0) REVERT: A 453 ARG cc_start: 0.7798 (mmp-170) cc_final: 0.7450 (mtt90) REVERT: C 152 ILE cc_start: 0.7519 (OUTLIER) cc_final: 0.7118 (tt) REVERT: C 271 ASP cc_start: 0.7473 (OUTLIER) cc_final: 0.7141 (t70) REVERT: C 387 TYR cc_start: 0.6742 (OUTLIER) cc_final: 0.6219 (t80) outliers start: 42 outliers final: 34 residues processed: 124 average time/residue: 0.2224 time to fit residues: 37.9812 Evaluate side-chains 116 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 79 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 283 ILE 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 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 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 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 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 81 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 9 optimal weight: 0.4980 chunk 85 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 77 optimal weight: 8.9990 chunk 48 optimal weight: 20.0000 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3998 r_free = 0.3998 target = 0.134279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.111195 restraints weight = 19885.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.113279 restraints weight = 12672.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.114609 restraints weight = 9510.272| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.5417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9141 Z= 0.202 Angle : 0.669 10.096 12366 Z= 0.339 Chirality : 0.045 0.200 1359 Planarity : 0.004 0.044 1580 Dihedral : 5.425 56.170 1208 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 4.42 % Allowed : 17.56 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.27), residues: 1063 helix: 1.67 (0.22), residues: 555 sheet: -1.96 (0.40), residues: 150 loop : -1.40 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 425 HIS 0.003 0.001 HIS A 336 PHE 0.023 0.001 PHE B 352 TYR 0.024 0.002 TYR C 376 ARG 0.006 0.000 ARG D 136 ********************** 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 127 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 85 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: A 304 ASP cc_start: 0.7740 (p0) cc_final: 0.7161 (t0) REVERT: A 453 ARG cc_start: 0.7802 (mmp-170) cc_final: 0.7534 (mtt90) REVERT: A 454 LYS cc_start: 0.7524 (mttt) cc_final: 0.7291 (tptt) REVERT: C 152 ILE cc_start: 0.7547 (OUTLIER) cc_final: 0.7051 (tt) REVERT: C 271 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7288 (t70) REVERT: C 285 THR cc_start: 0.8794 (m) cc_final: 0.8572 (p) REVERT: C 387 TYR cc_start: 0.6630 (OUTLIER) cc_final: 0.6227 (t80) REVERT: B 454 LYS cc_start: 0.7699 (mttt) cc_final: 0.7112 (pttt) REVERT: D 350 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7223 (tt) outliers start: 42 outliers final: 36 residues processed: 122 average time/residue: 0.2276 time to fit residues: 38.6189 Evaluate side-chains 121 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 81 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 336 HIS Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 382 THR 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 53 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 30.0000 chunk 14 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 44 optimal weight: 0.0970 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN B 148 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN D 167 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.130844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.107594 restraints weight = 20162.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.109584 restraints weight = 12921.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.110872 restraints weight = 9778.842| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.5395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9141 Z= 0.305 Angle : 0.733 9.976 12366 Z= 0.378 Chirality : 0.048 0.194 1359 Planarity : 0.005 0.044 1580 Dihedral : 5.634 58.997 1206 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 4.52 % Allowed : 17.88 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.26), residues: 1063 helix: 1.44 (0.22), residues: 562 sheet: -2.12 (0.40), residues: 150 loop : -1.63 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 425 HIS 0.004 0.001 HIS A 393 PHE 0.028 0.002 PHE A 282 TYR 0.028 0.002 TYR C 376 ARG 0.006 0.001 ARG D 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2593.15 seconds wall clock time: 47 minutes 23.78 seconds (2843.78 seconds total)