Starting phenix.real_space_refine on Thu Mar 5 12:40:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q3d_13789/03_2026/7q3d_13789.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q3d_13789/03_2026/7q3d_13789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7q3d_13789/03_2026/7q3d_13789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q3d_13789/03_2026/7q3d_13789.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7q3d_13789/03_2026/7q3d_13789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q3d_13789/03_2026/7q3d_13789.map" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 60 5.16 5 C 7123 2.51 5 N 1866 2.21 5 O 2000 1.98 5 H 11249 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22298 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 8887 Classifications: {'peptide': 545} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 525} Chain breaks: 7 Chain: "B" Number of atoms: 7247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 7247 Classifications: {'peptide': 453} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 427} Chain breaks: 7 Chain: "C" Number of atoms: 6164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 6164 Classifications: {'peptide': 393} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 359} Chain breaks: 1 Time building chain proxies: 3.61, per 1000 atoms: 0.16 Number of scatterers: 22298 At special positions: 0 Unit cell: (79.86, 118.8, 143.22, 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) S 60 16.00 O 2000 8.00 N 1866 7.00 C 7123 6.00 H 11249 1.00 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: 2.09 Conformation dependent library (CDL) restraints added in 596.6 milliseconds 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2632 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 12 sheets defined 37.5% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 73 through 86 Processing helix chain 'A' and resid 99 through 114 Processing helix chain 'A' and resid 153 through 158 removed outlier: 3.789A pdb=" N GLY A 157 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 487 through 498 Processing helix chain 'A' and resid 500 through 511 Processing helix chain 'A' and resid 512 through 515 removed outlier: 5.266A pdb=" N THR A 515 " --> pdb=" O ASN A 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 512 through 515' Processing helix chain 'A' and resid 516 through 533 Processing helix chain 'A' and resid 538 through 553 removed outlier: 4.154A pdb=" N PHE A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 583 removed outlier: 4.864A pdb=" N ASP A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N GLN A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 598 Processing helix chain 'A' and resid 603 through 612 removed outlier: 3.903A pdb=" N LEU A 609 " --> pdb=" O ASP A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 628 removed outlier: 4.218A pdb=" N GLU A 620 " --> pdb=" O LEU A 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 343 removed outlier: 3.621A pdb=" N GLN B 338 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS B 339 " --> pdb=" O GLU B 335 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LEU B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 358 removed outlier: 4.080A pdb=" N PHE B 347 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU B 355 " --> pdb=" O CYS B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 416 removed outlier: 3.770A pdb=" N ASN B 402 " --> pdb=" O PRO B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 424 Processing helix chain 'B' and resid 427 through 442 Processing helix chain 'B' and resid 444 through 448 removed outlier: 3.515A pdb=" N LYS B 447 " --> pdb=" O GLN B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 468 removed outlier: 3.934A pdb=" N VAL B 465 " --> pdb=" O ALA B 461 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 495 removed outlier: 4.801A pdb=" N GLU B 485 " --> pdb=" O GLU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 545 Processing helix chain 'B' and resid 546 through 554 Processing helix chain 'B' and resid 622 through 636 Processing helix chain 'B' and resid 638 through 648 Processing helix chain 'B' and resid 816 through 822 Processing helix chain 'B' and resid 827 through 860 removed outlier: 3.814A pdb=" N VAL B 845 " --> pdb=" O SER B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 938 Processing helix chain 'C' and resid 39 through 55 removed outlier: 3.597A pdb=" N HIS C 50 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 111 Processing helix chain 'C' and resid 120 through 128 removed outlier: 3.577A pdb=" N LEU C 124 " --> pdb=" O ASN C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 140 removed outlier: 4.366A pdb=" N LEU C 134 " --> pdb=" O ALA C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 150 Processing helix chain 'C' and resid 159 through 170 Processing helix chain 'C' and resid 193 through 197 Processing helix chain 'C' and resid 198 through 212 Proline residue: C 206 - end of helix Processing helix chain 'C' and resid 255 through 259 Processing helix chain 'C' and resid 260 through 269 removed outlier: 5.707A pdb=" N ARG C 266 " --> pdb=" O GLN C 262 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TRP C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 279 Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'C' and resid 322 through 338 Processing helix chain 'C' and resid 402 through 415 Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 61 removed outlier: 4.118A pdb=" N ILE A 403 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE A 413 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 9.609A pdb=" N LEU A 401 " --> pdb=" O ILE A 413 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 382 through 385 removed outlier: 9.609A pdb=" N LEU A 401 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE A 413 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE A 403 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLU A 467 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU A 438 " --> pdb=" O GLU A 467 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 116 through 123 removed outlier: 6.560A pdb=" N VAL A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU A 136 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ILE A 151 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N SER A 138 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N VAL A 149 " --> pdb=" O SER A 138 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER A 140 " --> pdb=" O GLU A 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 164 through 169 removed outlier: 6.931A pdb=" N SER A 177 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ALA A 167 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE A 175 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LEU A 169 " --> pdb=" O PHE A 173 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N PHE A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE A 178 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LYS A 183 " --> pdb=" O PHE A 178 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 228 through 231 removed outlier: 5.978A pdb=" N GLY A 268 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N VAL A 276 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA A 270 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LEU A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 286 through 291 removed outlier: 6.617A pdb=" N VAL A 302 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL A 289 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N PHE A 300 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A 330 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 286 through 291 removed outlier: 6.617A pdb=" N VAL A 302 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL A 289 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N PHE A 300 " --> pdb=" O VAL A 289 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 340 through 345 removed outlier: 6.578A pdb=" N GLY A 355 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N CYS A 343 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE A 353 " --> pdb=" O CYS A 343 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ARG A 345 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LYS A 351 " --> pdb=" O ARG A 345 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 327 through 331 removed outlier: 6.307A pdb=" N ILE B 327 " --> pdb=" O THR B 313 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR B 313 " --> pdb=" O ILE B 327 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N THR B 363 " --> pdb=" O TYR B 378 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ARG C 64 " --> pdb=" O THR B 363 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N SER B 365 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N SER C 62 " --> pdb=" O SER B 365 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU B 367 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU C 60 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 9.586A pdb=" N GLN C 59 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N SER C 74 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N SER C 61 " --> pdb=" O TRP C 72 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL C 10 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER C 27 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU C 12 " --> pdb=" O CYS C 25 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N CYS C 25 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N CYS C 14 " --> pdb=" O LEU C 23 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER C 27 " --> pdb=" O ALA C 34 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 474 through 475 removed outlier: 4.372A pdb=" N ILE B 811 " --> pdb=" O GLU B 806 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU B 806 " --> pdb=" O ILE B 811 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N VAL C 152 " --> pdb=" O CYS C 309 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N PHE C 311 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N CYS C 154 " --> pdb=" O PHE C 311 " (cutoff:3.500A) removed outlier: 9.361A pdb=" N VAL C 313 " --> pdb=" O CYS C 154 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 524 through 528 removed outlier: 6.937A pdb=" N LEU B 519 " --> pdb=" O ILE B 526 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N SER B 528 " --> pdb=" O SER B 517 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N SER B 517 " --> pdb=" O SER B 528 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU B 604 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER B 517 " --> pdb=" O CYS B 602 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N CYS B 602 " --> pdb=" O SER B 517 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU B 519 " --> pdb=" O MET B 600 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N MET B 600 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR B 589 " --> pdb=" O VAL B 565 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 186 through 190 removed outlier: 6.772A pdb=" N LEU C 181 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ALA C 190 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL C 179 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N PHE C 178 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU C 244 " --> pdb=" O LEU C 240 " (cutoff:3.500A) 568 hydrogen bonds defined for protein. 1599 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: 5.55 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 2332 1.05 - 1.25: 10663 1.25 - 1.44: 2958 1.44 - 1.64: 6501 1.64 - 1.83: 81 Bond restraints: 22535 Sorted by residual: bond pdb=" NE ARG C 196 " pdb=" HE ARG C 196 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.79e+01 bond pdb=" CD2 PHE A 481 " pdb=" HD2 PHE A 481 " ideal model delta sigma weight residual 0.930 1.095 -0.165 2.00e-02 2.50e+03 6.78e+01 bond pdb=" CD1 PHE A 291 " pdb=" HD1 PHE A 291 " ideal model delta sigma weight residual 0.930 1.094 -0.164 2.00e-02 2.50e+03 6.75e+01 bond pdb=" CD2 PHE B 909 " pdb=" HD2 PHE B 909 " ideal model delta sigma weight residual 0.930 1.094 -0.164 2.00e-02 2.50e+03 6.68e+01 bond pdb=" NH2 ARG B 399 " pdb="HH21 ARG B 399 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.66e+01 ... (remaining 22530 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 36820 2.77 - 5.55: 3015 5.55 - 8.32: 997 8.32 - 11.10: 5 11.10 - 13.87: 39 Bond angle restraints: 40876 Sorted by residual: angle pdb=" C GLY A 219 " pdb=" N PRO A 220 " pdb=" CA PRO A 220 " ideal model delta sigma weight residual 120.31 129.09 -8.78 9.80e-01 1.04e+00 8.03e+01 angle pdb=" C GLN A 295 " pdb=" N PRO A 296 " pdb=" CA PRO A 296 " ideal model delta sigma weight residual 119.28 127.87 -8.59 1.10e+00 8.26e-01 6.10e+01 angle pdb=" C GLN B 444 " pdb=" N PRO B 445 " pdb=" CA PRO B 445 " ideal model delta sigma weight residual 119.87 127.86 -7.99 1.04e+00 9.25e-01 5.90e+01 angle pdb=" C ASP A 285 " pdb=" N PRO A 286 " pdb=" CA PRO A 286 " ideal model delta sigma weight residual 119.78 127.45 -7.67 1.03e+00 9.43e-01 5.55e+01 angle pdb=" C PRO C 254 " pdb=" N PRO C 255 " pdb=" CA PRO C 255 " ideal model delta sigma weight residual 119.85 127.25 -7.40 1.01e+00 9.80e-01 5.36e+01 ... (remaining 40871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 9914 17.50 - 35.01: 467 35.01 - 52.51: 117 52.51 - 70.01: 54 70.01 - 87.51: 13 Dihedral angle restraints: 10565 sinusoidal: 5824 harmonic: 4741 Sorted by residual: dihedral pdb=" CA GLN A 295 " pdb=" C GLN A 295 " pdb=" N PRO A 296 " pdb=" CA PRO A 296 " ideal model delta harmonic sigma weight residual -180.00 -153.51 -26.49 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA LYS B 913 " pdb=" C LYS B 913 " pdb=" N PRO B 914 " pdb=" CA PRO B 914 " ideal model delta harmonic sigma weight residual 180.00 157.66 22.34 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA ILE B 308 " pdb=" C ILE B 308 " pdb=" N ILE B 309 " pdb=" CA ILE B 309 " ideal model delta harmonic sigma weight residual 180.00 158.17 21.83 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 10562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1242 0.076 - 0.151: 456 0.151 - 0.227: 71 0.227 - 0.302: 12 0.302 - 0.378: 3 Chirality restraints: 1784 Sorted by residual: chirality pdb=" CA THR C 199 " pdb=" N THR C 199 " pdb=" C THR C 199 " pdb=" CB THR C 199 " both_signs ideal model delta sigma weight residual False 2.53 2.15 0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CA SER C 253 " pdb=" N SER C 253 " pdb=" C SER C 253 " pdb=" CB SER C 253 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CG LEU B 942 " pdb=" CB LEU B 942 " pdb=" CD1 LEU B 942 " pdb=" CD2 LEU B 942 " both_signs ideal model delta sigma weight residual False -2.59 -2.91 0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 1781 not shown) Planarity restraints: 3227 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 566 " 0.120 2.00e-02 2.50e+03 5.23e-02 8.22e+01 pdb=" CG TYR A 566 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR A 566 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR A 566 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR A 566 " -0.040 2.00e-02 2.50e+03 pdb=" CE2 TYR A 566 " -0.025 2.00e-02 2.50e+03 pdb=" CZ TYR A 566 " -0.017 2.00e-02 2.50e+03 pdb=" OH TYR A 566 " 0.105 2.00e-02 2.50e+03 pdb=" HD1 TYR A 566 " -0.003 2.00e-02 2.50e+03 pdb=" HD2 TYR A 566 " -0.032 2.00e-02 2.50e+03 pdb=" HE1 TYR A 566 " -0.016 2.00e-02 2.50e+03 pdb=" HE2 TYR A 566 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 475 " -0.093 2.00e-02 2.50e+03 4.38e-02 7.67e+01 pdb=" CG TRP B 475 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 TRP B 475 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP B 475 " 0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP B 475 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TRP B 475 " 0.020 2.00e-02 2.50e+03 pdb=" CE3 TRP B 475 " 0.048 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 475 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 475 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 475 " -0.024 2.00e-02 2.50e+03 pdb=" HD1 TRP B 475 " -0.044 2.00e-02 2.50e+03 pdb=" HE1 TRP B 475 " 0.065 2.00e-02 2.50e+03 pdb=" HE3 TRP B 475 " 0.075 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 475 " -0.020 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 475 " -0.018 2.00e-02 2.50e+03 pdb=" HH2 TRP B 475 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 562 " -0.112 2.00e-02 2.50e+03 3.64e-02 5.30e+01 pdb=" CG TRP B 562 " 0.000 2.00e-02 2.50e+03 pdb=" CD1 TRP B 562 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP B 562 " 0.029 2.00e-02 2.50e+03 pdb=" NE1 TRP B 562 " 0.031 2.00e-02 2.50e+03 pdb=" CE2 TRP B 562 " 0.022 2.00e-02 2.50e+03 pdb=" CE3 TRP B 562 " 0.028 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 562 " -0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 562 " 0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP B 562 " -0.012 2.00e-02 2.50e+03 pdb=" HD1 TRP B 562 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 TRP B 562 " -0.003 2.00e-02 2.50e+03 pdb=" HE3 TRP B 562 " 0.033 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 562 " -0.037 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 562 " 0.007 2.00e-02 2.50e+03 pdb=" HH2 TRP B 562 " -0.036 2.00e-02 2.50e+03 ... (remaining 3224 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 2180 2.20 - 2.80: 45825 2.80 - 3.40: 64021 3.40 - 4.00: 87354 4.00 - 4.60: 130800 Nonbonded interactions: 330180 Sorted by model distance: nonbonded pdb=" H ALA C 285 " pdb=" HB THR C 312 " model vdw 1.604 2.270 nonbonded pdb=" HB3 ALA B 901 " pdb=" H ASP B 923 " model vdw 1.625 2.270 nonbonded pdb=" HB3 TRP A 513 " pdb=" H ASP A 514 " model vdw 1.666 2.270 nonbonded pdb="HG22 ILE A 217 " pdb=" H GLY A 219 " model vdw 1.677 2.270 nonbonded pdb=" HZ3 TRP B 475 " pdb=" HG1 THR B 477 " model vdw 1.678 2.100 ... (remaining 330175 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.47 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.130 Extract box with map and model: 0.360 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 21.810 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 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 : 0.013 0.087 11286 Z= 0.719 Angle : 1.348 8.779 15316 Z= 0.915 Chirality : 0.076 0.378 1784 Planarity : 0.013 0.078 1930 Dihedral : 11.905 87.514 4179 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.22), residues: 1355 helix: -1.26 (0.18), residues: 474 sheet: 1.43 (0.27), residues: 347 loop : 1.45 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 281 TYR 0.110 0.015 TYR A 566 PHE 0.066 0.011 PHE B 435 TRP 0.073 0.014 TRP B 562 HIS 0.011 0.003 HIS B 879 Details of bonding type rmsd covalent geometry : bond 0.01311 (11286) covalent geometry : angle 1.34781 (15316) hydrogen bonds : bond 0.18363 ( 563) hydrogen bonds : angle 7.86915 ( 1599) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 0.646 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.7706 (m-30) cc_final: 0.7393 (m-30) REVERT: A 176 LEU cc_start: 0.8918 (mt) cc_final: 0.8698 (mt) REVERT: A 177 SER cc_start: 0.8869 (t) cc_final: 0.8257 (p) REVERT: A 348 THR cc_start: 0.8756 (p) cc_final: 0.8518 (p) REVERT: A 560 ASP cc_start: 0.8901 (p0) cc_final: 0.8586 (p0) REVERT: A 604 MET cc_start: 0.6584 (mtt) cc_final: 0.6341 (ttm) REVERT: B 401 ARG cc_start: 0.9409 (ptt180) cc_final: 0.9164 (mmm160) REVERT: C 12 LEU cc_start: 0.9484 (tp) cc_final: 0.9252 (tp) REVERT: C 101 MET cc_start: 0.9336 (mmt) cc_final: 0.8866 (mmt) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.3091 time to fit residues: 123.2131 Evaluate side-chains 208 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.087327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.073897 restraints weight = 159379.102| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 6.57 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 11286 Z= 0.205 Angle : 0.692 6.230 15316 Z= 0.388 Chirality : 0.043 0.162 1784 Planarity : 0.005 0.048 1930 Dihedral : 6.194 46.535 1493 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.10 % Allowed : 8.94 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.22), residues: 1355 helix: 0.53 (0.22), residues: 485 sheet: 0.58 (0.26), residues: 347 loop : 0.84 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 423 TYR 0.019 0.002 TYR B 589 PHE 0.026 0.002 PHE B 435 TRP 0.013 0.002 TRP A 284 HIS 0.008 0.002 HIS A 607 Details of bonding type rmsd covalent geometry : bond 0.00407 (11286) covalent geometry : angle 0.69155 (15316) hydrogen bonds : bond 0.06767 ( 563) hydrogen bonds : angle 6.82463 ( 1599) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 216 time to evaluate : 0.587 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.7881 (m-30) cc_final: 0.7424 (m-30) REVERT: A 177 SER cc_start: 0.9013 (t) cc_final: 0.8339 (p) REVERT: A 559 LEU cc_start: 0.9301 (tp) cc_final: 0.9035 (tp) REVERT: A 560 ASP cc_start: 0.9234 (p0) cc_final: 0.9025 (p0) REVERT: B 599 TYR cc_start: 0.7943 (m-80) cc_final: 0.7079 (m-80) REVERT: B 606 GLU cc_start: 0.7489 (tt0) cc_final: 0.7077 (tm-30) REVERT: B 812 PHE cc_start: 0.7165 (m-80) cc_final: 0.6889 (m-80) REVERT: C 26 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8604 (mmp80) REVERT: C 101 MET cc_start: 0.9465 (mmt) cc_final: 0.9159 (tpp) REVERT: C 108 LEU cc_start: 0.9212 (mt) cc_final: 0.9005 (tt) outliers start: 26 outliers final: 20 residues processed: 227 average time/residue: 0.2811 time to fit residues: 88.5080 Evaluate side-chains 206 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 CYS Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 526 ILE Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 558 GLN Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 238 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 66 optimal weight: 0.0050 chunk 15 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 overall best weight: 3.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 ASN C 412 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.085120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.071742 restraints weight = 162641.528| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 6.55 r_work: 0.3682 rms_B_bonded: 6.54 restraints_weight: 2.0000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11286 Z= 0.242 Angle : 0.673 5.143 15316 Z= 0.367 Chirality : 0.042 0.179 1784 Planarity : 0.005 0.044 1930 Dihedral : 5.836 35.642 1493 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.74 % Allowed : 10.07 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.22), residues: 1355 helix: 0.67 (0.23), residues: 475 sheet: -0.04 (0.26), residues: 348 loop : 0.37 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 586 TYR 0.017 0.002 TYR B 624 PHE 0.022 0.002 PHE B 435 TRP 0.010 0.002 TRP B 379 HIS 0.009 0.002 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00485 (11286) covalent geometry : angle 0.67260 (15316) hydrogen bonds : bond 0.05526 ( 563) hydrogen bonds : angle 6.67182 ( 1599) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 0.652 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: 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: 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: 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 59 ILE cc_start: 0.7956 (mt) cc_final: 0.7680 (mt) REVERT: A 166 ASP cc_start: 0.7997 (m-30) cc_final: 0.7627 (m-30) REVERT: A 177 SER cc_start: 0.9155 (t) cc_final: 0.8707 (p) REVERT: A 313 MET cc_start: 0.8336 (mtp) cc_final: 0.8118 (ttm) REVERT: A 560 ASP cc_start: 0.9312 (p0) cc_final: 0.9055 (p0) REVERT: B 310 MET cc_start: 0.7882 (ptp) cc_final: 0.7679 (ptp) REVERT: B 812 PHE cc_start: 0.7652 (m-80) cc_final: 0.7432 (m-80) REVERT: B 878 GLU cc_start: 0.9194 (tt0) cc_final: 0.8800 (tt0) REVERT: B 900 MET cc_start: 0.7284 (ptm) cc_final: 0.6344 (mmt) REVERT: C 26 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8861 (mmp80) REVERT: C 101 MET cc_start: 0.9519 (mmt) cc_final: 0.9227 (tpp) outliers start: 34 outliers final: 28 residues processed: 210 average time/residue: 0.2548 time to fit residues: 75.1630 Evaluate side-chains 208 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 CYS Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 558 GLN Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 381 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 137 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 117 optimal weight: 0.0980 chunk 94 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.084778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.071486 restraints weight = 162941.300| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 6.52 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11286 Z= 0.183 Angle : 0.618 5.624 15316 Z= 0.332 Chirality : 0.041 0.150 1784 Planarity : 0.005 0.055 1930 Dihedral : 5.537 27.163 1493 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.42 % Allowed : 12.09 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.22), residues: 1355 helix: 0.84 (0.23), residues: 475 sheet: -0.12 (0.26), residues: 341 loop : 0.24 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 586 TYR 0.013 0.002 TYR B 589 PHE 0.018 0.002 PHE B 435 TRP 0.009 0.001 TRP C 268 HIS 0.006 0.001 HIS A 607 Details of bonding type rmsd covalent geometry : bond 0.00376 (11286) covalent geometry : angle 0.61760 (15316) hydrogen bonds : bond 0.04988 ( 563) hydrogen bonds : angle 6.45546 ( 1599) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 187 time to evaluate : 0.587 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: 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: 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: 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 166 ASP cc_start: 0.7619 (m-30) cc_final: 0.7218 (m-30) REVERT: A 177 SER cc_start: 0.9086 (t) cc_final: 0.8460 (p) REVERT: A 313 MET cc_start: 0.8308 (mtp) cc_final: 0.8097 (ttm) REVERT: A 560 ASP cc_start: 0.9247 (p0) cc_final: 0.8981 (p0) REVERT: B 482 ILE cc_start: 0.9263 (mt) cc_final: 0.8771 (tp) REVERT: B 600 MET cc_start: 0.6958 (mtm) cc_final: 0.6698 (mtt) REVERT: B 812 PHE cc_start: 0.7023 (m-80) cc_final: 0.6795 (m-80) REVERT: B 878 GLU cc_start: 0.9136 (tt0) cc_final: 0.8702 (tt0) REVERT: B 900 MET cc_start: 0.7580 (ptm) cc_final: 0.6542 (mmt) REVERT: C 26 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.8898 (mmp80) REVERT: C 101 MET cc_start: 0.9435 (mmt) cc_final: 0.9119 (tpp) REVERT: C 223 TYR cc_start: 0.8189 (m-80) cc_final: 0.7864 (m-80) outliers start: 30 outliers final: 24 residues processed: 200 average time/residue: 0.2602 time to fit residues: 73.4787 Evaluate side-chains 202 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 CYS Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 558 GLN Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 414 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 40 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 115 optimal weight: 20.0000 chunk 36 optimal weight: 0.5980 chunk 89 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.083632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.070495 restraints weight = 165292.058| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 6.44 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11286 Z= 0.230 Angle : 0.631 4.688 15316 Z= 0.339 Chirality : 0.041 0.149 1784 Planarity : 0.005 0.043 1930 Dihedral : 5.406 20.658 1493 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.66 % Allowed : 12.57 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.22), residues: 1355 helix: 0.79 (0.23), residues: 469 sheet: -0.46 (0.25), residues: 356 loop : 0.03 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 586 TYR 0.013 0.002 TYR A 566 PHE 0.017 0.002 PHE B 435 TRP 0.009 0.001 TRP C 268 HIS 0.007 0.001 HIS A 607 Details of bonding type rmsd covalent geometry : bond 0.00467 (11286) covalent geometry : angle 0.63077 (15316) hydrogen bonds : bond 0.04888 ( 563) hydrogen bonds : angle 6.46584 ( 1599) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 182 time to evaluate : 0.605 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: 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: 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: 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 166 ASP cc_start: 0.7833 (m-30) cc_final: 0.7423 (m-30) REVERT: A 177 SER cc_start: 0.9231 (t) cc_final: 0.8835 (p) REVERT: A 229 LEU cc_start: 0.8443 (mm) cc_final: 0.8009 (mm) REVERT: A 313 MET cc_start: 0.8369 (mtp) cc_final: 0.8163 (ttm) REVERT: A 560 ASP cc_start: 0.9250 (p0) cc_final: 0.8975 (p0) REVERT: B 482 ILE cc_start: 0.9321 (mt) cc_final: 0.8851 (tp) REVERT: B 600 MET cc_start: 0.6966 (mtm) cc_final: 0.6708 (mtt) REVERT: B 812 PHE cc_start: 0.7057 (m-80) cc_final: 0.6833 (m-80) REVERT: B 900 MET cc_start: 0.7642 (ptm) cc_final: 0.6611 (mmt) REVERT: C 26 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.8828 (mmp80) REVERT: C 101 MET cc_start: 0.9453 (mmt) cc_final: 0.9152 (tpp) outliers start: 33 outliers final: 29 residues processed: 198 average time/residue: 0.2698 time to fit residues: 75.1132 Evaluate side-chains 203 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 CYS Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 556 ARG Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 630 ASP Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 558 GLN Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 207 TRP Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 341 HIS Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 414 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 36 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 7 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.083830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.070707 restraints weight = 166577.346| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 6.54 r_work: 0.3646 rms_B_bonded: 6.54 restraints_weight: 2.0000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11286 Z= 0.182 Angle : 0.605 4.895 15316 Z= 0.321 Chirality : 0.041 0.148 1784 Planarity : 0.004 0.044 1930 Dihedral : 5.286 19.924 1493 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.58 % Allowed : 13.94 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.22), residues: 1355 helix: 0.93 (0.23), residues: 469 sheet: -0.47 (0.26), residues: 345 loop : -0.08 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 401 TYR 0.017 0.002 TYR A 566 PHE 0.016 0.002 PHE C 103 TRP 0.009 0.001 TRP C 268 HIS 0.006 0.001 HIS A 607 Details of bonding type rmsd covalent geometry : bond 0.00376 (11286) covalent geometry : angle 0.60467 (15316) hydrogen bonds : bond 0.04575 ( 563) hydrogen bonds : angle 6.31733 ( 1599) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 178 time to evaluate : 0.620 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: 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: 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: 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 166 ASP cc_start: 0.8052 (m-30) cc_final: 0.7815 (m-30) REVERT: A 177 SER cc_start: 0.9327 (t) cc_final: 0.9027 (p) REVERT: A 560 ASP cc_start: 0.9328 (p0) cc_final: 0.9115 (p0) REVERT: B 600 MET cc_start: 0.7312 (mtm) cc_final: 0.7051 (mtt) REVERT: B 812 PHE cc_start: 0.7417 (m-80) cc_final: 0.7203 (m-80) REVERT: B 878 GLU cc_start: 0.9182 (tt0) cc_final: 0.8829 (tt0) REVERT: B 900 MET cc_start: 0.7481 (ptm) cc_final: 0.6434 (mmt) REVERT: C 101 MET cc_start: 0.9468 (mmt) cc_final: 0.9251 (tpp) REVERT: C 223 TYR cc_start: 0.8216 (m-80) cc_final: 0.7910 (m-80) outliers start: 32 outliers final: 29 residues processed: 195 average time/residue: 0.2587 time to fit residues: 71.4073 Evaluate side-chains 201 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 CYS Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 556 ARG Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 630 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 207 TRP Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 341 HIS Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 414 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 39 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.083605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.070461 restraints weight = 167624.855| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 6.57 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11286 Z= 0.193 Angle : 0.608 5.533 15316 Z= 0.320 Chirality : 0.041 0.144 1784 Planarity : 0.004 0.041 1930 Dihedral : 5.229 19.691 1493 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.06 % Allowed : 13.86 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.22), residues: 1355 helix: 0.99 (0.23), residues: 468 sheet: -0.51 (0.26), residues: 343 loop : -0.20 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 586 TYR 0.012 0.002 TYR A 566 PHE 0.014 0.002 PHE B 435 TRP 0.009 0.001 TRP C 268 HIS 0.007 0.001 HIS A 607 Details of bonding type rmsd covalent geometry : bond 0.00398 (11286) covalent geometry : angle 0.60845 (15316) hydrogen bonds : bond 0.04483 ( 563) hydrogen bonds : angle 6.31366 ( 1599) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 174 time to evaluate : 0.624 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: 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: 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: 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 63 TYR cc_start: 0.8146 (OUTLIER) cc_final: 0.7596 (m-80) REVERT: A 166 ASP cc_start: 0.7920 (m-30) cc_final: 0.7537 (m-30) REVERT: A 177 SER cc_start: 0.9333 (t) cc_final: 0.8985 (p) REVERT: A 560 ASP cc_start: 0.9194 (p0) cc_final: 0.8994 (p0) REVERT: B 600 MET cc_start: 0.7042 (mtm) cc_final: 0.6772 (mtt) REVERT: B 812 PHE cc_start: 0.7005 (m-80) cc_final: 0.6797 (m-80) REVERT: B 878 GLU cc_start: 0.9150 (tt0) cc_final: 0.8724 (tt0) REVERT: B 900 MET cc_start: 0.7849 (ptm) cc_final: 0.6793 (mmt) REVERT: C 101 MET cc_start: 0.9405 (mmt) cc_final: 0.8956 (mmm) REVERT: C 223 TYR cc_start: 0.8082 (m-80) cc_final: 0.7702 (m-80) outliers start: 38 outliers final: 32 residues processed: 193 average time/residue: 0.2592 time to fit residues: 71.7073 Evaluate side-chains 201 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 CYS Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 556 ARG Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 630 ASP Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 207 TRP Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 341 HIS Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 414 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 136 optimal weight: 7.9990 chunk 121 optimal weight: 0.9990 chunk 133 optimal weight: 0.0570 chunk 32 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 135 optimal weight: 6.9990 overall best weight: 0.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.085487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.072262 restraints weight = 162002.198| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 6.57 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.5150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11286 Z= 0.115 Angle : 0.587 5.815 15316 Z= 0.301 Chirality : 0.042 0.152 1784 Planarity : 0.004 0.057 1930 Dihedral : 5.043 19.568 1493 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.34 % Allowed : 15.15 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.23), residues: 1355 helix: 1.29 (0.24), residues: 469 sheet: -0.52 (0.27), residues: 341 loop : -0.10 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG C 234 TYR 0.011 0.001 TYR A 566 PHE 0.016 0.001 PHE B 413 TRP 0.010 0.001 TRP C 268 HIS 0.004 0.001 HIS A 607 Details of bonding type rmsd covalent geometry : bond 0.00251 (11286) covalent geometry : angle 0.58738 (15316) hydrogen bonds : bond 0.04053 ( 563) hydrogen bonds : angle 6.04168 ( 1599) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 0.647 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: 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: 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: 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 63 TYR cc_start: 0.8130 (OUTLIER) cc_final: 0.7558 (m-80) REVERT: A 166 ASP cc_start: 0.7797 (m-30) cc_final: 0.7426 (m-30) REVERT: A 177 SER cc_start: 0.9296 (t) cc_final: 0.8912 (p) REVERT: B 600 MET cc_start: 0.6958 (mtm) cc_final: 0.6705 (mtt) REVERT: B 641 ARG cc_start: 0.8871 (mtp180) cc_final: 0.8516 (mtp85) REVERT: B 878 GLU cc_start: 0.9140 (tt0) cc_final: 0.8762 (tt0) REVERT: B 900 MET cc_start: 0.7987 (ptm) cc_final: 0.6801 (mmt) REVERT: C 101 MET cc_start: 0.9343 (mmt) cc_final: 0.9045 (mmm) REVERT: C 223 TYR cc_start: 0.8007 (m-80) cc_final: 0.7657 (m-80) outliers start: 29 outliers final: 27 residues processed: 191 average time/residue: 0.2622 time to fit residues: 71.8371 Evaluate side-chains 196 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 556 ARG Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 630 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 207 TRP Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 341 HIS Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 414 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 45 optimal weight: 0.0170 chunk 27 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 116 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 overall best weight: 3.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.083592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.070551 restraints weight = 168839.178| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 6.50 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11286 Z= 0.202 Angle : 0.607 5.422 15316 Z= 0.320 Chirality : 0.041 0.141 1784 Planarity : 0.004 0.040 1930 Dihedral : 5.025 21.327 1493 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.66 % Allowed : 15.31 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.22), residues: 1355 helix: 1.24 (0.24), residues: 469 sheet: -0.56 (0.26), residues: 339 loop : -0.24 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 234 TYR 0.010 0.001 TYR A 566 PHE 0.037 0.002 PHE B 812 TRP 0.011 0.001 TRP C 268 HIS 0.006 0.001 HIS A 607 Details of bonding type rmsd covalent geometry : bond 0.00416 (11286) covalent geometry : angle 0.60740 (15316) hydrogen bonds : bond 0.04285 ( 563) hydrogen bonds : angle 6.17301 ( 1599) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 0.606 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 TYR cc_start: 0.8212 (OUTLIER) cc_final: 0.7595 (m-80) REVERT: A 166 ASP cc_start: 0.8001 (m-30) cc_final: 0.7359 (m-30) REVERT: A 177 SER cc_start: 0.9373 (t) cc_final: 0.9030 (p) REVERT: B 600 MET cc_start: 0.7027 (mtm) cc_final: 0.6754 (mtt) REVERT: B 812 PHE cc_start: 0.7493 (m-80) cc_final: 0.7135 (m-80) REVERT: B 878 GLU cc_start: 0.9160 (tt0) cc_final: 0.8774 (tt0) REVERT: B 900 MET cc_start: 0.7928 (ptm) cc_final: 0.6798 (mmt) REVERT: C 101 MET cc_start: 0.9374 (mmt) cc_final: 0.9107 (mmm) outliers start: 33 outliers final: 30 residues processed: 186 average time/residue: 0.2513 time to fit residues: 67.1701 Evaluate side-chains 194 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 CYS Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 556 ARG Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 630 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 207 TRP Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 341 HIS Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 414 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 65 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.084303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.071264 restraints weight = 168212.755| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 6.49 r_work: 0.3655 rms_B_bonded: 6.45 restraints_weight: 2.0000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.5445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11286 Z= 0.148 Angle : 0.586 6.005 15316 Z= 0.304 Chirality : 0.041 0.161 1784 Planarity : 0.004 0.043 1930 Dihedral : 4.975 21.129 1493 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.66 % Allowed : 15.47 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.23), residues: 1355 helix: 1.28 (0.24), residues: 469 sheet: -0.56 (0.26), residues: 347 loop : -0.17 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 234 TYR 0.011 0.001 TYR A 566 PHE 0.027 0.001 PHE B 812 TRP 0.013 0.001 TRP C 268 HIS 0.008 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00312 (11286) covalent geometry : angle 0.58608 (15316) hydrogen bonds : bond 0.04067 ( 563) hydrogen bonds : angle 6.06298 ( 1599) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 0.643 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: 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: 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: 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 63 TYR cc_start: 0.8225 (OUTLIER) cc_final: 0.7573 (m-80) REVERT: A 166 ASP cc_start: 0.7885 (m-30) cc_final: 0.7650 (m-30) REVERT: A 177 SER cc_start: 0.9438 (t) cc_final: 0.9211 (p) REVERT: B 475 TRP cc_start: 0.8534 (t60) cc_final: 0.8279 (t60) REVERT: B 600 MET cc_start: 0.7305 (mtm) cc_final: 0.7052 (mtt) REVERT: B 812 PHE cc_start: 0.7786 (m-80) cc_final: 0.7412 (m-80) REVERT: B 878 GLU cc_start: 0.9222 (tt0) cc_final: 0.8923 (tt0) REVERT: B 900 MET cc_start: 0.7686 (ptm) cc_final: 0.6582 (mmt) REVERT: C 101 MET cc_start: 0.9423 (mmt) cc_final: 0.9138 (mmm) outliers start: 33 outliers final: 30 residues processed: 188 average time/residue: 0.2480 time to fit residues: 67.5161 Evaluate side-chains 195 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 CYS Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 556 ARG Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 630 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 916 GLU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 207 TRP Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 341 HIS Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 414 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 23 optimal weight: 5.9990 chunk 133 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.084696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.071671 restraints weight = 167466.651| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 6.49 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11286 Z= 0.138 Angle : 0.573 6.199 15316 Z= 0.296 Chirality : 0.041 0.144 1784 Planarity : 0.004 0.041 1930 Dihedral : 4.876 20.994 1493 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.26 % Allowed : 16.04 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.23), residues: 1355 helix: 1.39 (0.24), residues: 469 sheet: -0.61 (0.26), residues: 341 loop : -0.20 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 234 TYR 0.010 0.001 TYR A 566 PHE 0.028 0.001 PHE B 413 TRP 0.012 0.001 TRP C 268 HIS 0.007 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00292 (11286) covalent geometry : angle 0.57274 (15316) hydrogen bonds : bond 0.03901 ( 563) hydrogen bonds : angle 5.96894 ( 1599) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4794.31 seconds wall clock time: 82 minutes 12.53 seconds (4932.53 seconds total)