Starting phenix.real_space_refine on Mon Mar 11 17:24:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8e_41097/03_2024/8t8e_41097.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8e_41097/03_2024/8t8e_41097.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8e_41097/03_2024/8t8e_41097.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8e_41097/03_2024/8t8e_41097.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8e_41097/03_2024/8t8e_41097.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8e_41097/03_2024/8t8e_41097.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.062 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: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 5634 2.51 5 N 1463 2.21 5 O 1613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 1023": "OE1" <-> "OE2" Residue "C GLU 26": "OE1" <-> "OE2" Residue "C GLU 33": "OE1" <-> "OE2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "C GLU 286": "OE1" <-> "OE2" Residue "C GLU 474": "OE1" <-> "OE2" Residue "B GLU 210": "OE1" <-> "OE2" Residue "B GLU 268": "OE1" <-> "OE2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "B GLU 340": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8755 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2703 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 341} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 3966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3966 Classifications: {'peptide': 488} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 467} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2086 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 243} Chain breaks: 4 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 5.21, per 1000 atoms: 0.60 Number of scatterers: 8755 At special positions: 0 Unit cell: (92.568, 81.928, 148.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 1613 8.00 N 1463 7.00 C 5634 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.22 Conformation dependent library (CDL) restraints added in 1.8 seconds 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2086 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 3 sheets defined 50.1% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 114 through 125 removed outlier: 3.780A pdb=" N LEU A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 removed outlier: 3.922A pdb=" N PHE A 169 " --> pdb=" O GLN A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 211 removed outlier: 3.582A pdb=" N ILE A 204 " --> pdb=" O LYS A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 231 removed outlier: 3.725A pdb=" N PHE A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 247 removed outlier: 3.618A pdb=" N LYS A 239 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N SER A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 258 through 263 Processing helix chain 'A' and resid 951 through 959 Processing helix chain 'A' and resid 960 through 966 removed outlier: 3.527A pdb=" N TYR A 964 " --> pdb=" O ARG A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 981 removed outlier: 3.639A pdb=" N ASP A 978 " --> pdb=" O ASP A 974 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE A 979 " --> pdb=" O ALA A 975 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG A 980 " --> pdb=" O ASP A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1037 removed outlier: 3.622A pdb=" N LYS A1024 " --> pdb=" O SER A1020 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TRP A1036 " --> pdb=" O LEU A1032 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS A1037 " --> pdb=" O LEU A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1071 removed outlier: 3.975A pdb=" N ILE A1060 " --> pdb=" O VAL A1056 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASP A1071 " --> pdb=" O LYS A1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 41 removed outlier: 3.505A pdb=" N LEU C 30 " --> pdb=" O GLU C 26 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ALA C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN C 36 " --> pdb=" O PHE C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 53 removed outlier: 3.605A pdb=" N VAL C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU C 51 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 76 Processing helix chain 'C' and resid 84 through 91 removed outlier: 4.456A pdb=" N ASP C 91 " --> pdb=" O LEU C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 109 removed outlier: 3.531A pdb=" N ARG C 103 " --> pdb=" O THR C 99 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 105 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS C 106 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 116 removed outlier: 3.682A pdb=" N LEU C 115 " --> pdb=" O TYR C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 140 removed outlier: 3.566A pdb=" N ARG C 132 " --> pdb=" O LEU C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 209 removed outlier: 3.765A pdb=" N ASN C 209 " --> pdb=" O ASN C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 224 Processing helix chain 'C' and resid 229 through 234 Processing helix chain 'C' and resid 235 through 237 No H-bonds generated for 'chain 'C' and resid 235 through 237' Processing helix chain 'C' and resid 240 through 259 removed outlier: 3.618A pdb=" N ILE C 246 " --> pdb=" O PRO C 242 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N CYS C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN C 255 " --> pdb=" O PHE C 251 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP C 256 " --> pdb=" O SER C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 273 Processing helix chain 'C' and resid 274 through 276 No H-bonds generated for 'chain 'C' and resid 274 through 276' Processing helix chain 'C' and resid 279 through 287 removed outlier: 3.632A pdb=" N PHE C 285 " --> pdb=" O LEU C 281 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C 287 " --> pdb=" O VAL C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 301 removed outlier: 3.665A pdb=" N VAL C 301 " --> pdb=" O PHE C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 347 removed outlier: 3.529A pdb=" N LYS C 346 " --> pdb=" O TYR C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 356 removed outlier: 3.587A pdb=" N ARG C 351 " --> pdb=" O SER C 347 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS C 353 " --> pdb=" O ALA C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 392 removed outlier: 3.592A pdb=" N PHE C 392 " --> pdb=" O LEU C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 403 Processing helix chain 'C' and resid 413 through 430 removed outlier: 5.145A pdb=" N GLU C 419 " --> pdb=" O PRO C 415 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU C 424 " --> pdb=" O GLY C 420 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS C 427 " --> pdb=" O SER C 423 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASP C 428 " --> pdb=" O GLU C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 442 Processing helix chain 'C' and resid 444 through 458 Processing helix chain 'C' and resid 471 through 497 removed outlier: 3.925A pdb=" N LEU C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP C 483 " --> pdb=" O ILE C 479 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL C 484 " --> pdb=" O GLU C 480 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N CYS C 485 " --> pdb=" O LYS C 481 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU C 486 " --> pdb=" O CYS C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 528 Processing helix chain 'C' and resid 538 through 547 removed outlier: 4.033A pdb=" N VAL C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN C 544 " --> pdb=" O PRO C 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 220 Processing helix chain 'B' and resid 245 through 254 Processing helix chain 'B' and resid 270 through 274 removed outlier: 3.842A pdb=" N ARG B 274 " --> pdb=" O GLU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 292 removed outlier: 3.508A pdb=" N LYS B 289 " --> pdb=" O ASN B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 300 through 316 Processing helix chain 'B' and resid 317 through 322 Processing helix chain 'B' and resid 329 through 337 removed outlier: 3.795A pdb=" N LEU B 337 " --> pdb=" O LYS B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 346 removed outlier: 3.524A pdb=" N SER B 346 " --> pdb=" O HIS B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 363 removed outlier: 3.783A pdb=" N TYR B 360 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG B 361 " --> pdb=" O PHE B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 365 No H-bonds generated for 'chain 'B' and resid 364 through 365' Processing helix chain 'B' and resid 366 through 368 No H-bonds generated for 'chain 'B' and resid 366 through 368' Processing helix chain 'B' and resid 369 through 378 removed outlier: 3.905A pdb=" N LEU B 374 " --> pdb=" O GLN B 370 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG B 375 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 398 removed outlier: 3.741A pdb=" N ILE B 393 " --> pdb=" O GLN B 389 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU B 398 " --> pdb=" O LYS B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 416 removed outlier: 3.560A pdb=" N MET B 415 " --> pdb=" O PHE B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 440 removed outlier: 4.070A pdb=" N ILE B 440 " --> pdb=" O CYS B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 460 Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 99 removed outlier: 6.737A pdb=" N HIS A 155 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N VAL A 85 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ILE A 153 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LEU A 87 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LYS A 151 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 154 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 989 through 995 Processing sheet with id=AA3, first strand: chain 'A' and resid 1043 through 1044 295 hydrogen bonds defined for protein. 858 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.12 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1759 1.33 - 1.45: 2062 1.45 - 1.57: 5036 1.57 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 8923 Sorted by residual: bond pdb=" C HIS B 240 " pdb=" O HIS B 240 " ideal model delta sigma weight residual 1.235 1.208 0.028 1.13e-02 7.83e+03 6.02e+00 bond pdb=" CA LEU C 538 " pdb=" C LEU C 538 " ideal model delta sigma weight residual 1.523 1.504 0.020 8.40e-03 1.42e+04 5.39e+00 bond pdb=" N HIS B 240 " pdb=" CA HIS B 240 " ideal model delta sigma weight residual 1.460 1.434 0.026 1.17e-02 7.31e+03 4.79e+00 bond pdb=" C PHE A 211 " pdb=" O PHE A 211 " ideal model delta sigma weight residual 1.235 1.217 0.018 1.26e-02 6.30e+03 2.10e+00 bond pdb=" CA TYR C 539 " pdb=" C TYR C 539 " ideal model delta sigma weight residual 1.524 1.542 -0.018 1.26e-02 6.30e+03 2.09e+00 ... (remaining 8918 not shown) Histogram of bond angle deviations from ideal: 99.54 - 106.44: 167 106.44 - 113.33: 4816 113.33 - 120.23: 3372 120.23 - 127.13: 3612 127.13 - 134.03: 58 Bond angle restraints: 12025 Sorted by residual: angle pdb=" N TYR C 539 " pdb=" CA TYR C 539 " pdb=" C TYR C 539 " ideal model delta sigma weight residual 109.81 122.71 -12.90 2.21e+00 2.05e-01 3.41e+01 angle pdb=" N ILE C 68 " pdb=" CA ILE C 68 " pdb=" C ILE C 68 " ideal model delta sigma weight residual 112.29 106.90 5.39 9.40e-01 1.13e+00 3.29e+01 angle pdb=" N ILE B 437 " pdb=" CA ILE B 437 " pdb=" C ILE B 437 " ideal model delta sigma weight residual 111.91 107.25 4.66 8.90e-01 1.26e+00 2.74e+01 angle pdb=" N ILE B 450 " pdb=" CA ILE B 450 " pdb=" C ILE B 450 " ideal model delta sigma weight residual 113.71 108.78 4.93 9.50e-01 1.11e+00 2.69e+01 angle pdb=" N GLU A 968 " pdb=" CA GLU A 968 " pdb=" C GLU A 968 " ideal model delta sigma weight residual 112.94 107.11 5.83 1.41e+00 5.03e-01 1.71e+01 ... (remaining 12020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 4585 17.05 - 34.10: 607 34.10 - 51.15: 180 51.15 - 68.20: 20 68.20 - 85.26: 11 Dihedral angle restraints: 5403 sinusoidal: 2202 harmonic: 3201 Sorted by residual: dihedral pdb=" CA LYS C 308 " pdb=" C LYS C 308 " pdb=" N LEU C 309 " pdb=" CA LEU C 309 " ideal model delta harmonic sigma weight residual 180.00 -154.19 -25.81 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA TRP B 200 " pdb=" C TRP B 200 " pdb=" N HIS B 201 " pdb=" CA HIS B 201 " ideal model delta harmonic sigma weight residual 180.00 158.44 21.56 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA TYR B 347 " pdb=" C TYR B 347 " pdb=" N PHE B 348 " pdb=" CA PHE B 348 " ideal model delta harmonic sigma weight residual 180.00 158.75 21.25 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 5400 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1271 0.085 - 0.169: 83 0.169 - 0.253: 2 0.253 - 0.338: 0 0.338 - 0.422: 1 Chirality restraints: 1357 Sorted by residual: chirality pdb=" CA TYR C 539 " pdb=" N TYR C 539 " pdb=" C TYR C 539 " pdb=" CB TYR C 539 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" CA SER A 212 " pdb=" N SER A 212 " pdb=" C SER A 212 " pdb=" CB SER A 212 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA LYS A 987 " pdb=" N LYS A 987 " pdb=" C LYS A 987 " pdb=" CB LYS A 987 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.95e-01 ... (remaining 1354 not shown) Planarity restraints: 1525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 210 " -0.015 2.00e-02 2.50e+03 3.13e-02 9.77e+00 pdb=" C TYR A 210 " 0.054 2.00e-02 2.50e+03 pdb=" O TYR A 210 " -0.020 2.00e-02 2.50e+03 pdb=" N PHE A 211 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 77 " -0.036 5.00e-02 4.00e+02 5.59e-02 4.99e+00 pdb=" N PRO A 78 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 78 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 78 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 444 " 0.011 2.00e-02 2.50e+03 2.10e-02 4.39e+00 pdb=" C THR B 444 " -0.036 2.00e-02 2.50e+03 pdb=" O THR B 444 " 0.014 2.00e-02 2.50e+03 pdb=" N THR B 445 " 0.012 2.00e-02 2.50e+03 ... (remaining 1522 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 775 2.74 - 3.28: 8893 3.28 - 3.82: 13661 3.82 - 4.36: 16897 4.36 - 4.90: 28621 Nonbonded interactions: 68847 Sorted by model distance: nonbonded pdb=" OE1 GLN C 255 " pdb=" OG SER C 279 " model vdw 2.199 2.440 nonbonded pdb=" O ALA A 259 " pdb=" ND1 HIS A 263 " model vdw 2.214 2.520 nonbonded pdb=" OH TYR C 81 " pdb=" O GLU C 325 " model vdw 2.215 2.440 nonbonded pdb=" NZ LYS C 400 " pdb=" OG1 THR B 220 " model vdw 2.220 2.520 nonbonded pdb=" O GLU C 23 " pdb=" OH TYR C 126 " model vdw 2.247 2.440 ... (remaining 68842 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.410 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.570 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 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 : 0.003 0.029 8923 Z= 0.199 Angle : 0.694 12.904 12025 Z= 0.398 Chirality : 0.045 0.422 1357 Planarity : 0.004 0.056 1525 Dihedral : 16.794 85.255 3317 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.95 % Favored : 90.86 % Rotamer: Outliers : 1.03 % Allowed : 26.77 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.24), residues: 1061 helix: -2.29 (0.20), residues: 539 sheet: -2.02 (0.64), residues: 75 loop : -2.67 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 200 HIS 0.013 0.001 HIS C 513 PHE 0.014 0.001 PHE A1049 TYR 0.026 0.002 TYR B 295 ARG 0.003 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 PHE cc_start: 0.7718 (OUTLIER) cc_final: 0.7503 (m-80) REVERT: C 545 MET cc_start: 0.8568 (ttm) cc_final: 0.8328 (mtp) outliers start: 10 outliers final: 2 residues processed: 120 average time/residue: 0.1963 time to fit residues: 33.8237 Evaluate side-chains 112 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain C residue 273 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.1980 chunk 80 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8923 Z= 0.206 Angle : 0.581 7.326 12025 Z= 0.301 Chirality : 0.042 0.148 1357 Planarity : 0.003 0.045 1525 Dihedral : 5.233 25.873 1167 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 3.49 % Allowed : 26.15 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.24), residues: 1061 helix: -1.80 (0.21), residues: 533 sheet: -2.19 (0.60), residues: 75 loop : -2.45 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 220 HIS 0.005 0.001 HIS C 513 PHE 0.016 0.001 PHE A 973 TYR 0.012 0.002 TYR C 539 ARG 0.002 0.000 ARG A 952 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 117 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 537 LEU cc_start: 0.8319 (mm) cc_final: 0.7832 (tp) REVERT: C 538 LEU cc_start: 0.8051 (tt) cc_final: 0.7798 (tt) REVERT: B 210 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7621 (mm-30) REVERT: B 328 HIS cc_start: 0.7094 (OUTLIER) cc_final: 0.6771 (m-70) REVERT: B 361 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7930 (ttp-110) REVERT: B 405 TYR cc_start: 0.8712 (m-10) cc_final: 0.8479 (m-80) outliers start: 34 outliers final: 20 residues processed: 148 average time/residue: 0.1865 time to fit residues: 40.2348 Evaluate side-chains 132 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 110 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 307 TYR Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain B residue 200 TRP Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 328 HIS Chi-restraints excluded: chain B residue 361 ARG Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 456 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 GLN C 466 GLN C 544 GLN B 390 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8923 Z= 0.287 Angle : 0.610 6.913 12025 Z= 0.312 Chirality : 0.043 0.152 1357 Planarity : 0.004 0.041 1525 Dihedral : 5.270 25.162 1163 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 5.54 % Allowed : 25.95 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.24), residues: 1061 helix: -1.60 (0.21), residues: 539 sheet: -2.23 (0.60), residues: 75 loop : -2.51 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 525 HIS 0.006 0.001 HIS B 201 PHE 0.017 0.002 PHE A 973 TYR 0.015 0.002 TYR A 81 ARG 0.002 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 116 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 LEU cc_start: 0.2583 (OUTLIER) cc_final: 0.2237 (mp) REVERT: C 370 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7238 (ppt-90) REVERT: C 537 LEU cc_start: 0.8288 (mm) cc_final: 0.7791 (tp) REVERT: B 210 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7476 (mm-30) REVERT: B 238 PHE cc_start: 0.7624 (OUTLIER) cc_final: 0.7331 (t80) REVERT: B 328 HIS cc_start: 0.7114 (OUTLIER) cc_final: 0.6706 (m-70) REVERT: B 361 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.7900 (ttp-110) outliers start: 54 outliers final: 30 residues processed: 161 average time/residue: 0.1994 time to fit residues: 46.3116 Evaluate side-chains 139 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 104 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1057 ASN Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 307 TYR Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 370 ARG Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain B residue 200 TRP Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 328 HIS Chi-restraints excluded: chain B residue 361 ARG Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 456 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 102 optimal weight: 0.0070 chunk 91 optimal weight: 0.0570 chunk 27 optimal weight: 3.9990 chunk 85 optimal weight: 0.0770 overall best weight: 0.3474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 954 HIS C 183 ASN C 518 ASN B 322 ASN B 390 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8923 Z= 0.144 Angle : 0.530 7.373 12025 Z= 0.273 Chirality : 0.040 0.150 1357 Planarity : 0.003 0.036 1525 Dihedral : 4.839 25.495 1163 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 4.72 % Allowed : 26.67 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.25), residues: 1061 helix: -1.17 (0.22), residues: 540 sheet: -2.16 (0.59), residues: 75 loop : -2.49 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 200 HIS 0.002 0.000 HIS C 513 PHE 0.010 0.001 PHE A1049 TYR 0.013 0.001 TYR B 405 ARG 0.002 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 119 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 224 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.7825 (m-80) REVERT: B 316 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7786 (pt) REVERT: B 328 HIS cc_start: 0.6898 (OUTLIER) cc_final: 0.6638 (m-70) outliers start: 46 outliers final: 27 residues processed: 158 average time/residue: 0.1777 time to fit residues: 40.6522 Evaluate side-chains 138 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 108 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 307 TYR Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain B residue 200 TRP Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 328 HIS Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 70 optimal weight: 0.0270 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 91 optimal weight: 0.0870 chunk 25 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 390 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8923 Z= 0.396 Angle : 0.662 8.070 12025 Z= 0.334 Chirality : 0.045 0.156 1357 Planarity : 0.004 0.040 1525 Dihedral : 5.329 24.692 1163 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.27 % Favored : 89.73 % Rotamer: Outliers : 5.74 % Allowed : 26.46 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.25), residues: 1061 helix: -1.35 (0.21), residues: 544 sheet: -2.28 (0.57), residues: 75 loop : -2.48 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 200 HIS 0.008 0.001 HIS B 201 PHE 0.023 0.002 PHE C 258 TYR 0.016 0.002 TYR A 258 ARG 0.002 0.000 ARG A 952 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 112 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 CYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7898 (m) REVERT: A 256 LEU cc_start: 0.2708 (OUTLIER) cc_final: 0.2458 (mp) REVERT: C 370 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.7171 (ppt-90) REVERT: C 537 LEU cc_start: 0.8289 (mm) cc_final: 0.7680 (tp) REVERT: B 316 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.7911 (pp) REVERT: B 328 HIS cc_start: 0.6988 (OUTLIER) cc_final: 0.6545 (m-70) outliers start: 56 outliers final: 42 residues processed: 161 average time/residue: 0.1855 time to fit residues: 42.9557 Evaluate side-chains 153 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 106 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1057 ASN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 307 TYR Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 370 ARG Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 482 CYS Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain B residue 200 TRP Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 267 TYR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 328 HIS Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 456 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.5980 chunk 20 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 85 optimal weight: 0.1980 chunk 47 optimal weight: 0.6980 chunk 8 optimal weight: 10.0000 chunk 33 optimal weight: 0.0570 chunk 53 optimal weight: 0.8980 chunk 98 optimal weight: 0.0570 overall best weight: 0.3216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 390 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8923 Z= 0.145 Angle : 0.536 7.382 12025 Z= 0.276 Chirality : 0.040 0.149 1357 Planarity : 0.003 0.035 1525 Dihedral : 4.823 25.440 1163 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 5.13 % Allowed : 27.38 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.25), residues: 1061 helix: -1.03 (0.22), residues: 551 sheet: -2.15 (0.58), residues: 75 loop : -2.50 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 200 HIS 0.011 0.001 HIS C 513 PHE 0.021 0.001 PHE C 258 TYR 0.012 0.001 TYR C 412 ARG 0.001 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 118 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 CYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7989 (m) REVERT: C 479 ILE cc_start: 0.8723 (tp) cc_final: 0.8349 (tp) REVERT: B 224 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.7541 (m-80) REVERT: B 316 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7809 (pt) REVERT: B 328 HIS cc_start: 0.6940 (OUTLIER) cc_final: 0.6616 (m-70) outliers start: 50 outliers final: 33 residues processed: 153 average time/residue: 0.2000 time to fit residues: 42.9831 Evaluate side-chains 143 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 106 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 307 TYR Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain B residue 200 TRP Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 267 TYR Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 328 HIS Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 102 optimal weight: 0.2980 chunk 63 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8923 Z= 0.204 Angle : 0.570 13.360 12025 Z= 0.288 Chirality : 0.041 0.146 1357 Planarity : 0.003 0.036 1525 Dihedral : 4.831 24.535 1163 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 4.62 % Allowed : 28.31 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.25), residues: 1061 helix: -0.92 (0.22), residues: 543 sheet: -2.15 (0.58), residues: 75 loop : -2.45 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 200 HIS 0.004 0.001 HIS B 201 PHE 0.017 0.001 PHE C 258 TYR 0.019 0.001 TYR A 81 ARG 0.004 0.000 ARG B 230 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 113 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 479 ILE cc_start: 0.8743 (tp) cc_final: 0.8351 (tp) REVERT: B 224 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7488 (m-80) REVERT: B 316 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7876 (pt) REVERT: B 328 HIS cc_start: 0.6974 (OUTLIER) cc_final: 0.6674 (m-70) outliers start: 45 outliers final: 35 residues processed: 148 average time/residue: 0.1914 time to fit residues: 40.8489 Evaluate side-chains 146 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 108 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 307 TYR Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain B residue 200 TRP Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 267 TYR Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 328 HIS Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8923 Z= 0.286 Angle : 0.621 13.165 12025 Z= 0.313 Chirality : 0.043 0.152 1357 Planarity : 0.003 0.039 1525 Dihedral : 5.057 24.095 1163 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 4.82 % Allowed : 28.10 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.25), residues: 1061 helix: -1.03 (0.22), residues: 553 sheet: -2.16 (0.58), residues: 75 loop : -2.55 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 200 HIS 0.016 0.001 HIS C 513 PHE 0.017 0.002 PHE A 973 TYR 0.018 0.002 TYR A 81 ARG 0.002 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 109 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 CYS cc_start: 0.8268 (OUTLIER) cc_final: 0.8035 (m) REVERT: B 224 PHE cc_start: 0.7995 (OUTLIER) cc_final: 0.7460 (m-80) REVERT: B 230 ARG cc_start: 0.4476 (ttt-90) cc_final: 0.3923 (ttp80) REVERT: B 316 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7837 (pp) REVERT: B 328 HIS cc_start: 0.6921 (OUTLIER) cc_final: 0.6563 (m-70) outliers start: 47 outliers final: 37 residues processed: 148 average time/residue: 0.1792 time to fit residues: 38.6024 Evaluate side-chains 148 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 107 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 307 TYR Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain B residue 200 TRP Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 328 HIS Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 0.1980 chunk 74 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8923 Z= 0.229 Angle : 0.595 12.408 12025 Z= 0.300 Chirality : 0.042 0.148 1357 Planarity : 0.003 0.039 1525 Dihedral : 4.962 24.368 1163 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 4.31 % Allowed : 28.92 % Favored : 66.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.25), residues: 1061 helix: -0.96 (0.22), residues: 553 sheet: -2.12 (0.58), residues: 75 loop : -2.56 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 200 HIS 0.004 0.001 HIS B 201 PHE 0.016 0.002 PHE C 258 TYR 0.020 0.002 TYR A 81 ARG 0.001 0.000 ARG A 952 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 108 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 508 GLN cc_start: 0.7079 (mt0) cc_final: 0.6423 (pt0) REVERT: B 224 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.7462 (m-80) REVERT: B 230 ARG cc_start: 0.4522 (ttt-90) cc_final: 0.3959 (ttp80) REVERT: B 316 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8073 (pp) REVERT: B 328 HIS cc_start: 0.6905 (OUTLIER) cc_final: 0.6537 (m-70) outliers start: 42 outliers final: 36 residues processed: 142 average time/residue: 0.1859 time to fit residues: 38.2353 Evaluate side-chains 144 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 105 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 307 TYR Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain B residue 200 TRP Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 328 HIS Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 1.9990 chunk 47 optimal weight: 0.1980 chunk 69 optimal weight: 0.6980 chunk 105 optimal weight: 0.0050 chunk 97 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 chunk 8 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8923 Z= 0.160 Angle : 0.561 11.743 12025 Z= 0.283 Chirality : 0.041 0.150 1357 Planarity : 0.003 0.038 1525 Dihedral : 4.735 24.319 1163 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 4.10 % Allowed : 29.23 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.25), residues: 1061 helix: -0.84 (0.22), residues: 559 sheet: -2.07 (0.59), residues: 75 loop : -2.56 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 200 HIS 0.003 0.001 HIS A 93 PHE 0.016 0.001 PHE C 258 TYR 0.020 0.001 TYR A 81 ARG 0.003 0.000 ARG A 177 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 114 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 508 GLN cc_start: 0.6899 (mt0) cc_final: 0.6348 (pt0) REVERT: B 224 PHE cc_start: 0.7817 (OUTLIER) cc_final: 0.7611 (m-80) REVERT: B 230 ARG cc_start: 0.4502 (ttt-90) cc_final: 0.3947 (ttp80) REVERT: B 316 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7819 (pt) REVERT: B 328 HIS cc_start: 0.7062 (OUTLIER) cc_final: 0.6776 (m-70) outliers start: 40 outliers final: 33 residues processed: 145 average time/residue: 0.1898 time to fit residues: 39.8612 Evaluate side-chains 146 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 110 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 307 TYR Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain B residue 200 TRP Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 328 HIS Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.171865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.129446 restraints weight = 10929.045| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.50 r_work: 0.3347 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8923 Z= 0.300 Angle : 0.635 12.394 12025 Z= 0.319 Chirality : 0.044 0.152 1357 Planarity : 0.003 0.039 1525 Dihedral : 5.043 23.766 1163 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 4.31 % Allowed : 29.03 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.25), residues: 1061 helix: -1.00 (0.22), residues: 556 sheet: -2.16 (0.58), residues: 75 loop : -2.60 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 220 HIS 0.007 0.001 HIS B 201 PHE 0.018 0.002 PHE A 973 TYR 0.019 0.002 TYR B 295 ARG 0.002 0.000 ARG B 274 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2010.69 seconds wall clock time: 37 minutes 18.02 seconds (2238.02 seconds total)