Starting phenix.real_space_refine on Mon Mar 18 21:53:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3d_13789/03_2024/7q3d_13789.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3d_13789/03_2024/7q3d_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3d_13789/03_2024/7q3d_13789.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3d_13789/03_2024/7q3d_13789.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3d_13789/03_2024/7q3d_13789.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3d_13789/03_2024/7q3d_13789.pdb" } resolution = 3.35 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= -0.003 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 Residue "A ASP 166": "OD1" <-> "OD2" Residue "B TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: 10.00, per 1000 atoms: 0.45 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 - 3.50 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: 18.14 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.75 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: 8.72 Time building geometry restraints manager: 18.88 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: 95.13 - 102.90: 204 102.90 - 110.67: 23695 110.67 - 118.43: 6493 118.43 - 126.20: 10263 126.20 - 133.97: 221 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 ========== 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: 2.890 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: 0.310 Extract box with map and model: 12.130 Check model and map are aligned: 0.310 Set scattering table: 0.210 Process input model: 71.150 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 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:2.900 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.360 ------------------------------------------------------------------------------- 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= 0.848 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (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 TRP 0.073 0.014 TRP B 562 HIS 0.011 0.003 HIS B 879 PHE 0.066 0.011 PHE B 435 TYR 0.110 0.015 TYR A 566 ARG 0.013 0.001 ARG A 281 *********************** 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 fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 1.965 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: 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: 0.8258 (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: 0.6173 time to fit residues: 247.0768 Evaluate side-chains 205 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 412 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 11286 Z= 0.288 Angle : 0.685 6.698 15316 Z= 0.378 Chirality : 0.042 0.161 1784 Planarity : 0.005 0.043 1930 Dihedral : 6.176 41.631 1493 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.58 % Allowed : 8.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.22), residues: 1355 helix: 0.59 (0.22), residues: 474 sheet: 0.61 (0.26), residues: 347 loop : 0.83 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 284 HIS 0.009 0.002 HIS A 607 PHE 0.026 0.002 PHE B 413 TYR 0.017 0.002 TYR B 589 ARG 0.005 0.001 ARG A 115 *********************** 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 243 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 211 time to evaluate : 1.753 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: A 177 SER cc_start: 0.8784 (t) cc_final: 0.8358 (p) REVERT: A 511 MET cc_start: 0.7824 (mmt) cc_final: 0.7516 (mmm) REVERT: A 559 LEU cc_start: 0.9315 (tp) cc_final: 0.9102 (tp) REVERT: B 599 TYR cc_start: 0.7858 (m-80) cc_final: 0.7062 (m-80) REVERT: B 812 PHE cc_start: 0.7471 (m-80) cc_final: 0.7198 (m-80) REVERT: B 900 MET cc_start: 0.8039 (ptm) cc_final: 0.6732 (mmt) REVERT: C 26 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8712 (mmp80) REVERT: C 101 MET cc_start: 0.9307 (mmt) cc_final: 0.9017 (tpp) REVERT: C 108 LEU cc_start: 0.9314 (mt) cc_final: 0.9085 (tt) REVERT: C 223 TYR cc_start: 0.8193 (m-80) cc_final: 0.7656 (m-80) outliers start: 32 outliers final: 26 residues processed: 223 average time/residue: 0.5724 time to fit residues: 178.6290 Evaluate side-chains 209 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 182 time to evaluate : 1.868 ------------------------------------------------------------------------------- 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 316 SER 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 493 LEU 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 13 LEU Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 51 MET 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 257 SER Chi-restraints excluded: chain C residue 371 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 104 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 135 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 124 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 GLN A 414 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11286 Z= 0.284 Angle : 0.639 5.322 15316 Z= 0.350 Chirality : 0.041 0.147 1784 Planarity : 0.005 0.041 1930 Dihedral : 5.766 34.483 1493 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.82 % Allowed : 10.56 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.22), residues: 1355 helix: 0.77 (0.23), residues: 475 sheet: 0.24 (0.26), residues: 354 loop : 0.39 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 268 HIS 0.009 0.001 HIS B 330 PHE 0.021 0.002 PHE B 435 TYR 0.017 0.002 TYR A 566 ARG 0.003 0.000 ARG C 218 *********************** 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 223 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 188 time to evaluate : 1.526 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: A 181 GLN cc_start: 0.8628 (mt0) cc_final: 0.8416 (mp10) REVERT: B 812 PHE cc_start: 0.7387 (m-80) cc_final: 0.7076 (m-80) REVERT: B 900 MET cc_start: 0.8026 (ptm) cc_final: 0.6750 (mmt) REVERT: C 101 MET cc_start: 0.9304 (mmt) cc_final: 0.9007 (tpp) REVERT: C 108 LEU cc_start: 0.9319 (mt) cc_final: 0.9062 (tt) outliers start: 35 outliers final: 30 residues processed: 200 average time/residue: 0.5462 time to fit residues: 153.4995 Evaluate side-chains 204 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 174 time to evaluate : 1.675 ------------------------------------------------------------------------------- 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 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 309 ASP Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 316 SER 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 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 558 GLN Chi-restraints excluded: chain B residue 631 THR 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 119 ARG Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 371 THR 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 124 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 133 optimal weight: 0.9980 chunk 119 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11286 Z= 0.201 Angle : 0.584 5.470 15316 Z= 0.311 Chirality : 0.041 0.148 1784 Planarity : 0.004 0.056 1930 Dihedral : 5.410 27.846 1493 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.18 % Allowed : 12.81 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.22), residues: 1355 helix: 1.10 (0.23), residues: 469 sheet: 0.07 (0.26), residues: 351 loop : 0.30 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 268 HIS 0.006 0.001 HIS A 386 PHE 0.025 0.002 PHE A 428 TYR 0.016 0.001 TYR A 566 ARG 0.003 0.000 ARG A 273 *********************** 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 213 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 186 time to evaluate : 1.671 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 181 GLN cc_start: 0.8620 (mt0) cc_final: 0.8377 (mp10) REVERT: B 812 PHE cc_start: 0.7161 (m-80) cc_final: 0.6857 (m-80) REVERT: B 900 MET cc_start: 0.8105 (ptm) cc_final: 0.6760 (mmt) REVERT: C 101 MET cc_start: 0.9257 (mmt) cc_final: 0.8953 (tpp) REVERT: C 108 LEU cc_start: 0.9289 (mt) cc_final: 0.9054 (tt) outliers start: 27 outliers final: 25 residues processed: 197 average time/residue: 0.5288 time to fit residues: 147.5329 Evaluate side-chains 197 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 172 time to evaluate : 1.918 ------------------------------------------------------------------------------- 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 309 ASP Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 316 SER 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 388 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 405 GLU 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 119 ARG Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 240 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 75 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 11286 Z= 0.347 Angle : 0.654 5.153 15316 Z= 0.352 Chirality : 0.040 0.150 1784 Planarity : 0.005 0.043 1930 Dihedral : 5.400 21.927 1493 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.82 % Allowed : 13.54 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.22), residues: 1355 helix: 0.88 (0.23), residues: 468 sheet: -0.25 (0.26), residues: 354 loop : -0.08 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 241 HIS 0.008 0.002 HIS A 607 PHE 0.017 0.002 PHE B 435 TYR 0.015 0.002 TYR A 566 ARG 0.006 0.001 ARG C 218 *********************** 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 205 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 170 time to evaluate : 1.816 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 181 GLN cc_start: 0.8665 (mt0) cc_final: 0.8411 (mp10) REVERT: B 812 PHE cc_start: 0.7306 (m-80) cc_final: 0.6950 (m-80) REVERT: B 900 MET cc_start: 0.8137 (ptm) cc_final: 0.6962 (mmt) REVERT: C 101 MET cc_start: 0.9295 (mmt) cc_final: 0.9008 (tpp) REVERT: C 108 LEU cc_start: 0.9313 (mt) cc_final: 0.9053 (tt) outliers start: 35 outliers final: 30 residues processed: 187 average time/residue: 0.5326 time to fit residues: 141.6263 Evaluate side-chains 197 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 167 time to evaluate : 1.639 ------------------------------------------------------------------------------- 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 309 ASP Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 358 ASP 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 630 ASP 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 638 VAL Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain C residue 13 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11286 Z= 0.227 Angle : 0.588 5.875 15316 Z= 0.311 Chirality : 0.040 0.144 1784 Planarity : 0.004 0.045 1930 Dihedral : 5.219 20.658 1493 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.50 % Allowed : 14.75 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.22), residues: 1355 helix: 1.05 (0.23), residues: 469 sheet: -0.47 (0.26), residues: 354 loop : -0.06 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 241 HIS 0.006 0.001 HIS A 607 PHE 0.016 0.001 PHE B 435 TYR 0.015 0.001 TYR A 566 ARG 0.004 0.000 ARG A 273 *********************** 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 201 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 170 time to evaluate : 1.884 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 181 GLN cc_start: 0.8672 (mt0) cc_final: 0.8396 (mp10) REVERT: B 482 ILE cc_start: 0.9261 (mt) cc_final: 0.8745 (tp) REVERT: B 600 MET cc_start: 0.5942 (mtt) cc_final: 0.5691 (mtm) REVERT: B 812 PHE cc_start: 0.7241 (m-80) cc_final: 0.6932 (m-80) REVERT: B 900 MET cc_start: 0.8186 (ptm) cc_final: 0.6928 (mmt) REVERT: C 101 MET cc_start: 0.9253 (mmt) cc_final: 0.9027 (tpp) REVERT: C 108 LEU cc_start: 0.9297 (mt) cc_final: 0.9043 (tt) outliers start: 31 outliers final: 29 residues processed: 186 average time/residue: 0.4966 time to fit residues: 132.7286 Evaluate side-chains 195 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 166 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 CYS 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 309 ASP Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 316 SER 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 309 ILE 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 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 257 SER 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 15 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 75 optimal weight: 0.8980 chunk 112 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.4911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11286 Z= 0.188 Angle : 0.565 5.793 15316 Z= 0.295 Chirality : 0.040 0.145 1784 Planarity : 0.004 0.043 1930 Dihedral : 5.028 20.020 1493 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.26 % Allowed : 15.31 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.23), residues: 1355 helix: 1.31 (0.23), residues: 468 sheet: -0.42 (0.26), residues: 353 loop : -0.01 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 268 HIS 0.006 0.001 HIS A 607 PHE 0.015 0.001 PHE B 413 TYR 0.015 0.001 TYR A 566 ARG 0.003 0.000 ARG A 273 *********************** 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 205 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 177 time to evaluate : 1.949 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: A 181 GLN cc_start: 0.8675 (mt0) cc_final: 0.8379 (mp10) REVERT: B 482 ILE cc_start: 0.9267 (mt) cc_final: 0.8750 (tp) REVERT: B 600 MET cc_start: 0.5900 (mtt) cc_final: 0.5653 (mtm) REVERT: B 812 PHE cc_start: 0.7120 (m-80) cc_final: 0.6838 (m-80) REVERT: B 900 MET cc_start: 0.8284 (ptm) cc_final: 0.6961 (mmt) REVERT: C 101 MET cc_start: 0.9209 (mmt) cc_final: 0.8975 (tpp) REVERT: C 108 LEU cc_start: 0.9279 (mt) cc_final: 0.9018 (tt) outliers start: 28 outliers final: 25 residues processed: 190 average time/residue: 0.5013 time to fit residues: 137.9809 Evaluate side-chains 194 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 169 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 CYS 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 316 SER Chi-restraints excluded: chain A residue 354 LEU 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 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 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 53 optimal weight: 8.9990 chunk 79 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 104 optimal weight: 8.9990 chunk 120 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 11286 Z= 0.346 Angle : 0.634 5.897 15316 Z= 0.339 Chirality : 0.040 0.141 1784 Planarity : 0.004 0.041 1930 Dihedral : 5.175 21.193 1493 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.22 % Allowed : 14.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.22), residues: 1355 helix: 0.90 (0.23), residues: 468 sheet: -0.60 (0.26), residues: 359 loop : -0.24 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 268 HIS 0.008 0.001 HIS A 607 PHE 0.017 0.002 PHE C 103 TYR 0.017 0.002 TYR A 125 ARG 0.005 0.001 ARG C 218 *********************** 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 206 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 166 time to evaluate : 2.207 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: A 63 TYR cc_start: 0.8285 (OUTLIER) cc_final: 0.7723 (m-80) REVERT: A 181 GLN cc_start: 0.8719 (mt0) cc_final: 0.8405 (mp10) REVERT: B 482 ILE cc_start: 0.9314 (mt) cc_final: 0.8835 (tp) REVERT: B 812 PHE cc_start: 0.7281 (m-80) cc_final: 0.6966 (m-80) REVERT: B 900 MET cc_start: 0.8285 (ptm) cc_final: 0.7082 (mmt) REVERT: C 108 LEU cc_start: 0.9325 (mt) cc_final: 0.9069 (tt) REVERT: C 207 TRP cc_start: 0.8821 (OUTLIER) cc_final: 0.7513 (t60) outliers start: 40 outliers final: 35 residues processed: 185 average time/residue: 0.5320 time to fit residues: 142.1136 Evaluate side-chains 197 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 160 time to evaluate : 1.755 ------------------------------------------------------------------------------- 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 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 229 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 547 SER 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 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 484 MET Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 194 TRP 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 257 SER Chi-restraints excluded: chain C residue 341 HIS Chi-restraints excluded: chain C residue 381 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 0.0970 chunk 116 optimal weight: 7.9990 chunk 123 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 117 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 131 optimal weight: 5.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.5315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11286 Z= 0.170 Angle : 0.576 6.559 15316 Z= 0.297 Chirality : 0.041 0.145 1784 Planarity : 0.004 0.045 1930 Dihedral : 4.992 20.450 1493 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.18 % Allowed : 16.36 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.23), residues: 1355 helix: 1.23 (0.23), residues: 469 sheet: -0.44 (0.26), residues: 353 loop : -0.06 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 268 HIS 0.006 0.001 HIS A 386 PHE 0.016 0.001 PHE B 413 TYR 0.016 0.001 TYR A 566 ARG 0.003 0.000 ARG A 273 *********************** 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 fitting. rotamer outliers: 27 poor density : 174 time to evaluate : 1.924 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: A 63 TYR cc_start: 0.8291 (OUTLIER) cc_final: 0.7637 (m-80) REVERT: A 181 GLN cc_start: 0.8683 (mt0) cc_final: 0.8335 (mp10) REVERT: B 812 PHE cc_start: 0.7098 (m-80) cc_final: 0.6833 (m-80) REVERT: B 900 MET cc_start: 0.8316 (ptm) cc_final: 0.7001 (mmt) REVERT: C 101 MET cc_start: 0.9219 (mmt) cc_final: 0.8895 (mmp) REVERT: C 108 LEU cc_start: 0.9273 (mt) cc_final: 0.9015 (tt) REVERT: C 207 TRP cc_start: 0.8765 (OUTLIER) cc_final: 0.7420 (t60) outliers start: 27 outliers final: 24 residues processed: 186 average time/residue: 0.5184 time to fit residues: 138.3595 Evaluate side-chains 195 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 169 time to evaluate : 1.820 ------------------------------------------------------------------------------- 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 127 CYS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 547 SER 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 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 484 MET Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain C residue 13 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 79 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 116 optimal weight: 8.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.5468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11286 Z= 0.209 Angle : 0.576 6.359 15316 Z= 0.300 Chirality : 0.040 0.140 1784 Planarity : 0.004 0.037 1930 Dihedral : 4.928 21.822 1493 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.01 % Allowed : 16.84 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.23), residues: 1355 helix: 1.29 (0.24), residues: 469 sheet: -0.42 (0.26), residues: 353 loop : -0.11 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 268 HIS 0.006 0.001 HIS A 607 PHE 0.014 0.001 PHE C 103 TYR 0.015 0.001 TYR A 566 ARG 0.003 0.000 ARG A 273 ********************** 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 191 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 166 time to evaluate : 1.831 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: A 63 TYR cc_start: 0.8293 (OUTLIER) cc_final: 0.7648 (m-80) REVERT: A 181 GLN cc_start: 0.8718 (mt0) cc_final: 0.8458 (mt0) REVERT: B 812 PHE cc_start: 0.7121 (m-80) cc_final: 0.6848 (m-80) REVERT: B 900 MET cc_start: 0.8309 (ptm) cc_final: 0.6993 (mmt) REVERT: C 101 MET cc_start: 0.9229 (mmt) cc_final: 0.8924 (mmm) REVERT: C 108 LEU cc_start: 0.9277 (mt) cc_final: 0.9013 (tt) REVERT: C 207 TRP cc_start: 0.8800 (OUTLIER) cc_final: 0.7478 (t60) REVERT: C 414 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.8926 (pp) outliers start: 25 outliers final: 22 residues processed: 177 average time/residue: 0.4961 time to fit residues: 126.1796 Evaluate side-chains 189 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 164 time to evaluate : 1.625 ------------------------------------------------------------------------------- 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 127 CYS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 309 ASP 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 547 SER 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 458 GLN Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain C residue 13 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 33 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.083308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.070809 restraints weight = 176298.123| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 6.36 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.5631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11286 Z= 0.281 Angle : 0.612 6.526 15316 Z= 0.322 Chirality : 0.040 0.141 1784 Planarity : 0.004 0.037 1930 Dihedral : 5.005 21.670 1493 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.50 % Allowed : 16.60 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.23), residues: 1355 helix: 1.01 (0.23), residues: 469 sheet: -0.56 (0.26), residues: 357 loop : -0.24 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 268 HIS 0.007 0.001 HIS A 607 PHE 0.017 0.002 PHE C 103 TYR 0.016 0.002 TYR A 125 ARG 0.004 0.001 ARG A 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5011.43 seconds wall clock time: 89 minutes 2.73 seconds (5342.73 seconds total)