Starting phenix.real_space_refine on Tue Dec 12 18:13:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3d_13789/12_2023/7q3d_13789.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3d_13789/12_2023/7q3d_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_13789/12_2023/7q3d_13789.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3d_13789/12_2023/7q3d_13789.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3d_13789/12_2023/7q3d_13789.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3d_13789/12_2023/7q3d_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 10.29, per 1000 atoms: 0.46 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: 23.16 Conformation dependent library (CDL) restraints added in 2.1 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: 2.10 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: 9.49 Time building geometry restraints manager: 21.53 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: 9797 17.50 - 35.01: 427 35.01 - 52.51: 67 52.51 - 70.01: 26 70.01 - 87.51: 13 Dihedral angle restraints: 10330 sinusoidal: 5589 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 10327 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: 3.580 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: 0.360 Extract box with map and model: 13.310 Check model and map are aligned: 0.320 Set scattering table: 0.210 Process input model: 78.050 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.330 ------------------------------------------------------------------------------- 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 : 2.043 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 outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.6403 time to fit residues: 256.3243 Evaluate side-chains 202 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.843 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3002 ------------------------------------------------------------------------------- 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: 1.9990 chunk 70 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 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: A 375 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 11286 Z= 0.276 Angle : 0.689 6.343 15316 Z= 0.384 Chirality : 0.042 0.160 1784 Planarity : 0.005 0.045 1930 Dihedral : 6.178 42.509 1493 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.50 % Allowed : 9.02 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.87 (0.22), residues: 1355 helix: 0.55 (0.22), residues: 477 sheet: 0.66 (0.26), residues: 347 loop : 0.81 (0.27), residues: 531 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 0.019 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 239 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 208 time to evaluate : 1.864 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 outliers start: 31 outliers final: 26 residues processed: 220 average time/residue: 0.5568 time to fit residues: 171.8981 Evaluate side-chains 206 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 180 time to evaluate : 1.793 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.3161 time to fit residues: 15.9912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 104 optimal weight: 0.0980 chunk 85 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 125 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 124 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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** C 412 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11286 Z= 0.239 Angle : 0.631 5.418 15316 Z= 0.343 Chirality : 0.041 0.154 1784 Planarity : 0.005 0.041 1930 Dihedral : 5.755 35.542 1493 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.05 % Allowed : 11.28 % Favored : 87.67 % 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: 0.70 (0.22), residues: 1355 helix: 0.83 (0.23), residues: 475 sheet: 0.27 (0.26), residues: 353 loop : 0.50 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 268 HIS 0.008 0.001 HIS B 330 PHE 0.020 0.002 PHE B 435 TYR 0.016 0.002 TYR A 566 ARG 0.003 0.000 ARG A 115 *********************** 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 205 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 192 time to evaluate : 1.803 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 outliers start: 13 outliers final: 9 residues processed: 195 average time/residue: 0.5046 time to fit residues: 142.5244 Evaluate side-chains 186 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 177 time to evaluate : 2.061 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3178 time to fit residues: 6.9642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 634 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 11286 Z= 0.308 Angle : 0.647 5.811 15316 Z= 0.348 Chirality : 0.041 0.174 1784 Planarity : 0.005 0.053 1930 Dihedral : 5.557 30.851 1493 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.37 % Allowed : 12.49 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.42 (0.22), residues: 1355 helix: 0.86 (0.23), residues: 469 sheet: -0.06 (0.26), residues: 353 loop : 0.21 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 268 HIS 0.007 0.001 HIS A 607 PHE 0.024 0.002 PHE A 428 TYR 0.016 0.002 TYR A 566 ARG 0.004 0.000 ARG C 218 *********************** 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 194 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 177 time to evaluate : 1.912 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 outliers start: 17 outliers final: 14 residues processed: 184 average time/residue: 0.5334 time to fit residues: 140.8206 Evaluate side-chains 179 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 165 time to evaluate : 2.018 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2910 time to fit residues: 9.4651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 119 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11286 Z= 0.283 Angle : 0.621 5.876 15316 Z= 0.331 Chirality : 0.041 0.154 1784 Planarity : 0.005 0.043 1930 Dihedral : 5.393 28.473 1493 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.05 % Allowed : 13.78 % Favored : 85.17 % 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: 0.94 (0.23), residues: 469 sheet: -0.31 (0.26), residues: 348 loop : -0.08 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 268 HIS 0.006 0.001 HIS A 607 PHE 0.016 0.002 PHE B 435 TYR 0.020 0.002 TYR A 210 ARG 0.004 0.000 ARG B 641 *********************** 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 185 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 172 time to evaluate : 2.156 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 outliers start: 13 outliers final: 10 residues processed: 181 average time/residue: 0.5222 time to fit residues: 137.1275 Evaluate side-chains 175 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 165 time to evaluate : 1.806 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 10 average time/residue: 0.4007 time to fit residues: 8.8228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 128 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: 0.7600 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 11286 Z= 0.350 Angle : 0.652 5.227 15316 Z= 0.351 Chirality : 0.041 0.207 1784 Planarity : 0.005 0.044 1930 Dihedral : 5.444 28.674 1493 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.85 % Allowed : 14.02 % Favored : 84.13 % 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: -0.16 (0.22), residues: 1355 helix: 0.74 (0.23), residues: 468 sheet: -0.64 (0.25), residues: 364 loop : -0.29 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 268 HIS 0.008 0.002 HIS A 607 PHE 0.021 0.002 PHE A 428 TYR 0.017 0.002 TYR A 566 ARG 0.014 0.001 ARG B 641 *********************** 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 189 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 166 time to evaluate : 2.241 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 outliers start: 23 outliers final: 19 residues processed: 178 average time/residue: 0.5083 time to fit residues: 131.8565 Evaluate side-chains 178 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 159 time to evaluate : 1.845 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 2 residues processed: 19 average time/residue: 0.3130 time to fit residues: 12.2489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 74 optimal weight: 0.8980 chunk 133 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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: 0.7558 moved from start: 0.5226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11286 Z= 0.224 Angle : 0.594 4.954 15316 Z= 0.313 Chirality : 0.040 0.146 1784 Planarity : 0.004 0.043 1930 Dihedral : 5.279 27.552 1493 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.89 % Allowed : 15.47 % 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: 0.02 (0.22), residues: 1355 helix: 1.00 (0.23), residues: 468 sheet: -0.57 (0.26), residues: 358 loop : -0.28 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 268 HIS 0.006 0.001 HIS A 607 PHE 0.016 0.002 PHE C 103 TYR 0.017 0.001 TYR A 566 ARG 0.002 0.000 ARG A 115 *********************** 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 178 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 167 time to evaluate : 2.086 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 outliers start: 11 outliers final: 7 residues processed: 174 average time/residue: 0.5018 time to fit residues: 127.4669 Evaluate side-chains 170 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 163 time to evaluate : 1.935 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 7 average time/residue: 0.4039 time to fit residues: 6.6270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.5337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11286 Z= 0.191 Angle : 0.573 5.213 15316 Z= 0.300 Chirality : 0.040 0.151 1784 Planarity : 0.004 0.050 1930 Dihedral : 5.117 27.189 1493 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.05 % Allowed : 16.44 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.19 (0.22), residues: 1355 helix: 1.24 (0.24), residues: 468 sheet: -0.54 (0.26), residues: 360 loop : -0.24 (0.27), residues: 527 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 C 103 TYR 0.016 0.001 TYR A 566 ARG 0.002 0.000 ARG C 379 *********************** 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 179 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 166 time to evaluate : 1.839 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 outliers start: 13 outliers final: 9 residues processed: 172 average time/residue: 0.5202 time to fit residues: 130.4507 Evaluate side-chains 173 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 164 time to evaluate : 1.795 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 9 average time/residue: 0.3609 time to fit residues: 7.4338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 117 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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: 0.7523 moved from start: 0.5438 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= 0.164 Angle : 0.568 6.081 15316 Z= 0.293 Chirality : 0.041 0.142 1784 Planarity : 0.004 0.044 1930 Dihedral : 4.953 26.463 1493 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.48 % Allowed : 17.08 % 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: 1.41 (0.24), residues: 468 sheet: -0.35 (0.26), residues: 354 loop : -0.18 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 268 HIS 0.005 0.001 HIS A 607 PHE 0.016 0.001 PHE B 413 TYR 0.015 0.001 TYR A 566 ARG 0.002 0.000 ARG B 401 *********************** 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 180 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 174 time to evaluate : 1.742 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 outliers start: 6 outliers final: 6 residues processed: 178 average time/residue: 0.5163 time to fit residues: 133.4778 Evaluate side-chains 171 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 165 time to evaluate : 1.848 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 6 average time/residue: 0.4732 time to fit residues: 6.4489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 126 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 116 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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: 0.7528 moved from start: 0.5584 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= 0.171 Angle : 0.569 6.161 15316 Z= 0.294 Chirality : 0.040 0.147 1784 Planarity : 0.004 0.040 1930 Dihedral : 4.883 26.151 1493 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.64 % Allowed : 17.32 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.42 (0.23), residues: 1355 helix: 1.46 (0.24), residues: 469 sheet: -0.38 (0.26), residues: 354 loop : -0.16 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 268 HIS 0.005 0.001 HIS A 607 PHE 0.015 0.001 PHE C 103 TYR 0.020 0.001 TYR A 566 ARG 0.002 0.000 ARG A 586 ********************** 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 176 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 168 time to evaluate : 1.723 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 outliers start: 8 outliers final: 6 residues processed: 172 average time/residue: 0.5210 time to fit residues: 130.9034 Evaluate side-chains 168 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 162 time to evaluate : 1.889 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 6 average time/residue: 0.4232 time to fit residues: 6.2220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 112 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 96 optimal weight: 0.6980 chunk 6 optimal weight: 10.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.083787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.071341 restraints weight = 176814.933| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 6.39 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.5740 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 : 0.608 6.150 15316 Z= 0.321 Chirality : 0.040 0.139 1784 Planarity : 0.004 0.038 1930 Dihedral : 4.975 26.344 1493 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.64 % Allowed : 17.41 % Favored : 81.95 % 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: 0.18 (0.23), residues: 1355 helix: 1.21 (0.24), residues: 469 sheet: -0.47 (0.26), residues: 352 loop : -0.31 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 268 HIS 0.007 0.001 HIS A 607 PHE 0.014 0.002 PHE C 103 TYR 0.016 0.002 TYR A 125 ARG 0.003 0.000 ARG C 218 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5088.54 seconds wall clock time: 90 minutes 52.75 seconds (5452.75 seconds total)