Starting phenix.real_space_refine on Tue Jul 29 02:25:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n0z_48799/07_2025/9n0z_48799.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n0z_48799/07_2025/9n0z_48799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n0z_48799/07_2025/9n0z_48799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n0z_48799/07_2025/9n0z_48799.map" model { file = "/net/cci-nas-00/data/ceres_data/9n0z_48799/07_2025/9n0z_48799.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n0z_48799/07_2025/9n0z_48799.cif" } resolution = 3.5 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= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 61 5.16 5 C 6861 2.51 5 N 1856 2.21 5 O 2069 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10847 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4527 Classifications: {'peptide': 581} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 554} Chain: "B" Number of atoms: 3529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3529 Classifications: {'peptide': 431} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 415} Chain breaks: 1 Chain: "C" Number of atoms: 2496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2496 Classifications: {'peptide': 308} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 294} Chain: "D" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 295 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 32} Time building chain proxies: 7.15, per 1000 atoms: 0.66 Number of scatterers: 10847 At special positions: 0 Unit cell: (105.165, 102.6, 129.105, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 61 16.00 O 2069 8.00 N 1856 7.00 C 6861 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.15 Conformation dependent library (CDL) restraints added in 1.4 seconds 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2600 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 14 sheets defined 48.4% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 10 through 20 removed outlier: 3.619A pdb=" N ASP A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 43 removed outlier: 5.083A pdb=" N SER A 36 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N THR A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 56 removed outlier: 4.214A pdb=" N LEU A 52 " --> pdb=" O ARG A 48 " (cutoff:3.500A) Proline residue: A 53 - end of helix Processing helix chain 'A' and resid 62 through 74 removed outlier: 3.861A pdb=" N ALA A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 89 Processing helix chain 'A' and resid 90 through 95 removed outlier: 3.721A pdb=" N SER A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 117 removed outlier: 3.978A pdb=" N HIS A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 128 through 136 Processing helix chain 'A' and resid 142 through 148 Processing helix chain 'A' and resid 159 through 174 Processing helix chain 'A' and resid 178 through 194 removed outlier: 3.596A pdb=" N ARG A 182 " --> pdb=" O THR A 178 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N GLY A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N GLU A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 214 removed outlier: 4.216A pdb=" N ILE A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Proline residue: A 207 - end of helix Processing helix chain 'A' and resid 222 through 235 removed outlier: 4.373A pdb=" N GLU A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 253 removed outlier: 3.596A pdb=" N GLU A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 266 removed outlier: 3.594A pdb=" N ARG A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 275 Processing helix chain 'A' and resid 275 through 292 removed outlier: 4.935A pdb=" N VAL A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 296 through 305 removed outlier: 3.658A pdb=" N LYS A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 312 removed outlier: 3.654A pdb=" N ASN A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 325 Processing helix chain 'A' and resid 326 through 335 removed outlier: 4.154A pdb=" N SER A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 349 removed outlier: 3.953A pdb=" N LYS A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 356 removed outlier: 3.525A pdb=" N SER A 353 " --> pdb=" O MET A 350 " (cutoff:3.500A) Proline residue: A 354 - end of helix No H-bonds generated for 'chain 'A' and resid 350 through 356' Processing helix chain 'A' and resid 358 through 375 removed outlier: 4.346A pdb=" N LEU A 366 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Proline residue: A 367 - end of helix Processing helix chain 'A' and resid 379 through 387 removed outlier: 3.662A pdb=" N ASN A 387 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 393 Processing helix chain 'A' and resid 400 through 413 Proline residue: A 406 - end of helix removed outlier: 4.020A pdb=" N GLU A 413 " --> pdb=" O VAL A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 435 removed outlier: 3.944A pdb=" N ARG A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) Proline residue: A 428 - end of helix removed outlier: 3.829A pdb=" N GLY A 435 " --> pdb=" O ALA A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 442 Processing helix chain 'A' and resid 443 through 452 removed outlier: 3.653A pdb=" N VAL A 452 " --> pdb=" O MET A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 480 removed outlier: 7.217A pdb=" N LYS A 475 " --> pdb=" O GLU A 471 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N GLU A 476 " --> pdb=" O LYS A 472 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TRP A 477 " --> pdb=" O PHE A 473 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA A 478 " --> pdb=" O GLY A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 489 removed outlier: 4.509A pdb=" N LYS A 485 " --> pdb=" O THR A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 494 through 513 removed outlier: 3.712A pdb=" N ARG A 498 " --> pdb=" O ASN A 494 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLU A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL A 511 " --> pdb=" O VAL A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 529 removed outlier: 4.344A pdb=" N LYS A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU A 522 " --> pdb=" O THR A 518 " (cutoff:3.500A) Proline residue: A 523 - end of helix Processing helix chain 'A' and resid 533 through 548 removed outlier: 3.679A pdb=" N ASN A 539 " --> pdb=" O ASN A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 551 No H-bonds generated for 'chain 'A' and resid 549 through 551' Processing helix chain 'A' and resid 552 through 568 removed outlier: 3.920A pdb=" N SER A 558 " --> pdb=" O SER A 554 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LYS A 561 " --> pdb=" O GLN A 557 " (cutoff:3.500A) Proline residue: A 562 - end of helix Processing helix chain 'A' and resid 572 through 586 removed outlier: 3.801A pdb=" N LYS A 576 " --> pdb=" O ASP A 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 30 removed outlier: 3.794A pdb=" N ILE B 30 " --> pdb=" O GLU B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 330 Processing helix chain 'B' and resid 334 through 338 removed outlier: 3.853A pdb=" N GLU B 338 " --> pdb=" O SER B 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 19 Processing helix chain 'C' and resid 24 through 41 removed outlier: 3.938A pdb=" N VAL C 28 " --> pdb=" O SER C 24 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS C 41 " --> pdb=" O GLU C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 73 Processing helix chain 'C' and resid 92 through 107 Processing helix chain 'C' and resid 120 through 127 Processing helix chain 'C' and resid 128 through 137 Processing helix chain 'C' and resid 140 through 153 removed outlier: 3.623A pdb=" N TYR C 152 " --> pdb=" O ASP C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 182 Processing helix chain 'C' and resid 193 through 201 Processing helix chain 'C' and resid 221 through 233 removed outlier: 3.665A pdb=" N SER C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 268 removed outlier: 3.833A pdb=" N ARG C 268 " --> pdb=" O TYR C 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 8 removed outlier: 4.195A pdb=" N LYS D 7 " --> pdb=" O GLU D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 13 Processing helix chain 'D' and resid 20 through 32 removed outlier: 4.221A pdb=" N LYS D 24 " --> pdb=" O ASP D 20 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE D 31 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS D 32 " --> pdb=" O ARG D 28 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 12 through 13 Processing sheet with id=AA2, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA3, first strand: chain 'B' and resid 51 through 52 removed outlier: 3.584A pdb=" N VAL B 52 " --> pdb=" O PHE B 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 109 through 114 removed outlier: 3.552A pdb=" N LEU B 111 " --> pdb=" O TRP B 122 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER B 125 " --> pdb=" O GLU B 165 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 109 through 114 removed outlier: 3.552A pdb=" N LEU B 111 " --> pdb=" O TRP B 122 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG B 170 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 129 through 132 Processing sheet with id=AA7, first strand: chain 'B' and resid 184 through 185 removed outlier: 3.653A pdb=" N TYR B 192 " --> pdb=" O TRP B 203 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE B 200 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE B 212 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N THR C 301 " --> pdb=" O SER B 211 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN B 213 " --> pdb=" O THR C 301 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 251 through 252 Processing sheet with id=AA9, first strand: chain 'B' and resid 302 through 303 removed outlier: 3.706A pdb=" N GLU B 321 " --> pdb=" O ILE B 310 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 348 through 350 removed outlier: 3.801A pdb=" N LEU B 379 " --> pdb=" O PHE B 366 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 421 through 424 removed outlier: 4.249A pdb=" N HIS B 421 " --> pdb=" O ALA B 434 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA B 432 " --> pdb=" O ALA B 423 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 45 through 48 removed outlier: 3.771A pdb=" N VAL C 48 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE C 164 " --> pdb=" O SER C 238 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL C 257 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS C 251 " --> pdb=" O VAL C 256 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 80 through 81 removed outlier: 6.658A pdb=" N TYR C 80 " --> pdb=" O THR C 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 276 through 278 removed outlier: 3.575A pdb=" N SER C 285 " --> pdb=" O GLU C 277 " (cutoff:3.500A) 412 hydrogen bonds defined for protein. 1173 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: 3.21 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3557 1.34 - 1.46: 1463 1.46 - 1.57: 5951 1.57 - 1.69: 0 1.69 - 1.81: 89 Bond restraints: 11060 Sorted by residual: bond pdb=" N VAL A 394 " pdb=" CA VAL A 394 " ideal model delta sigma weight residual 1.458 1.495 -0.037 9.00e-03 1.23e+04 1.68e+01 bond pdb=" N PRO A 285 " pdb=" CD PRO A 285 " ideal model delta sigma weight residual 1.473 1.524 -0.051 1.40e-02 5.10e+03 1.33e+01 bond pdb=" N ILE A 355 " pdb=" CA ILE A 355 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.09e-02 8.42e+03 1.12e+01 bond pdb=" N ILE A 483 " pdb=" CA ILE A 483 " ideal model delta sigma weight residual 1.461 1.502 -0.041 1.23e-02 6.61e+03 1.10e+01 bond pdb=" N ILE A 482 " pdb=" CA ILE A 482 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.21e-02 6.83e+03 9.98e+00 ... (remaining 11055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 14327 1.81 - 3.62: 584 3.62 - 5.43: 61 5.43 - 7.24: 7 7.24 - 9.05: 2 Bond angle restraints: 14981 Sorted by residual: angle pdb=" N LYS B 88 " pdb=" CA LYS B 88 " pdb=" C LYS B 88 " ideal model delta sigma weight residual 113.01 107.65 5.36 1.20e+00 6.94e-01 2.00e+01 angle pdb=" N GLU A 471 " pdb=" CA GLU A 471 " pdb=" C GLU A 471 " ideal model delta sigma weight residual 112.89 107.75 5.14 1.24e+00 6.50e-01 1.72e+01 angle pdb=" N LEU A 466 " pdb=" CA LEU A 466 " pdb=" C LEU A 466 " ideal model delta sigma weight residual 111.07 106.66 4.41 1.07e+00 8.73e-01 1.70e+01 angle pdb=" N ILE B 285 " pdb=" CA ILE B 285 " pdb=" C ILE B 285 " ideal model delta sigma weight residual 111.77 107.77 4.00 1.04e+00 9.25e-01 1.48e+01 angle pdb=" C GLU A 363 " pdb=" N HIS A 364 " pdb=" CA HIS A 364 " ideal model delta sigma weight residual 122.08 116.22 5.86 1.53e+00 4.27e-01 1.46e+01 ... (remaining 14976 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5983 17.98 - 35.96: 561 35.96 - 53.94: 158 53.94 - 71.92: 31 71.92 - 89.90: 23 Dihedral angle restraints: 6756 sinusoidal: 2764 harmonic: 3992 Sorted by residual: dihedral pdb=" CD ARG A 420 " pdb=" NE ARG A 420 " pdb=" CZ ARG A 420 " pdb=" NH1 ARG A 420 " ideal model delta sinusoidal sigma weight residual 0.00 59.29 -59.29 1 1.00e+01 1.00e-02 4.70e+01 dihedral pdb=" CD ARG A 527 " pdb=" NE ARG A 527 " pdb=" CZ ARG A 527 " pdb=" NH1 ARG A 527 " ideal model delta sinusoidal sigma weight residual 0.00 56.23 -56.23 1 1.00e+01 1.00e-02 4.26e+01 dihedral pdb=" CD ARG A 134 " pdb=" NE ARG A 134 " pdb=" CZ ARG A 134 " pdb=" NH1 ARG A 134 " ideal model delta sinusoidal sigma weight residual 0.00 55.93 -55.93 1 1.00e+01 1.00e-02 4.22e+01 ... (remaining 6753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1244 0.050 - 0.100: 336 0.100 - 0.151: 94 0.151 - 0.201: 17 0.201 - 0.251: 3 Chirality restraints: 1694 Sorted by residual: chirality pdb=" CA VAL A 533 " pdb=" N VAL A 533 " pdb=" C VAL A 533 " pdb=" CB VAL A 533 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA ILE A 355 " pdb=" N ILE A 355 " pdb=" C ILE A 355 " pdb=" CB ILE A 355 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CG LEU A 411 " pdb=" CB LEU A 411 " pdb=" CD1 LEU A 411 " pdb=" CD2 LEU A 411 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1691 not shown) Planarity restraints: 1938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 420 " -0.943 9.50e-02 1.11e+02 4.23e-01 1.08e+02 pdb=" NE ARG A 420 " 0.057 2.00e-02 2.50e+03 pdb=" CZ ARG A 420 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 420 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 420 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 527 " 0.920 9.50e-02 1.11e+02 4.12e-01 1.03e+02 pdb=" NE ARG A 527 " -0.055 2.00e-02 2.50e+03 pdb=" CZ ARG A 527 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 527 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 527 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 134 " -0.913 9.50e-02 1.11e+02 4.09e-01 1.01e+02 pdb=" NE ARG A 134 " 0.055 2.00e-02 2.50e+03 pdb=" CZ ARG A 134 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 134 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 134 " -0.024 2.00e-02 2.50e+03 ... (remaining 1935 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 3 2.23 - 2.90: 4452 2.90 - 3.56: 14983 3.56 - 4.23: 23565 4.23 - 4.90: 41109 Nonbonded interactions: 84112 Sorted by model distance: nonbonded pdb=" CE MET B 301 " pdb=" CG2 VAL B 308 " model vdw 1.559 3.880 nonbonded pdb=" O MET C 83 " pdb=" ND1 HIS C 167 " model vdw 1.917 3.120 nonbonded pdb=" OD2 ASP C 57 " pdb=" OD2 ASP C 85 " model vdw 2.110 3.040 nonbonded pdb=" O SER B 15 " pdb=" OE1 GLN B 16 " model vdw 2.300 3.040 nonbonded pdb=" OH TYR B 74 " pdb=" OE2 GLU B 126 " model vdw 2.312 3.040 ... (remaining 84107 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.650 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: 0.000 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 28.600 Find NCS groups from input model: 0.110 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: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 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 : 0.006 0.055 11060 Z= 0.357 Angle : 0.778 9.048 14981 Z= 0.502 Chirality : 0.051 0.251 1694 Planarity : 0.018 0.423 1938 Dihedral : 16.264 89.895 4156 Min Nonbonded Distance : 1.559 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 0.00 % Allowed : 19.95 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.23), residues: 1345 helix: -0.20 (0.23), residues: 568 sheet: -4.97 (0.28), residues: 164 loop : -2.30 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 143 HIS 0.006 0.001 HIS B 326 PHE 0.021 0.001 PHE B 242 TYR 0.020 0.001 TYR B 74 ARG 0.007 0.000 ARG C 185 Details of bonding type rmsd hydrogen bonds : bond 0.17048 ( 407) hydrogen bonds : angle 6.68013 ( 1173) covalent geometry : bond 0.00614 (11060) covalent geometry : angle 0.77849 (14981) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 1.347 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: B 134 TYR cc_start: 0.7088 (m-80) cc_final: 0.6767 (m-80) REVERT: B 396 LYS cc_start: 0.8586 (mmtt) cc_final: 0.8199 (mmtm) REVERT: C 92 TYR cc_start: 0.5415 (m-80) cc_final: 0.5039 (m-80) REVERT: C 144 LYS cc_start: 0.8303 (mtpp) cc_final: 0.7844 (mmmt) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.2835 time to fit residues: 95.8564 Evaluate side-chains 155 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 8.9990 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 40 optimal weight: 0.4980 chunk 63 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN C 63 HIS ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 GLN ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.176783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.112245 restraints weight = 13556.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.109387 restraints weight = 9812.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.109158 restraints weight = 9000.412| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11060 Z= 0.214 Angle : 0.696 8.266 14981 Z= 0.359 Chirality : 0.045 0.185 1694 Planarity : 0.005 0.055 1938 Dihedral : 5.354 69.702 1472 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 3.96 % Allowed : 20.45 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.24), residues: 1345 helix: 0.35 (0.23), residues: 574 sheet: -4.38 (0.30), residues: 185 loop : -2.02 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 143 HIS 0.009 0.001 HIS A 364 PHE 0.025 0.002 PHE A 503 TYR 0.020 0.002 TYR A 577 ARG 0.008 0.001 ARG A 420 Details of bonding type rmsd hydrogen bonds : bond 0.04504 ( 407) hydrogen bonds : angle 5.16155 ( 1173) covalent geometry : bond 0.00520 (11060) covalent geometry : angle 0.69585 (14981) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 161 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 HIS cc_start: 0.8189 (OUTLIER) cc_final: 0.7230 (t-90) REVERT: A 332 GLU cc_start: 0.8304 (tm-30) cc_final: 0.8000 (tm-30) REVERT: A 453 ASP cc_start: 0.8599 (t0) cc_final: 0.8057 (t0) REVERT: A 537 ARG cc_start: 0.8684 (ttm-80) cc_final: 0.8325 (ttm-80) REVERT: B 37 ASN cc_start: 0.8697 (OUTLIER) cc_final: 0.8279 (p0) REVERT: B 58 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7132 (mt-10) REVERT: B 135 ASN cc_start: 0.7226 (OUTLIER) cc_final: 0.6479 (t0) REVERT: B 196 ASP cc_start: 0.8925 (p0) cc_final: 0.8667 (p0) REVERT: B 214 ILE cc_start: 0.8872 (tp) cc_final: 0.8500 (pt) REVERT: C 92 TYR cc_start: 0.4718 (m-80) cc_final: 0.4342 (m-80) REVERT: C 144 LYS cc_start: 0.8381 (mtpp) cc_final: 0.7859 (mmmt) REVERT: C 195 MET cc_start: 0.5649 (ttt) cc_final: 0.5239 (tmm) REVERT: C 260 PHE cc_start: 0.6407 (t80) cc_final: 0.5685 (m-80) outliers start: 48 outliers final: 30 residues processed: 200 average time/residue: 0.2304 time to fit residues: 66.3510 Evaluate side-chains 171 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 137 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 37 ASN Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 69 PHE Chi-restraints excluded: chain C residue 238 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 39 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 117 optimal weight: 9.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.179627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.114663 restraints weight = 13605.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.112362 restraints weight = 9376.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112390 restraints weight = 9176.831| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11060 Z= 0.143 Angle : 0.624 10.302 14981 Z= 0.319 Chirality : 0.043 0.256 1694 Planarity : 0.005 0.044 1938 Dihedral : 5.142 66.956 1472 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.77 % Favored : 93.16 % Rotamer: Outliers : 3.87 % Allowed : 20.69 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: -1.70 (0.24), residues: 1345 helix: 0.59 (0.23), residues: 576 sheet: -3.93 (0.32), residues: 187 loop : -1.87 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 143 HIS 0.004 0.001 HIS B 326 PHE 0.016 0.001 PHE B 242 TYR 0.018 0.001 TYR A 577 ARG 0.004 0.000 ARG C 185 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 407) hydrogen bonds : angle 4.82630 ( 1173) covalent geometry : bond 0.00336 (11060) covalent geometry : angle 0.62394 (14981) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 156 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 304 HIS cc_start: 0.8179 (OUTLIER) cc_final: 0.7267 (t-90) REVERT: A 453 ASP cc_start: 0.8566 (t0) cc_final: 0.8001 (t0) REVERT: A 528 MET cc_start: 0.6652 (ttm) cc_final: 0.6346 (ttm) REVERT: A 537 ARG cc_start: 0.8687 (ttm-80) cc_final: 0.8431 (ttm-80) REVERT: B 58 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.7070 (mt-10) REVERT: B 135 ASN cc_start: 0.7151 (OUTLIER) cc_final: 0.6390 (t0) REVERT: B 196 ASP cc_start: 0.8824 (p0) cc_final: 0.8485 (p0) REVERT: B 214 ILE cc_start: 0.8887 (tp) cc_final: 0.8522 (pt) REVERT: B 234 PHE cc_start: 0.8871 (OUTLIER) cc_final: 0.8571 (m-80) REVERT: C 92 TYR cc_start: 0.4559 (m-80) cc_final: 0.4187 (m-80) REVERT: C 144 LYS cc_start: 0.8392 (mtpp) cc_final: 0.7919 (mmmt) REVERT: C 195 MET cc_start: 0.5543 (ttt) cc_final: 0.5249 (tmm) REVERT: C 218 TYR cc_start: 0.6098 (t80) cc_final: 0.5847 (t80) REVERT: C 239 ARG cc_start: 0.6168 (ptt90) cc_final: 0.5958 (ptm-80) REVERT: C 260 PHE cc_start: 0.6446 (t80) cc_final: 0.5679 (m-80) REVERT: C 268 ARG cc_start: 0.6816 (mmm160) cc_final: 0.5563 (mtm110) REVERT: D 28 ARG cc_start: 0.6720 (OUTLIER) cc_final: 0.5193 (ttm170) outliers start: 47 outliers final: 29 residues processed: 194 average time/residue: 0.2473 time to fit residues: 67.9529 Evaluate side-chains 173 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain B residue 13 CYS Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 69 PHE Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 28 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 92 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN B 174 ASN ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.188120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 139)---------------| | r_work = 0.3452 r_free = 0.3452 target = 0.126803 restraints weight = 13300.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.127429 restraints weight = 11570.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.126537 restraints weight = 10303.059| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11060 Z= 0.141 Angle : 0.618 12.690 14981 Z= 0.311 Chirality : 0.043 0.224 1694 Planarity : 0.004 0.041 1938 Dihedral : 4.982 63.499 1472 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.95 % Favored : 93.98 % Rotamer: Outliers : 4.53 % Allowed : 20.86 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: -1.55 (0.24), residues: 1345 helix: 0.63 (0.23), residues: 583 sheet: -3.40 (0.33), residues: 206 loop : -1.81 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 143 HIS 0.003 0.001 HIS B 176 PHE 0.033 0.002 PHE B 442 TYR 0.018 0.001 TYR A 577 ARG 0.002 0.000 ARG B 210 Details of bonding type rmsd hydrogen bonds : bond 0.03451 ( 407) hydrogen bonds : angle 4.65609 ( 1173) covalent geometry : bond 0.00334 (11060) covalent geometry : angle 0.61792 (14981) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 146 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8489 (mptp) REVERT: A 304 HIS cc_start: 0.8130 (OUTLIER) cc_final: 0.7328 (t-90) REVERT: A 453 ASP cc_start: 0.8542 (t0) cc_final: 0.8002 (t0) REVERT: A 528 MET cc_start: 0.6726 (ttm) cc_final: 0.6502 (ttm) REVERT: A 537 ARG cc_start: 0.8742 (ttm-80) cc_final: 0.8355 (ttm-80) REVERT: B 37 ASN cc_start: 0.8452 (OUTLIER) cc_final: 0.8021 (p0) REVERT: B 58 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.7089 (mt-10) REVERT: B 214 ILE cc_start: 0.8942 (tp) cc_final: 0.8544 (pt) REVERT: B 234 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.8566 (m-80) REVERT: B 252 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7836 (mtt90) REVERT: B 280 PHE cc_start: 0.8175 (t80) cc_final: 0.7935 (t80) REVERT: C 92 TYR cc_start: 0.4718 (m-80) cc_final: 0.4294 (m-80) REVERT: C 144 LYS cc_start: 0.8401 (mtpp) cc_final: 0.7918 (mmmt) REVERT: C 195 MET cc_start: 0.5686 (ttt) cc_final: 0.5293 (tmm) REVERT: C 218 TYR cc_start: 0.6243 (t80) cc_final: 0.5965 (t80) REVERT: C 260 PHE cc_start: 0.6416 (t80) cc_final: 0.5793 (m-80) REVERT: C 268 ARG cc_start: 0.6827 (mmm160) cc_final: 0.5611 (mtm110) REVERT: D 28 ARG cc_start: 0.6798 (OUTLIER) cc_final: 0.5680 (ttm170) outliers start: 55 outliers final: 36 residues processed: 187 average time/residue: 0.2254 time to fit residues: 60.1325 Evaluate side-chains 182 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 139 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain B residue 13 CYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 37 ASN Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 ARG Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 69 PHE Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 28 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 87 optimal weight: 0.6980 chunk 57 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 55 optimal weight: 5.9990 chunk 122 optimal weight: 0.0060 chunk 103 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 52 optimal weight: 0.0970 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 ASN B 438 ASN ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.182783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.120399 restraints weight = 13385.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.116609 restraints weight = 10804.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.118699 restraints weight = 9986.397| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11060 Z= 0.111 Angle : 0.586 9.595 14981 Z= 0.297 Chirality : 0.041 0.188 1694 Planarity : 0.004 0.040 1938 Dihedral : 4.778 59.937 1472 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.87 % Favored : 94.05 % Rotamer: Outliers : 3.54 % Allowed : 21.60 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: -1.27 (0.24), residues: 1345 helix: 0.86 (0.23), residues: 576 sheet: -3.05 (0.34), residues: 208 loop : -1.71 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 143 HIS 0.003 0.001 HIS A 87 PHE 0.027 0.001 PHE B 442 TYR 0.018 0.001 TYR A 577 ARG 0.004 0.000 ARG A 171 Details of bonding type rmsd hydrogen bonds : bond 0.03017 ( 407) hydrogen bonds : angle 4.48989 ( 1173) covalent geometry : bond 0.00247 (11060) covalent geometry : angle 0.58613 (14981) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 143 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8585 (mttp) REVERT: A 262 MET cc_start: 0.8609 (tpp) cc_final: 0.8386 (tpt) REVERT: A 304 HIS cc_start: 0.8196 (OUTLIER) cc_final: 0.7418 (t-90) REVERT: A 383 ASN cc_start: 0.8434 (m-40) cc_final: 0.8177 (m-40) REVERT: A 414 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7921 (m-30) REVERT: A 453 ASP cc_start: 0.8391 (t0) cc_final: 0.7953 (t0) REVERT: A 537 ARG cc_start: 0.8811 (ttm-80) cc_final: 0.8376 (ttm-80) REVERT: B 214 ILE cc_start: 0.8933 (tp) cc_final: 0.8580 (pt) REVERT: B 234 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.8594 (m-80) REVERT: B 280 PHE cc_start: 0.8116 (t80) cc_final: 0.7490 (t80) REVERT: C 92 TYR cc_start: 0.4817 (m-80) cc_final: 0.4374 (m-80) REVERT: C 144 LYS cc_start: 0.8380 (mtpp) cc_final: 0.7925 (mmmt) REVERT: C 185 ARG cc_start: 0.6300 (ptp-110) cc_final: 0.5976 (ptp-110) REVERT: C 195 MET cc_start: 0.5741 (ttt) cc_final: 0.5510 (tmm) REVERT: C 218 TYR cc_start: 0.6242 (t80) cc_final: 0.6038 (t80) REVERT: C 260 PHE cc_start: 0.6423 (t80) cc_final: 0.5873 (m-80) REVERT: C 268 ARG cc_start: 0.6804 (mmm160) cc_final: 0.5825 (ttp-110) REVERT: D 28 ARG cc_start: 0.6892 (OUTLIER) cc_final: 0.5794 (ttm170) outliers start: 43 outliers final: 27 residues processed: 176 average time/residue: 0.2287 time to fit residues: 57.8263 Evaluate side-chains 170 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain B residue 13 CYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 69 PHE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 28 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 97 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 127 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 ASN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 ASN B 372 ASN ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.182144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.118867 restraints weight = 13631.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.115365 restraints weight = 10115.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.116731 restraints weight = 9608.183| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11060 Z= 0.133 Angle : 0.602 8.807 14981 Z= 0.302 Chirality : 0.042 0.206 1694 Planarity : 0.004 0.041 1938 Dihedral : 4.701 56.357 1472 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.72 % Favored : 94.20 % Rotamer: Outliers : 4.29 % Allowed : 20.69 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: -1.25 (0.24), residues: 1345 helix: 0.85 (0.23), residues: 584 sheet: -2.95 (0.35), residues: 203 loop : -1.78 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 143 HIS 0.003 0.001 HIS B 326 PHE 0.028 0.001 PHE B 442 TYR 0.012 0.001 TYR B 74 ARG 0.004 0.000 ARG A 171 Details of bonding type rmsd hydrogen bonds : bond 0.03146 ( 407) hydrogen bonds : angle 4.44779 ( 1173) covalent geometry : bond 0.00318 (11060) covalent geometry : angle 0.60173 (14981) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 145 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7302 (mtm-85) REVERT: A 34 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8573 (mttp) REVERT: A 262 MET cc_start: 0.8610 (tpp) cc_final: 0.8363 (tpt) REVERT: A 304 HIS cc_start: 0.8206 (OUTLIER) cc_final: 0.7347 (t-90) REVERT: A 414 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7938 (m-30) REVERT: A 453 ASP cc_start: 0.8438 (t0) cc_final: 0.7948 (t0) REVERT: A 537 ARG cc_start: 0.8810 (ttm-80) cc_final: 0.8356 (ttm-80) REVERT: B 214 ILE cc_start: 0.8977 (tp) cc_final: 0.8582 (pt) REVERT: B 234 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8575 (m-80) REVERT: B 280 PHE cc_start: 0.8108 (t80) cc_final: 0.7887 (t80) REVERT: B 396 LYS cc_start: 0.8412 (mmtt) cc_final: 0.7806 (ptpt) REVERT: C 92 TYR cc_start: 0.4823 (m-80) cc_final: 0.4370 (m-80) REVERT: C 144 LYS cc_start: 0.8371 (mtpp) cc_final: 0.7909 (mmmt) REVERT: C 185 ARG cc_start: 0.6296 (ptp-110) cc_final: 0.5879 (ptm160) REVERT: C 195 MET cc_start: 0.5759 (ttt) cc_final: 0.5479 (tmm) REVERT: C 260 PHE cc_start: 0.6400 (t80) cc_final: 0.5851 (m-80) REVERT: C 268 ARG cc_start: 0.6820 (mmm160) cc_final: 0.5860 (ttp-110) REVERT: D 28 ARG cc_start: 0.6971 (OUTLIER) cc_final: 0.5878 (ttm170) outliers start: 52 outliers final: 41 residues processed: 183 average time/residue: 0.2499 time to fit residues: 64.6522 Evaluate side-chains 183 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 136 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain B residue 13 CYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 69 PHE Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 31 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 115 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 5 optimal weight: 0.1980 chunk 125 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 ASN B 174 ASN B 372 ASN ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.186990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 118)---------------| | r_work = 0.3570 r_free = 0.3570 target = 0.134322 restraints weight = 13653.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.124299 restraints weight = 17447.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.125293 restraints weight = 13245.848| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11060 Z= 0.161 Angle : 0.632 12.668 14981 Z= 0.317 Chirality : 0.043 0.211 1694 Planarity : 0.004 0.041 1938 Dihedral : 4.762 53.406 1472 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.32 % Favored : 93.61 % Rotamer: Outliers : 4.45 % Allowed : 21.10 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: -1.25 (0.24), residues: 1345 helix: 0.81 (0.23), residues: 586 sheet: -2.93 (0.36), residues: 198 loop : -1.77 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 143 HIS 0.004 0.001 HIS B 326 PHE 0.024 0.002 PHE B 442 TYR 0.014 0.001 TYR C 218 ARG 0.004 0.000 ARG A 171 Details of bonding type rmsd hydrogen bonds : bond 0.03369 ( 407) hydrogen bonds : angle 4.52967 ( 1173) covalent geometry : bond 0.00391 (11060) covalent geometry : angle 0.63162 (14981) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 143 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8562 (mttp) REVERT: A 262 MET cc_start: 0.8577 (tpp) cc_final: 0.8322 (tpt) REVERT: A 304 HIS cc_start: 0.8166 (OUTLIER) cc_final: 0.7293 (t-90) REVERT: A 414 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7951 (m-30) REVERT: A 453 ASP cc_start: 0.8556 (t0) cc_final: 0.7950 (t0) REVERT: A 528 MET cc_start: 0.6065 (ttm) cc_final: 0.5838 (ttm) REVERT: A 537 ARG cc_start: 0.8643 (ttm-80) cc_final: 0.8267 (ttm-80) REVERT: B 37 ASN cc_start: 0.8655 (OUTLIER) cc_final: 0.8209 (p0) REVERT: B 214 ILE cc_start: 0.9009 (tp) cc_final: 0.8526 (pt) REVERT: B 234 PHE cc_start: 0.8816 (OUTLIER) cc_final: 0.8518 (m-80) REVERT: B 280 PHE cc_start: 0.8071 (t80) cc_final: 0.7482 (t80) REVERT: B 396 LYS cc_start: 0.8364 (mmtt) cc_final: 0.7653 (ptpt) REVERT: C 92 TYR cc_start: 0.4547 (m-80) cc_final: 0.4149 (m-80) REVERT: C 144 LYS cc_start: 0.8415 (mtpp) cc_final: 0.8011 (mmmt) REVERT: C 260 PHE cc_start: 0.6404 (t80) cc_final: 0.5755 (m-80) REVERT: C 268 ARG cc_start: 0.6786 (mmm160) cc_final: 0.5735 (ttp-110) REVERT: D 28 ARG cc_start: 0.6659 (OUTLIER) cc_final: 0.5636 (ttm170) outliers start: 54 outliers final: 42 residues processed: 182 average time/residue: 0.2269 time to fit residues: 58.5214 Evaluate side-chains 183 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 135 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain B residue 13 CYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 37 ASN Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 69 PHE Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 31 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 64 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 128 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 82 optimal weight: 8.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 ASN B 372 ASN ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 GLN ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.185615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.124571 restraints weight = 13402.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.121278 restraints weight = 13765.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.124054 restraints weight = 12162.885| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11060 Z= 0.129 Angle : 0.619 11.401 14981 Z= 0.310 Chirality : 0.042 0.208 1694 Planarity : 0.004 0.041 1938 Dihedral : 4.692 50.738 1472 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.72 % Favored : 94.20 % Rotamer: Outliers : 4.12 % Allowed : 21.93 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: -1.20 (0.24), residues: 1345 helix: 0.83 (0.23), residues: 587 sheet: -2.90 (0.35), residues: 205 loop : -1.69 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 143 HIS 0.003 0.001 HIS B 326 PHE 0.023 0.001 PHE B 442 TYR 0.011 0.001 TYR B 74 ARG 0.004 0.000 ARG A 171 Details of bonding type rmsd hydrogen bonds : bond 0.03117 ( 407) hydrogen bonds : angle 4.47939 ( 1173) covalent geometry : bond 0.00304 (11060) covalent geometry : angle 0.61936 (14981) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 133 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8602 (mttp) REVERT: A 262 MET cc_start: 0.8637 (tpp) cc_final: 0.8381 (tpt) REVERT: A 304 HIS cc_start: 0.8234 (OUTLIER) cc_final: 0.7370 (t-90) REVERT: A 453 ASP cc_start: 0.8393 (t0) cc_final: 0.7986 (t0) REVERT: A 537 ARG cc_start: 0.8840 (ttm-80) cc_final: 0.8454 (ttm-80) REVERT: B 214 ILE cc_start: 0.9021 (tp) cc_final: 0.8572 (pt) REVERT: B 234 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.8514 (m-80) REVERT: C 92 TYR cc_start: 0.5169 (m-80) cc_final: 0.4689 (m-80) REVERT: C 144 LYS cc_start: 0.8451 (mtpp) cc_final: 0.8007 (mmmt) REVERT: C 195 MET cc_start: 0.6239 (ttt) cc_final: 0.5604 (tmm) REVERT: C 260 PHE cc_start: 0.6209 (t80) cc_final: 0.5831 (m-80) REVERT: C 268 ARG cc_start: 0.6812 (mmm160) cc_final: 0.5774 (mtm110) REVERT: D 28 ARG cc_start: 0.6891 (OUTLIER) cc_final: 0.5618 (ttm170) outliers start: 50 outliers final: 40 residues processed: 172 average time/residue: 0.2272 time to fit residues: 56.1925 Evaluate side-chains 173 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 129 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain B residue 13 CYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 69 PHE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 31 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 97 optimal weight: 0.0570 chunk 20 optimal weight: 0.7980 chunk 82 optimal weight: 0.0970 chunk 98 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 56 optimal weight: 8.9990 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 ASN B 174 ASN B 372 ASN ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.188023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.144271 restraints weight = 13507.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.136512 restraints weight = 20032.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.132679 restraints weight = 19529.491| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11060 Z= 0.114 Angle : 0.611 10.798 14981 Z= 0.305 Chirality : 0.042 0.201 1694 Planarity : 0.004 0.041 1938 Dihedral : 4.532 46.080 1472 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.87 % Favored : 94.05 % Rotamer: Outliers : 3.71 % Allowed : 22.26 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: -1.04 (0.24), residues: 1345 helix: 0.95 (0.23), residues: 582 sheet: -2.68 (0.36), residues: 205 loop : -1.63 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 143 HIS 0.003 0.001 HIS A 364 PHE 0.024 0.001 PHE B 442 TYR 0.009 0.001 TYR B 74 ARG 0.005 0.000 ARG A 171 Details of bonding type rmsd hydrogen bonds : bond 0.02939 ( 407) hydrogen bonds : angle 4.39640 ( 1173) covalent geometry : bond 0.00262 (11060) covalent geometry : angle 0.61056 (14981) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 136 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8599 (mttp) REVERT: A 262 MET cc_start: 0.8587 (tpp) cc_final: 0.8337 (tpt) REVERT: A 304 HIS cc_start: 0.8187 (OUTLIER) cc_final: 0.7432 (t-90) REVERT: A 440 ASP cc_start: 0.6813 (t0) cc_final: 0.6601 (t0) REVERT: A 453 ASP cc_start: 0.8355 (t0) cc_final: 0.7930 (t0) REVERT: A 537 ARG cc_start: 0.8845 (ttm-80) cc_final: 0.8455 (ttm-80) REVERT: B 214 ILE cc_start: 0.8995 (tp) cc_final: 0.8546 (pt) REVERT: B 234 PHE cc_start: 0.8823 (OUTLIER) cc_final: 0.8550 (m-80) REVERT: B 280 PHE cc_start: 0.8211 (t80) cc_final: 0.7624 (t80) REVERT: C 92 TYR cc_start: 0.5258 (m-80) cc_final: 0.4763 (m-80) REVERT: C 144 LYS cc_start: 0.8346 (mtpp) cc_final: 0.7962 (mmmt) REVERT: C 195 MET cc_start: 0.6186 (ttt) cc_final: 0.5597 (tmm) REVERT: C 260 PHE cc_start: 0.6004 (t80) cc_final: 0.5721 (m-80) REVERT: C 268 ARG cc_start: 0.6831 (mmm160) cc_final: 0.5910 (mtm110) REVERT: D 28 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6287 (ttm170) outliers start: 45 outliers final: 35 residues processed: 170 average time/residue: 0.2401 time to fit residues: 58.7913 Evaluate side-chains 166 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 127 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain B residue 13 CYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 69 PHE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 28 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 3 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 15 optimal weight: 0.3980 chunk 30 optimal weight: 0.2980 chunk 44 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 ASN B 372 ASN ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.190642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.141003 restraints weight = 13452.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.139839 restraints weight = 19251.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.140502 restraints weight = 16673.076| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11060 Z= 0.118 Angle : 0.609 10.406 14981 Z= 0.305 Chirality : 0.042 0.200 1694 Planarity : 0.004 0.041 1938 Dihedral : 4.472 43.038 1472 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.50 % Favored : 94.42 % Rotamer: Outliers : 3.22 % Allowed : 22.51 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: -1.01 (0.24), residues: 1345 helix: 0.96 (0.23), residues: 580 sheet: -2.56 (0.36), residues: 205 loop : -1.63 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP C 143 HIS 0.003 0.001 HIS B 326 PHE 0.024 0.001 PHE B 442 TYR 0.010 0.001 TYR B 74 ARG 0.005 0.000 ARG A 171 Details of bonding type rmsd hydrogen bonds : bond 0.02943 ( 407) hydrogen bonds : angle 4.41676 ( 1173) covalent geometry : bond 0.00273 (11060) covalent geometry : angle 0.60863 (14981) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 1.205 Fit side-chains revert: symmetry clash REVERT: A 34 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8584 (mttp) REVERT: A 262 MET cc_start: 0.8604 (tpp) cc_final: 0.8352 (tpt) REVERT: A 304 HIS cc_start: 0.8192 (OUTLIER) cc_final: 0.7444 (t-90) REVERT: A 453 ASP cc_start: 0.8324 (t0) cc_final: 0.7930 (t0) REVERT: A 537 ARG cc_start: 0.8907 (ttm-80) cc_final: 0.8594 (ttm-80) REVERT: B 214 ILE cc_start: 0.9024 (tp) cc_final: 0.8568 (pt) REVERT: B 223 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7199 (mm-30) REVERT: B 234 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.8526 (m-80) REVERT: C 92 TYR cc_start: 0.5341 (m-80) cc_final: 0.4820 (m-80) REVERT: C 144 LYS cc_start: 0.8311 (mtpp) cc_final: 0.7971 (mmmt) REVERT: C 195 MET cc_start: 0.6161 (ttt) cc_final: 0.5581 (tmm) REVERT: C 260 PHE cc_start: 0.5952 (t80) cc_final: 0.5723 (m-80) REVERT: C 268 ARG cc_start: 0.6875 (mmm160) cc_final: 0.5958 (mtm110) REVERT: D 28 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6602 (ttm170) outliers start: 39 outliers final: 32 residues processed: 160 average time/residue: 0.2239 time to fit residues: 51.5208 Evaluate side-chains 161 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain B residue 13 CYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 69 PHE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 28 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 41 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 48 optimal weight: 6.9990 chunk 126 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 108 optimal weight: 0.0060 chunk 52 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 ASN B 372 ASN ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.187830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 146)---------------| | r_work = 0.3554 r_free = 0.3554 target = 0.133005 restraints weight = 13316.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 76)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.127403 restraints weight = 16006.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.123686 restraints weight = 12506.583| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11060 Z= 0.119 Angle : 0.609 10.051 14981 Z= 0.305 Chirality : 0.042 0.192 1694 Planarity : 0.004 0.042 1938 Dihedral : 4.418 38.317 1472 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.87 % Favored : 94.05 % Rotamer: Outliers : 3.13 % Allowed : 22.67 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: -0.95 (0.24), residues: 1345 helix: 0.99 (0.23), residues: 580 sheet: -2.48 (0.37), residues: 206 loop : -1.59 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP C 143 HIS 0.003 0.001 HIS B 326 PHE 0.041 0.002 PHE B 280 TYR 0.012 0.001 TYR B 74 ARG 0.005 0.000 ARG A 171 Details of bonding type rmsd hydrogen bonds : bond 0.02924 ( 407) hydrogen bonds : angle 4.42055 ( 1173) covalent geometry : bond 0.00278 (11060) covalent geometry : angle 0.60871 (14981) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4293.56 seconds wall clock time: 75 minutes 17.52 seconds (4517.52 seconds total)