Starting phenix.real_space_refine on Tue Jun 10 04:34:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c5c_45214/06_2025/9c5c_45214.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c5c_45214/06_2025/9c5c_45214.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c5c_45214/06_2025/9c5c_45214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c5c_45214/06_2025/9c5c_45214.map" model { file = "/net/cci-nas-00/data/ceres_data/9c5c_45214/06_2025/9c5c_45214.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c5c_45214/06_2025/9c5c_45214.cif" } resolution = 3.6 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= 0.025 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 63 5.16 5 C 7280 2.51 5 N 1928 2.21 5 O 2093 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 11364 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 4606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4606 Classifications: {'peptide': 584} Link IDs: {'PTRANS': 20, 'TRANS': 563} Chain: "B" Number of atoms: 4530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4530 Classifications: {'peptide': 570} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 545} Chain breaks: 1 Chain: "M" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1008 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 117} Chain: "S" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1220 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 148} Time building chain proxies: 8.94, per 1000 atoms: 0.79 Number of scatterers: 11364 At special positions: 0 Unit cell: (97.468, 90.86, 132.16, 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 63 16.00 O 2093 8.00 N 1928 7.00 C 7280 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: 3.22 Conformation dependent library (CDL) restraints added in 1.8 seconds 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2766 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 4 sheets defined 78.4% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'D' and resid 18 through 28 Processing helix chain 'D' and resid 31 through 47 Processing helix chain 'D' and resid 51 through 69 removed outlier: 3.535A pdb=" N LYS D 55 " --> pdb=" O ASN D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 74 No H-bonds generated for 'chain 'D' and resid 72 through 74' Processing helix chain 'D' and resid 75 through 84 Processing helix chain 'D' and resid 87 through 100 removed outlier: 3.880A pdb=" N ILE D 93 " --> pdb=" O THR D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 111 Processing helix chain 'D' and resid 112 through 122 Processing helix chain 'D' and resid 124 through 136 Processing helix chain 'D' and resid 140 through 155 removed outlier: 5.182A pdb=" N ASN D 149 " --> pdb=" O ARG D 145 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ASP D 150 " --> pdb=" O ASP D 146 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR D 153 " --> pdb=" O ASN D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 177 removed outlier: 3.670A pdb=" N ARG D 163 " --> pdb=" O LYS D 159 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU D 168 " --> pdb=" O LYS D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 192 Proline residue: D 183 - end of helix Proline residue: D 186 - end of helix Processing helix chain 'D' and resid 196 through 212 Processing helix chain 'D' and resid 214 through 220 removed outlier: 3.609A pdb=" N LEU D 219 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N SER D 220 " --> pdb=" O ASN D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 232 Processing helix chain 'D' and resid 234 through 249 removed outlier: 3.682A pdb=" N LEU D 238 " --> pdb=" O ASN D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 270 removed outlier: 4.140A pdb=" N GLY D 256 " --> pdb=" O GLU D 252 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLU D 261 " --> pdb=" O LYS D 257 " (cutoff:3.500A) Proline residue: D 262 - end of helix Processing helix chain 'D' and resid 272 through 291 Processing helix chain 'D' and resid 297 through 314 removed outlier: 3.874A pdb=" N ASP D 314 " --> pdb=" O ILE D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 334 Processing helix chain 'D' and resid 334 through 339 removed outlier: 3.896A pdb=" N VAL D 338 " --> pdb=" O HIS D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 349 Processing helix chain 'D' and resid 353 through 368 Processing helix chain 'D' and resid 372 through 387 Processing helix chain 'D' and resid 389 through 406 Processing helix chain 'D' and resid 414 through 427 Processing helix chain 'D' and resid 433 through 448 removed outlier: 3.526A pdb=" N VAL D 448 " --> pdb=" O VAL D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 465 Processing helix chain 'D' and resid 465 through 470 Processing helix chain 'D' and resid 477 through 492 removed outlier: 3.953A pdb=" N VAL D 481 " --> pdb=" O GLY D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 496 Processing helix chain 'D' and resid 498 through 507 Processing helix chain 'D' and resid 508 through 514 removed outlier: 3.798A pdb=" N THR D 513 " --> pdb=" O ARG D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 541 removed outlier: 3.714A pdb=" N LYS D 528 " --> pdb=" O GLN D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 555 Processing helix chain 'D' and resid 557 through 562 Processing helix chain 'D' and resid 565 through 588 Processing helix chain 'D' and resid 592 through 600 removed outlier: 3.820A pdb=" N PHE D 600 " --> pdb=" O VAL D 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 55 through 73 Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 through 78' Processing helix chain 'B' and resid 79 through 86 removed outlier: 3.835A pdb=" N LYS B 85 " --> pdb=" O PRO B 81 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 106 Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 116 through 124 removed outlier: 3.641A pdb=" N PHE B 120 " --> pdb=" O SER B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 142 Processing helix chain 'B' and resid 147 through 161 Processing helix chain 'B' and resid 163 through 181 Processing helix chain 'B' and resid 184 through 197 removed outlier: 3.743A pdb=" N LYS B 197 " --> pdb=" O GLU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 215 removed outlier: 4.346A pdb=" N SER B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 225 removed outlier: 3.684A pdb=" N ASN B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 233 Processing helix chain 'B' and resid 237 through 256 Processing helix chain 'B' and resid 295 through 305 removed outlier: 3.661A pdb=" N ILE B 301 " --> pdb=" O HIS B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 310 removed outlier: 3.761A pdb=" N GLN B 309 " --> pdb=" O PRO B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 327 Processing helix chain 'B' and resid 331 through 333 No H-bonds generated for 'chain 'B' and resid 331 through 333' Processing helix chain 'B' and resid 334 through 342 removed outlier: 4.498A pdb=" N SER B 338 " --> pdb=" O ILE B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 345 No H-bonds generated for 'chain 'B' and resid 343 through 345' Processing helix chain 'B' and resid 346 through 364 removed outlier: 3.622A pdb=" N ILE B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN B 363 " --> pdb=" O THR B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 376 Processing helix chain 'B' and resid 382 through 396 Processing helix chain 'B' and resid 401 through 414 removed outlier: 4.256A pdb=" N LYS B 414 " --> pdb=" O GLN B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 435 removed outlier: 3.674A pdb=" N GLY B 429 " --> pdb=" O ILE B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 448 removed outlier: 3.650A pdb=" N CYS B 448 " --> pdb=" O ASN B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 452 Processing helix chain 'B' and resid 454 through 472 removed outlier: 3.727A pdb=" N VAL B 463 " --> pdb=" O ALA B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 487 removed outlier: 5.262A pdb=" N HIS B 482 " --> pdb=" O GLU B 478 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS B 485 " --> pdb=" O LYS B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 490 No H-bonds generated for 'chain 'B' and resid 488 through 490' Processing helix chain 'B' and resid 492 through 506 Processing helix chain 'B' and resid 513 through 525 removed outlier: 3.737A pdb=" N LYS B 523 " --> pdb=" O ARG B 519 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER B 524 " --> pdb=" O LYS B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 528 No H-bonds generated for 'chain 'B' and resid 526 through 528' Processing helix chain 'B' and resid 529 through 564 removed outlier: 3.568A pdb=" N LEU B 534 " --> pdb=" O ASP B 530 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN B 535 " --> pdb=" O LEU B 531 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR B 546 " --> pdb=" O LYS B 542 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LYS B 549 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N GLN B 550 " --> pdb=" O THR B 546 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU B 553 " --> pdb=" O LYS B 549 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N LEU B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR B 564 " --> pdb=" O ASN B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 582 Processing helix chain 'B' and resid 583 through 587 Processing helix chain 'B' and resid 588 through 593 removed outlier: 3.679A pdb=" N TYR B 593 " --> pdb=" O ALA B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 599 Processing helix chain 'B' and resid 611 through 617 removed outlier: 3.749A pdb=" N HIS B 616 " --> pdb=" O ASP B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 627 Processing helix chain 'B' and resid 645 through 650 removed outlier: 4.034A pdb=" N ARG B 649 " --> pdb=" O ASP B 645 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN B 650 " --> pdb=" O PRO B 646 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 645 through 650' Processing helix chain 'M' and resid 25 through 28 Processing helix chain 'M' and resid 29 through 39 Processing helix chain 'M' and resid 75 through 95 Processing helix chain 'M' and resid 98 through 105 Processing helix chain 'M' and resid 105 through 116 Processing helix chain 'S' and resid 24 through 41 removed outlier: 3.815A pdb=" N LYS S 41 " --> pdb=" O HIS S 37 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 101 Processing helix chain 'S' and resid 105 through 112 Processing helix chain 'S' and resid 112 through 123 Processing helix chain 'S' and resid 133 through 151 Processing sheet with id=AA1, first strand: chain 'M' and resid 14 through 19 removed outlier: 3.823A pdb=" N SER M 4 " --> pdb=" O VAL M 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 117 through 118 removed outlier: 3.609A pdb=" N ASP M 118 " --> pdb=" O PHE M 121 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 14 through 19 removed outlier: 6.314A pdb=" N ILE S 7 " --> pdb=" O ARG S 15 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER S 17 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE S 5 " --> pdb=" O SER S 17 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N PHE S 19 " --> pdb=" O LYS S 3 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N LYS S 3 " --> pdb=" O PHE S 19 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N CYS S 76 " --> pdb=" O LYS S 3 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ILE S 5 " --> pdb=" O VAL S 74 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL S 74 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE S 7 " --> pdb=" O TYR S 72 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TYR S 72 " --> pdb=" O ILE S 7 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 124 through 125 749 hydrogen bonds defined for protein. 2175 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: 3.88 Time building geometry restraints manager: 3.79 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: 3690 1.34 - 1.46: 2254 1.46 - 1.58: 5513 1.58 - 1.70: 0 1.70 - 1.82: 102 Bond restraints: 11559 Sorted by residual: bond pdb=" N MET D 459 " pdb=" CA MET D 459 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.23e-02 6.61e+03 4.92e+00 bond pdb=" N PHE D 174 " pdb=" CA PHE D 174 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.20e-02 6.94e+03 4.53e+00 bond pdb=" CB ASN D 408 " pdb=" CG ASN D 408 " ideal model delta sigma weight residual 1.516 1.554 -0.038 2.50e-02 1.60e+03 2.36e+00 bond pdb=" CG LEU D 244 " pdb=" CD1 LEU D 244 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.86e+00 bond pdb=" C PHE D 174 " pdb=" O PHE D 174 " ideal model delta sigma weight residual 1.236 1.251 -0.015 1.15e-02 7.56e+03 1.74e+00 ... (remaining 11554 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 15289 2.07 - 4.13: 287 4.13 - 6.20: 43 6.20 - 8.27: 16 8.27 - 10.34: 5 Bond angle restraints: 15640 Sorted by residual: angle pdb=" CB LYS D 257 " pdb=" CG LYS D 257 " pdb=" CD LYS D 257 " ideal model delta sigma weight residual 111.30 119.26 -7.96 2.30e+00 1.89e-01 1.20e+01 angle pdb=" C ASN B 547 " pdb=" CA ASN B 547 " pdb=" CB ASN B 547 " ideal model delta sigma weight residual 111.35 117.14 -5.79 1.72e+00 3.38e-01 1.13e+01 angle pdb=" CA ARG B 227 " pdb=" CB ARG B 227 " pdb=" CG ARG B 227 " ideal model delta sigma weight residual 114.10 120.32 -6.22 2.00e+00 2.50e-01 9.66e+00 angle pdb=" CA GLN B 601 " pdb=" CB GLN B 601 " pdb=" CG GLN B 601 " ideal model delta sigma weight residual 114.10 120.25 -6.15 2.00e+00 2.50e-01 9.45e+00 angle pdb=" CA ASN D 408 " pdb=" CB ASN D 408 " pdb=" CG ASN D 408 " ideal model delta sigma weight residual 112.60 115.57 -2.97 1.00e+00 1.00e+00 8.79e+00 ... (remaining 15635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 6313 17.62 - 35.25: 616 35.25 - 52.87: 163 52.87 - 70.49: 35 70.49 - 88.12: 12 Dihedral angle restraints: 7139 sinusoidal: 2902 harmonic: 4237 Sorted by residual: dihedral pdb=" CA SER M 22 " pdb=" C SER M 22 " pdb=" N VAL M 23 " pdb=" CA VAL M 23 " ideal model delta harmonic sigma weight residual -180.00 -160.79 -19.21 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA ASP B 161 " pdb=" C ASP B 161 " pdb=" N LEU B 162 " pdb=" CA LEU B 162 " ideal model delta harmonic sigma weight residual -180.00 -162.52 -17.48 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA THR D 112 " pdb=" C THR D 112 " pdb=" N THR D 113 " pdb=" CA THR D 113 " ideal model delta harmonic sigma weight residual -180.00 -163.09 -16.91 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 7136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1247 0.037 - 0.075: 459 0.075 - 0.112: 110 0.112 - 0.149: 27 0.149 - 0.186: 7 Chirality restraints: 1850 Sorted by residual: chirality pdb=" CB ILE M 2 " pdb=" CA ILE M 2 " pdb=" CG1 ILE M 2 " pdb=" CG2 ILE M 2 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.69e-01 chirality pdb=" CA ASN D 408 " pdb=" N ASN D 408 " pdb=" C ASN D 408 " pdb=" CB ASN D 408 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.62e-01 chirality pdb=" CB THR S 35 " pdb=" CA THR S 35 " pdb=" OG1 THR S 35 " pdb=" CG2 THR S 35 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.39e-01 ... (remaining 1847 not shown) Planarity restraints: 1971 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 475 " -0.251 9.50e-02 1.11e+02 1.13e-01 8.38e+00 pdb=" NE ARG D 475 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG D 475 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG D 475 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG D 475 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 212 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.97e+00 pdb=" CD GLU B 212 " 0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU B 212 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU B 212 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE M 32 " 0.008 2.00e-02 2.50e+03 1.67e-02 4.86e+00 pdb=" CG PHE M 32 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE M 32 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE M 32 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE M 32 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE M 32 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE M 32 " -0.001 2.00e-02 2.50e+03 ... (remaining 1968 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1057 2.74 - 3.28: 12707 3.28 - 3.82: 19717 3.82 - 4.36: 23390 4.36 - 4.90: 38622 Nonbonded interactions: 95493 Sorted by model distance: nonbonded pdb=" O VAL D 423 " pdb=" OG1 THR D 426 " model vdw 2.202 3.040 nonbonded pdb=" NE2 GLN B 175 " pdb=" OE1 GLU B 213 " model vdw 2.204 3.120 nonbonded pdb=" OE2 GLU B 391 " pdb=" OG SER B 609 " model vdw 2.214 3.040 nonbonded pdb=" OG SER S 24 " pdb=" OG1 THR S 27 " model vdw 2.216 3.040 nonbonded pdb=" O THR D 133 " pdb=" OG SER D 136 " model vdw 2.221 3.040 ... (remaining 95488 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: 3.410 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: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 32.800 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.010 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5917 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 : 0.004 0.045 11559 Z= 0.169 Angle : 0.734 10.337 15640 Z= 0.400 Chirality : 0.042 0.186 1850 Planarity : 0.005 0.113 1971 Dihedral : 15.741 88.116 4373 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 20.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.08 % Allowed : 19.66 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.23), residues: 1419 helix: 0.60 (0.16), residues: 976 sheet: 0.83 (0.83), residues: 42 loop : 0.67 (0.35), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 74 HIS 0.008 0.001 HIS S 117 PHE 0.036 0.002 PHE M 32 TYR 0.023 0.002 TYR D 161 ARG 0.014 0.001 ARG D 475 Details of bonding type rmsd hydrogen bonds : bond 0.18433 ( 749) hydrogen bonds : angle 6.65637 ( 2175) covalent geometry : bond 0.00365 (11559) covalent geometry : angle 0.73447 (15640) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 419 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 83 MET cc_start: 0.5285 (ttp) cc_final: 0.4972 (ptt) REVERT: D 91 LYS cc_start: 0.7665 (mttt) cc_final: 0.7436 (mttt) REVERT: D 92 ARG cc_start: 0.6693 (ttt180) cc_final: 0.6239 (ttt180) REVERT: D 168 LEU cc_start: 0.6675 (mt) cc_final: 0.5961 (mt) REVERT: D 177 TYR cc_start: 0.5552 (t80) cc_final: 0.5223 (t80) REVERT: D 180 SER cc_start: 0.5130 (p) cc_final: 0.4862 (p) REVERT: D 194 ASP cc_start: 0.5509 (t70) cc_final: 0.4804 (t70) REVERT: D 301 ILE cc_start: 0.7921 (mt) cc_final: 0.7589 (tt) REVERT: D 308 LEU cc_start: 0.6941 (mt) cc_final: 0.6527 (mt) REVERT: D 321 TYR cc_start: 0.5814 (t80) cc_final: 0.5433 (t80) REVERT: D 327 MET cc_start: 0.5209 (mtp) cc_final: 0.4991 (ttm) REVERT: D 356 ILE cc_start: 0.6555 (tp) cc_final: 0.6316 (tp) REVERT: D 418 TYR cc_start: 0.5426 (t80) cc_final: 0.5210 (t80) REVERT: D 442 LEU cc_start: 0.7351 (mt) cc_final: 0.7116 (mt) REVERT: D 443 ASP cc_start: 0.6298 (t70) cc_final: 0.5286 (t0) REVERT: D 475 ARG cc_start: 0.6986 (mmm160) cc_final: 0.6736 (mmm160) REVERT: D 480 GLU cc_start: 0.6293 (tp30) cc_final: 0.5700 (tp30) REVERT: D 567 GLU cc_start: 0.6795 (tp30) cc_final: 0.6065 (tp30) REVERT: D 584 LYS cc_start: 0.7467 (mttt) cc_final: 0.7217 (mttt) REVERT: B 59 LYS cc_start: 0.7795 (mtmt) cc_final: 0.7565 (mtmm) REVERT: B 64 LYS cc_start: 0.8490 (mttm) cc_final: 0.8255 (mttt) REVERT: B 83 VAL cc_start: 0.7239 (t) cc_final: 0.7038 (p) REVERT: B 153 LEU cc_start: 0.8345 (tp) cc_final: 0.8066 (tt) REVERT: B 194 LYS cc_start: 0.7713 (mttt) cc_final: 0.7496 (mtpp) REVERT: B 243 VAL cc_start: 0.7522 (t) cc_final: 0.7315 (m) REVERT: B 302 ARG cc_start: 0.7689 (tpt90) cc_final: 0.7168 (tpt90) REVERT: B 420 PHE cc_start: 0.7194 (t80) cc_final: 0.6627 (t80) REVERT: B 426 GLN cc_start: 0.8399 (mm-40) cc_final: 0.7963 (mm110) REVERT: B 523 LYS cc_start: 0.7966 (mttt) cc_final: 0.7736 (mmtm) REVERT: B 526 THR cc_start: 0.9012 (p) cc_final: 0.8573 (m) REVERT: B 556 GLN cc_start: 0.7756 (tm-30) cc_final: 0.7548 (tm-30) REVERT: B 559 LEU cc_start: 0.7845 (mt) cc_final: 0.7641 (mm) REVERT: B 564 TYR cc_start: 0.7669 (m-80) cc_final: 0.7416 (m-10) REVERT: B 577 ILE cc_start: 0.8607 (mt) cc_final: 0.8325 (mm) REVERT: B 593 TYR cc_start: 0.7487 (m-80) cc_final: 0.6243 (m-80) REVERT: B 618 GLN cc_start: 0.6457 (tt0) cc_final: 0.6097 (tt0) REVERT: B 650 ASN cc_start: 0.7195 (m110) cc_final: 0.6833 (p0) REVERT: S 115 LYS cc_start: 0.8445 (ttpt) cc_final: 0.8057 (ttpt) outliers start: 1 outliers final: 0 residues processed: 419 average time/residue: 0.2649 time to fit residues: 150.9301 Evaluate side-chains 363 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 66 GLN D 100 GLN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN D 500 HIS D 559 GLN D 586 GLN B 91 ASN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 GLN B 579 GLN ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 HIS ** M 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 ASN S 30 GLN ** S 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.148758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.130535 restraints weight = 22573.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.134840 restraints weight = 13278.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.137920 restraints weight = 8618.277| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11559 Z= 0.193 Angle : 0.731 11.805 15640 Z= 0.377 Chirality : 0.045 0.217 1850 Planarity : 0.005 0.049 1971 Dihedral : 4.683 24.165 1535 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.99 % Allowed : 17.07 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.22), residues: 1419 helix: 0.74 (0.16), residues: 1003 sheet: 0.63 (0.83), residues: 44 loop : 0.75 (0.35), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 236 HIS 0.022 0.002 HIS S 117 PHE 0.025 0.002 PHE D 245 TYR 0.024 0.002 TYR B 101 ARG 0.005 0.001 ARG D 475 Details of bonding type rmsd hydrogen bonds : bond 0.05192 ( 749) hydrogen bonds : angle 5.19018 ( 2175) covalent geometry : bond 0.00408 (11559) covalent geometry : angle 0.73124 (15640) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 387 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 92 ARG cc_start: 0.7996 (ttt180) cc_final: 0.7427 (ttt180) REVERT: D 93 ILE cc_start: 0.8644 (mm) cc_final: 0.8029 (tp) REVERT: D 170 MET cc_start: 0.7588 (mmm) cc_final: 0.7291 (mmm) REVERT: D 177 TYR cc_start: 0.7039 (t80) cc_final: 0.6130 (t80) REVERT: D 194 ASP cc_start: 0.6665 (t70) cc_final: 0.6461 (t70) REVERT: D 207 ILE cc_start: 0.8210 (tt) cc_final: 0.7796 (mt) REVERT: D 242 ILE cc_start: 0.8763 (mm) cc_final: 0.8337 (mm) REVERT: D 245 PHE cc_start: 0.8189 (m-80) cc_final: 0.7611 (m-80) REVERT: D 257 LYS cc_start: 0.8545 (tppt) cc_final: 0.8218 (tppt) REVERT: D 306 GLN cc_start: 0.8610 (tp-100) cc_final: 0.8186 (tp-100) REVERT: D 307 LYS cc_start: 0.8669 (mmtm) cc_final: 0.8395 (mmtm) REVERT: D 308 LEU cc_start: 0.8593 (mt) cc_final: 0.8386 (mt) REVERT: D 314 ASP cc_start: 0.6958 (t0) cc_final: 0.6582 (t0) REVERT: D 341 HIS cc_start: 0.6943 (m-70) cc_final: 0.6508 (m-70) REVERT: D 371 LYS cc_start: 0.8102 (ttpp) cc_final: 0.7686 (ttpp) REVERT: D 372 ASN cc_start: 0.8083 (p0) cc_final: 0.7813 (p0) REVERT: D 375 GLU cc_start: 0.8196 (mp0) cc_final: 0.7626 (pm20) REVERT: D 379 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7533 (mppt) REVERT: D 395 GLU cc_start: 0.8308 (pt0) cc_final: 0.7904 (pt0) REVERT: D 416 GLU cc_start: 0.7879 (tt0) cc_final: 0.7613 (mm-30) REVERT: D 442 LEU cc_start: 0.8761 (mt) cc_final: 0.8493 (mt) REVERT: D 443 ASP cc_start: 0.8254 (t70) cc_final: 0.7917 (t0) REVERT: D 449 LYS cc_start: 0.8088 (tttt) cc_final: 0.7831 (tttt) REVERT: D 523 VAL cc_start: 0.8011 (t) cc_final: 0.7653 (p) REVERT: D 535 GLN cc_start: 0.7367 (OUTLIER) cc_final: 0.6908 (tp-100) REVERT: D 547 GLN cc_start: 0.8588 (tp-100) cc_final: 0.8017 (tp-100) REVERT: B 50 MET cc_start: 0.7034 (tpp) cc_final: 0.6660 (tpp) REVERT: B 59 LYS cc_start: 0.8417 (mtmt) cc_final: 0.7532 (mmmt) REVERT: B 63 MET cc_start: 0.7964 (mmm) cc_final: 0.7500 (mmm) REVERT: B 83 VAL cc_start: 0.7779 (t) cc_final: 0.7450 (p) REVERT: B 87 VAL cc_start: 0.8787 (m) cc_final: 0.8455 (t) REVERT: B 97 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7441 (mm) REVERT: B 121 GLN cc_start: 0.8366 (tt0) cc_final: 0.8161 (tp40) REVERT: B 125 LYS cc_start: 0.8686 (mmtp) cc_final: 0.8271 (mmtm) REVERT: B 169 ASN cc_start: 0.8369 (m-40) cc_final: 0.7936 (m-40) REVERT: B 190 GLU cc_start: 0.8229 (tp30) cc_final: 0.8010 (tp30) REVERT: B 209 MET cc_start: 0.7947 (ttm) cc_final: 0.7292 (ttm) REVERT: B 243 VAL cc_start: 0.7194 (t) cc_final: 0.6893 (m) REVERT: B 255 GLN cc_start: 0.7763 (mm110) cc_final: 0.7491 (mm110) REVERT: B 302 ARG cc_start: 0.8344 (tpt90) cc_final: 0.8048 (tpp80) REVERT: B 312 ASN cc_start: 0.7997 (t0) cc_final: 0.7675 (t0) REVERT: B 317 MET cc_start: 0.7356 (tpp) cc_final: 0.7016 (tpp) REVERT: B 346 ASN cc_start: 0.7281 (p0) cc_final: 0.7044 (p0) REVERT: B 424 THR cc_start: 0.8393 (m) cc_final: 0.8121 (m) REVERT: B 426 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8278 (mm110) REVERT: B 503 ILE cc_start: 0.8371 (tt) cc_final: 0.8095 (tt) REVERT: B 523 LYS cc_start: 0.8621 (mttt) cc_final: 0.8007 (mmtm) REVERT: B 531 LEU cc_start: 0.8314 (tp) cc_final: 0.8038 (mp) REVERT: B 538 ASN cc_start: 0.7056 (m110) cc_final: 0.6837 (m110) REVERT: B 556 GLN cc_start: 0.8171 (tm130) cc_final: 0.7688 (tm-30) REVERT: B 564 TYR cc_start: 0.8203 (m-80) cc_final: 0.7777 (m-10) REVERT: B 565 ASP cc_start: 0.8064 (t70) cc_final: 0.7862 (t70) REVERT: B 573 ARG cc_start: 0.7907 (mmt90) cc_final: 0.7655 (tpp-160) REVERT: B 579 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.6799 (tp-100) REVERT: B 601 GLN cc_start: 0.8300 (tm-30) cc_final: 0.8062 (tm-30) REVERT: B 624 HIS cc_start: 0.8306 (t-90) cc_final: 0.8043 (t70) REVERT: M 1 MET cc_start: 0.5422 (mmm) cc_final: 0.4833 (mmm) REVERT: M 17 GLU cc_start: 0.5734 (OUTLIER) cc_final: 0.5462 (tt0) REVERT: M 43 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8186 (mm-30) REVERT: M 61 ARG cc_start: 0.7068 (ptm160) cc_final: 0.6638 (ptm160) REVERT: M 116 MET cc_start: 0.7062 (tpp) cc_final: 0.6674 (tpp) REVERT: S 1 MET cc_start: 0.6836 (OUTLIER) cc_final: 0.6617 (tpt) REVERT: S 93 PHE cc_start: 0.7429 (t80) cc_final: 0.7169 (t80) REVERT: S 96 THR cc_start: 0.9006 (m) cc_final: 0.8711 (p) REVERT: S 115 LYS cc_start: 0.8677 (ttpt) cc_final: 0.8066 (ttpt) outliers start: 51 outliers final: 25 residues processed: 411 average time/residue: 0.2785 time to fit residues: 158.7035 Evaluate side-chains 407 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 376 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 100 GLN Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 383 HIS Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 522 TYR Chi-restraints excluded: chain D residue 535 GLN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 355 GLN Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 579 GLN Chi-restraints excluded: chain B residue 598 PHE Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 10 CYS Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 38 LYS Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 51 THR Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain M residue 97 CYS Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 89 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 85 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 57 optimal weight: 0.3980 chunk 88 optimal weight: 0.2980 chunk 124 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 583 GLN D 586 GLN B 363 GLN ** B 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 638 ASN B 650 ASN ** M 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.149878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.131402 restraints weight = 22873.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.135862 restraints weight = 13434.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.138869 restraints weight = 8606.373| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11559 Z= 0.151 Angle : 0.681 12.306 15640 Z= 0.342 Chirality : 0.043 0.273 1850 Planarity : 0.004 0.048 1971 Dihedral : 4.561 24.472 1535 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.84 % Allowed : 19.58 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.22), residues: 1419 helix: 0.93 (0.16), residues: 998 sheet: 0.72 (0.85), residues: 45 loop : 0.66 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 236 HIS 0.006 0.001 HIS B 223 PHE 0.023 0.002 PHE D 226 TYR 0.023 0.001 TYR B 101 ARG 0.007 0.001 ARG D 447 Details of bonding type rmsd hydrogen bonds : bond 0.04633 ( 749) hydrogen bonds : angle 4.98053 ( 2175) covalent geometry : bond 0.00327 (11559) covalent geometry : angle 0.68059 (15640) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 388 time to evaluate : 1.306 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: D 32 GLU cc_start: 0.7912 (pm20) cc_final: 0.7214 (pm20) REVERT: D 59 VAL cc_start: 0.6517 (OUTLIER) cc_final: 0.6093 (m) REVERT: D 67 MET cc_start: 0.5821 (ttt) cc_final: 0.5455 (tpt) REVERT: D 92 ARG cc_start: 0.7978 (ttt180) cc_final: 0.7345 (ttt180) REVERT: D 93 ILE cc_start: 0.8661 (mm) cc_final: 0.8053 (tp) REVERT: D 118 LYS cc_start: 0.8614 (ptpp) cc_final: 0.8266 (ptpp) REVERT: D 170 MET cc_start: 0.7489 (mmm) cc_final: 0.7131 (mmm) REVERT: D 177 TYR cc_start: 0.6947 (t80) cc_final: 0.6087 (t80) REVERT: D 182 ARG cc_start: 0.7632 (mmm160) cc_final: 0.7374 (mmm160) REVERT: D 207 ILE cc_start: 0.8231 (tt) cc_final: 0.7745 (mt) REVERT: D 242 ILE cc_start: 0.8675 (mm) cc_final: 0.8337 (mm) REVERT: D 245 PHE cc_start: 0.8086 (m-80) cc_final: 0.7734 (m-80) REVERT: D 257 LYS cc_start: 0.8461 (tppt) cc_final: 0.8197 (tppt) REVERT: D 307 LYS cc_start: 0.8640 (mmtm) cc_final: 0.8379 (mmtm) REVERT: D 314 ASP cc_start: 0.6970 (t0) cc_final: 0.6604 (t0) REVERT: D 345 ILE cc_start: 0.9005 (mt) cc_final: 0.8485 (tp) REVERT: D 346 LEU cc_start: 0.8978 (mt) cc_final: 0.8667 (mt) REVERT: D 357 ARG cc_start: 0.7562 (mtm-85) cc_final: 0.6952 (mtm-85) REVERT: D 359 ARG cc_start: 0.7727 (tpp80) cc_final: 0.7404 (mmm-85) REVERT: D 371 LYS cc_start: 0.8082 (ttpp) cc_final: 0.7627 (ttpp) REVERT: D 372 ASN cc_start: 0.8067 (p0) cc_final: 0.7553 (p0) REVERT: D 375 GLU cc_start: 0.8101 (mp0) cc_final: 0.7459 (pm20) REVERT: D 378 LYS cc_start: 0.8731 (mttp) cc_final: 0.8414 (mttp) REVERT: D 379 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7526 (mppt) REVERT: D 418 TYR cc_start: 0.7401 (t80) cc_final: 0.7124 (t80) REVERT: D 442 LEU cc_start: 0.8727 (mt) cc_final: 0.8448 (mt) REVERT: D 443 ASP cc_start: 0.8193 (t70) cc_final: 0.7940 (t0) REVERT: D 449 LYS cc_start: 0.8088 (tttt) cc_final: 0.7858 (tttt) REVERT: D 535 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.6838 (tp-100) REVERT: D 567 GLU cc_start: 0.7528 (tp30) cc_final: 0.6711 (mm-30) REVERT: D 577 GLN cc_start: 0.7356 (tp40) cc_final: 0.6994 (tm-30) REVERT: B 50 MET cc_start: 0.6985 (tpp) cc_final: 0.6545 (tpp) REVERT: B 52 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7313 (mt-10) REVERT: B 59 LYS cc_start: 0.8371 (mtmt) cc_final: 0.7647 (mmmt) REVERT: B 87 VAL cc_start: 0.8827 (m) cc_final: 0.8494 (t) REVERT: B 97 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7418 (mm) REVERT: B 104 ARG cc_start: 0.7812 (tpt90) cc_final: 0.7315 (tpt90) REVERT: B 130 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8361 (tt) REVERT: B 156 LYS cc_start: 0.9121 (mmtm) cc_final: 0.8867 (mmtm) REVERT: B 169 ASN cc_start: 0.8367 (m-40) cc_final: 0.7995 (m-40) REVERT: B 190 GLU cc_start: 0.8258 (tp30) cc_final: 0.7851 (tp30) REVERT: B 194 LYS cc_start: 0.8580 (mttt) cc_final: 0.8253 (mttt) REVERT: B 209 MET cc_start: 0.7915 (ttm) cc_final: 0.7131 (ttm) REVERT: B 243 VAL cc_start: 0.7149 (t) cc_final: 0.6815 (m) REVERT: B 255 GLN cc_start: 0.7715 (mm110) cc_final: 0.7492 (mm110) REVERT: B 302 ARG cc_start: 0.8322 (tpt90) cc_final: 0.8083 (tpp80) REVERT: B 312 ASN cc_start: 0.8077 (t0) cc_final: 0.7661 (t0) REVERT: B 346 ASN cc_start: 0.7283 (p0) cc_final: 0.7041 (p0) REVERT: B 418 LYS cc_start: 0.7453 (mmtt) cc_final: 0.7165 (mmmt) REVERT: B 426 GLN cc_start: 0.8662 (mm-40) cc_final: 0.8342 (mm-40) REVERT: B 503 ILE cc_start: 0.8347 (tt) cc_final: 0.8049 (tt) REVERT: B 531 LEU cc_start: 0.8288 (tp) cc_final: 0.8044 (mp) REVERT: B 533 LYS cc_start: 0.8754 (mtpp) cc_final: 0.7962 (mttp) REVERT: B 535 GLN cc_start: 0.7061 (mm-40) cc_final: 0.6677 (mm-40) REVERT: B 554 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.6944 (tp) REVERT: B 556 GLN cc_start: 0.8211 (tm130) cc_final: 0.7995 (tm-30) REVERT: B 564 TYR cc_start: 0.8263 (m-80) cc_final: 0.7785 (m-10) REVERT: B 565 ASP cc_start: 0.8068 (t70) cc_final: 0.7846 (t70) REVERT: B 572 ASP cc_start: 0.8058 (t0) cc_final: 0.7698 (t0) REVERT: B 573 ARG cc_start: 0.7890 (mmt90) cc_final: 0.7620 (tpp-160) REVERT: B 597 ILE cc_start: 0.8230 (pt) cc_final: 0.7974 (pt) REVERT: B 618 GLN cc_start: 0.7343 (tt0) cc_final: 0.6828 (tt0) REVERT: B 624 HIS cc_start: 0.8347 (t-90) cc_final: 0.8097 (t70) REVERT: M 1 MET cc_start: 0.5356 (mmm) cc_final: 0.4718 (mmm) REVERT: M 17 GLU cc_start: 0.5827 (OUTLIER) cc_final: 0.5613 (tt0) REVERT: M 116 MET cc_start: 0.6997 (tpp) cc_final: 0.6643 (tpp) outliers start: 49 outliers final: 26 residues processed: 408 average time/residue: 0.2624 time to fit residues: 147.3153 Evaluate side-chains 413 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 380 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 382 THR Chi-restraints excluded: chain D residue 383 HIS Chi-restraints excluded: chain D residue 417 TRP Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 522 TYR Chi-restraints excluded: chain D residue 535 GLN Chi-restraints excluded: chain D residue 588 LYS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 579 GLN Chi-restraints excluded: chain B residue 592 LYS Chi-restraints excluded: chain B residue 598 PHE Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 10 CYS Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 51 THR Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 97 CYS Chi-restraints excluded: chain S residue 13 LYS Chi-restraints excluded: chain S residue 24 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 61 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 57 optimal weight: 0.0370 chunk 46 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 100 GLN ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 GLN B 579 GLN B 601 GLN B 638 ASN B 650 ASN ** M 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.149681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.130871 restraints weight = 22644.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.135205 restraints weight = 13249.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.138302 restraints weight = 8590.136| |-----------------------------------------------------------------------------| r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11559 Z= 0.154 Angle : 0.671 11.337 15640 Z= 0.336 Chirality : 0.043 0.229 1850 Planarity : 0.004 0.047 1971 Dihedral : 4.560 24.352 1535 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.62 % Allowed : 20.28 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.22), residues: 1419 helix: 0.92 (0.16), residues: 1004 sheet: 0.86 (0.84), residues: 45 loop : 0.54 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 236 HIS 0.006 0.001 HIS S 117 PHE 0.048 0.002 PHE D 226 TYR 0.013 0.001 TYR D 522 ARG 0.005 0.000 ARG B 250 Details of bonding type rmsd hydrogen bonds : bond 0.04461 ( 749) hydrogen bonds : angle 4.91797 ( 2175) covalent geometry : bond 0.00333 (11559) covalent geometry : angle 0.67056 (15640) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 375 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 67 MET cc_start: 0.5966 (ttt) cc_final: 0.5598 (tpt) REVERT: D 92 ARG cc_start: 0.7781 (ttt180) cc_final: 0.7116 (ttt180) REVERT: D 93 ILE cc_start: 0.8646 (mm) cc_final: 0.8115 (tp) REVERT: D 118 LYS cc_start: 0.8640 (ptpp) cc_final: 0.8319 (ptpp) REVERT: D 170 MET cc_start: 0.7443 (mmm) cc_final: 0.7059 (mmm) REVERT: D 177 TYR cc_start: 0.6994 (t80) cc_final: 0.6083 (t80) REVERT: D 182 ARG cc_start: 0.7807 (mmm160) cc_final: 0.7581 (mmm160) REVERT: D 207 ILE cc_start: 0.8249 (tt) cc_final: 0.7751 (mt) REVERT: D 242 ILE cc_start: 0.8703 (mm) cc_final: 0.8332 (tp) REVERT: D 245 PHE cc_start: 0.8123 (m-80) cc_final: 0.7744 (m-80) REVERT: D 307 LYS cc_start: 0.8683 (mmtm) cc_final: 0.8472 (mmtm) REVERT: D 314 ASP cc_start: 0.7058 (t0) cc_final: 0.6669 (t0) REVERT: D 345 ILE cc_start: 0.8994 (mt) cc_final: 0.8494 (tp) REVERT: D 346 LEU cc_start: 0.8996 (mt) cc_final: 0.8611 (mt) REVERT: D 357 ARG cc_start: 0.7626 (mtm-85) cc_final: 0.6952 (mtm-85) REVERT: D 359 ARG cc_start: 0.7798 (tpp80) cc_final: 0.7409 (mpp80) REVERT: D 372 ASN cc_start: 0.8136 (p0) cc_final: 0.7796 (p0) REVERT: D 375 GLU cc_start: 0.8045 (mp0) cc_final: 0.7558 (mp0) REVERT: D 378 LYS cc_start: 0.8764 (mttp) cc_final: 0.8253 (mttp) REVERT: D 379 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7544 (mppt) REVERT: D 399 LYS cc_start: 0.8605 (mmtp) cc_final: 0.8004 (mmtp) REVERT: D 418 TYR cc_start: 0.7502 (t80) cc_final: 0.7267 (t80) REVERT: D 440 GLN cc_start: 0.8107 (mt0) cc_final: 0.7511 (tt0) REVERT: D 442 LEU cc_start: 0.8700 (mt) cc_final: 0.8463 (mt) REVERT: D 449 LYS cc_start: 0.8105 (tttt) cc_final: 0.7884 (tttt) REVERT: D 528 LYS cc_start: 0.7686 (mttt) cc_final: 0.7248 (mttp) REVERT: D 535 GLN cc_start: 0.7307 (tp-100) cc_final: 0.6858 (tp-100) REVERT: D 567 GLU cc_start: 0.7665 (tp30) cc_final: 0.6669 (mm-30) REVERT: D 570 GLU cc_start: 0.8330 (tm-30) cc_final: 0.8106 (tm-30) REVERT: D 577 GLN cc_start: 0.7350 (tp-100) cc_final: 0.6910 (tm-30) REVERT: B 50 MET cc_start: 0.7021 (tpp) cc_final: 0.6559 (tpp) REVERT: B 52 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7435 (mt-10) REVERT: B 69 MET cc_start: 0.7453 (ppp) cc_final: 0.7213 (ppp) REVERT: B 87 VAL cc_start: 0.8846 (m) cc_final: 0.8558 (t) REVERT: B 97 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7484 (mm) REVERT: B 101 TYR cc_start: 0.8341 (t80) cc_final: 0.7974 (t80) REVERT: B 125 LYS cc_start: 0.8691 (mmtp) cc_final: 0.8063 (tptp) REVERT: B 130 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8377 (tt) REVERT: B 156 LYS cc_start: 0.9135 (mmtm) cc_final: 0.8885 (mmtm) REVERT: B 169 ASN cc_start: 0.8420 (m-40) cc_final: 0.8104 (m-40) REVERT: B 190 GLU cc_start: 0.8256 (tp30) cc_final: 0.7812 (tp30) REVERT: B 194 LYS cc_start: 0.8542 (mttt) cc_final: 0.8200 (mttt) REVERT: B 209 MET cc_start: 0.7961 (ttm) cc_final: 0.6861 (ttm) REVERT: B 243 VAL cc_start: 0.7180 (t) cc_final: 0.6850 (m) REVERT: B 255 GLN cc_start: 0.7663 (mm110) cc_final: 0.7426 (mm110) REVERT: B 302 ARG cc_start: 0.8240 (tpt90) cc_final: 0.8038 (tpp80) REVERT: B 317 MET cc_start: 0.7300 (tpp) cc_final: 0.6976 (tpp) REVERT: B 346 ASN cc_start: 0.7218 (p0) cc_final: 0.6944 (p0) REVERT: B 469 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7320 (tt) REVERT: B 503 ILE cc_start: 0.8339 (tt) cc_final: 0.8040 (tt) REVERT: B 531 LEU cc_start: 0.8287 (tp) cc_final: 0.8049 (mp) REVERT: B 535 GLN cc_start: 0.7268 (mm-40) cc_final: 0.6770 (mm-40) REVERT: B 554 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.6973 (tp) REVERT: B 556 GLN cc_start: 0.8243 (tm130) cc_final: 0.8038 (tm-30) REVERT: B 563 LYS cc_start: 0.7473 (tttp) cc_final: 0.7161 (ttpp) REVERT: B 564 TYR cc_start: 0.8236 (m-80) cc_final: 0.7636 (m-10) REVERT: B 565 ASP cc_start: 0.8087 (t70) cc_final: 0.7884 (t70) REVERT: B 572 ASP cc_start: 0.8090 (t0) cc_final: 0.7532 (t0) REVERT: B 573 ARG cc_start: 0.7886 (mmt90) cc_final: 0.7588 (tpp-160) REVERT: B 579 GLN cc_start: 0.7356 (OUTLIER) cc_final: 0.6489 (tp-100) REVERT: B 618 GLN cc_start: 0.7268 (tt0) cc_final: 0.6975 (tt0) REVERT: B 624 HIS cc_start: 0.8333 (t-90) cc_final: 0.8123 (t70) REVERT: M 1 MET cc_start: 0.5313 (mmm) cc_final: 0.4284 (mmm) REVERT: M 17 GLU cc_start: 0.6012 (OUTLIER) cc_final: 0.5804 (tt0) REVERT: M 21 LYS cc_start: 0.8585 (mttp) cc_final: 0.8181 (mmtt) REVERT: M 116 MET cc_start: 0.6964 (tpp) cc_final: 0.6638 (tpp) REVERT: S 1 MET cc_start: 0.6587 (OUTLIER) cc_final: 0.6294 (tpt) REVERT: S 128 MET cc_start: 0.7382 (mmm) cc_final: 0.7138 (mmp) outliers start: 59 outliers final: 32 residues processed: 398 average time/residue: 0.2617 time to fit residues: 143.9863 Evaluate side-chains 409 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 369 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 382 THR Chi-restraints excluded: chain D residue 383 HIS Chi-restraints excluded: chain D residue 417 TRP Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 522 TYR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 579 GLN Chi-restraints excluded: chain B residue 592 LYS Chi-restraints excluded: chain B residue 598 PHE Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 10 CYS Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 51 THR Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 97 CYS Chi-restraints excluded: chain M residue 110 TYR Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 13 LYS Chi-restraints excluded: chain S residue 24 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 101 optimal weight: 0.0010 chunk 79 optimal weight: 0.8980 chunk 10 optimal weight: 0.0870 chunk 26 optimal weight: 0.5980 chunk 124 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 61 optimal weight: 0.1980 overall best weight: 0.2964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 638 ASN B 650 ASN ** M 26 GLN ** 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 = 0.4205 r_free = 0.4205 target = 0.150927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.132140 restraints weight = 22249.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.136461 restraints weight = 13053.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.139566 restraints weight = 8474.364| |-----------------------------------------------------------------------------| r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 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 0.034 11559 Z= 0.134 Angle : 0.676 12.316 15640 Z= 0.332 Chirality : 0.042 0.296 1850 Planarity : 0.004 0.047 1971 Dihedral : 4.442 21.388 1535 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.60 % Allowed : 22.47 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.22), residues: 1419 helix: 1.00 (0.16), residues: 1002 sheet: 1.23 (0.86), residues: 43 loop : 0.48 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP D 236 HIS 0.007 0.001 HIS S 117 PHE 0.050 0.002 PHE D 226 TYR 0.016 0.001 TYR D 277 ARG 0.004 0.000 ARG B 250 Details of bonding type rmsd hydrogen bonds : bond 0.04214 ( 749) hydrogen bonds : angle 4.79842 ( 2175) covalent geometry : bond 0.00291 (11559) covalent geometry : angle 0.67610 (15640) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 385 time to evaluate : 1.160 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: D 92 ARG cc_start: 0.7739 (ttt180) cc_final: 0.7031 (ttt180) REVERT: D 93 ILE cc_start: 0.8629 (mm) cc_final: 0.8095 (tp) REVERT: D 118 LYS cc_start: 0.8616 (ptpp) cc_final: 0.8272 (ptpp) REVERT: D 170 MET cc_start: 0.7422 (mmm) cc_final: 0.6893 (mmm) REVERT: D 177 TYR cc_start: 0.6899 (t80) cc_final: 0.6020 (t80) REVERT: D 207 ILE cc_start: 0.8211 (tt) cc_final: 0.7601 (mm) REVERT: D 242 ILE cc_start: 0.8678 (mm) cc_final: 0.8276 (tp) REVERT: D 245 PHE cc_start: 0.8124 (m-80) cc_final: 0.7774 (m-80) REVERT: D 257 LYS cc_start: 0.8463 (tppt) cc_final: 0.8206 (tppt) REVERT: D 307 LYS cc_start: 0.8638 (mmtm) cc_final: 0.8421 (mmtm) REVERT: D 314 ASP cc_start: 0.7054 (t0) cc_final: 0.6699 (t0) REVERT: D 345 ILE cc_start: 0.8908 (mt) cc_final: 0.8463 (tp) REVERT: D 357 ARG cc_start: 0.7585 (mtm-85) cc_final: 0.6922 (mtm-85) REVERT: D 359 ARG cc_start: 0.7740 (tpp80) cc_final: 0.7348 (mpp80) REVERT: D 371 LYS cc_start: 0.8122 (ttpp) cc_final: 0.7693 (ttpp) REVERT: D 372 ASN cc_start: 0.8076 (p0) cc_final: 0.7648 (p0) REVERT: D 375 GLU cc_start: 0.7990 (mp0) cc_final: 0.7496 (mp0) REVERT: D 378 LYS cc_start: 0.8744 (mttp) cc_final: 0.8233 (mttp) REVERT: D 379 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7482 (mppt) REVERT: D 399 LYS cc_start: 0.8592 (mmtp) cc_final: 0.7994 (mmtp) REVERT: D 406 GLN cc_start: 0.7776 (pt0) cc_final: 0.7342 (pm20) REVERT: D 418 TYR cc_start: 0.7453 (t80) cc_final: 0.6895 (t80) REVERT: D 440 GLN cc_start: 0.8065 (mt0) cc_final: 0.7420 (tt0) REVERT: D 442 LEU cc_start: 0.8644 (mt) cc_final: 0.8404 (mt) REVERT: D 449 LYS cc_start: 0.8049 (tttt) cc_final: 0.7831 (tttt) REVERT: D 523 VAL cc_start: 0.7948 (t) cc_final: 0.7456 (p) REVERT: D 528 LYS cc_start: 0.7622 (mttt) cc_final: 0.7181 (mttp) REVERT: D 535 GLN cc_start: 0.7248 (OUTLIER) cc_final: 0.6790 (tp-100) REVERT: D 577 GLN cc_start: 0.7279 (tp-100) cc_final: 0.6587 (tm-30) REVERT: D 582 ILE cc_start: 0.8088 (mt) cc_final: 0.7844 (mm) REVERT: D 584 LYS cc_start: 0.8434 (mttt) cc_final: 0.8071 (mptt) REVERT: D 595 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7196 (tt0) REVERT: B 50 MET cc_start: 0.6984 (tpp) cc_final: 0.6505 (tpp) REVERT: B 63 MET cc_start: 0.7849 (mmm) cc_final: 0.7416 (mmm) REVERT: B 69 MET cc_start: 0.7646 (ppp) cc_final: 0.7349 (ppp) REVERT: B 97 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7424 (mm) REVERT: B 101 TYR cc_start: 0.8345 (t80) cc_final: 0.8077 (t80) REVERT: B 130 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8384 (tt) REVERT: B 137 ARG cc_start: 0.7861 (mtm110) cc_final: 0.7400 (mtp85) REVERT: B 156 LYS cc_start: 0.9147 (mmtm) cc_final: 0.8924 (mmmm) REVERT: B 169 ASN cc_start: 0.8385 (m-40) cc_final: 0.7920 (m-40) REVERT: B 190 GLU cc_start: 0.8254 (tp30) cc_final: 0.7740 (tp30) REVERT: B 194 LYS cc_start: 0.8496 (mttt) cc_final: 0.8099 (mttt) REVERT: B 209 MET cc_start: 0.7998 (ttm) cc_final: 0.7064 (ttm) REVERT: B 243 VAL cc_start: 0.7140 (t) cc_final: 0.6827 (m) REVERT: B 346 ASN cc_start: 0.7129 (p0) cc_final: 0.6848 (p0) REVERT: B 420 PHE cc_start: 0.6324 (t80) cc_final: 0.6053 (t80) REVERT: B 469 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7293 (tt) REVERT: B 503 ILE cc_start: 0.8303 (tt) cc_final: 0.7997 (tt) REVERT: B 523 LYS cc_start: 0.8562 (mttt) cc_final: 0.8025 (mptt) REVERT: B 531 LEU cc_start: 0.8269 (tp) cc_final: 0.8004 (mp) REVERT: B 535 GLN cc_start: 0.7261 (mm-40) cc_final: 0.7061 (mm-40) REVERT: B 556 GLN cc_start: 0.8227 (tm130) cc_final: 0.7948 (tm-30) REVERT: B 563 LYS cc_start: 0.7419 (tttp) cc_final: 0.7122 (ttpp) REVERT: B 564 TYR cc_start: 0.8212 (m-80) cc_final: 0.7620 (m-10) REVERT: B 565 ASP cc_start: 0.8119 (t70) cc_final: 0.7890 (t70) REVERT: B 572 ASP cc_start: 0.8082 (t0) cc_final: 0.7543 (t0) REVERT: B 573 ARG cc_start: 0.7797 (mmt90) cc_final: 0.7499 (tpp-160) REVERT: B 577 ILE cc_start: 0.8613 (mt) cc_final: 0.8403 (mm) REVERT: B 593 TYR cc_start: 0.7935 (m-80) cc_final: 0.7713 (m-80) REVERT: B 618 GLN cc_start: 0.7194 (tt0) cc_final: 0.6860 (tt0) REVERT: B 644 PRO cc_start: 0.8456 (Cg_endo) cc_final: 0.7676 (Cg_exo) REVERT: M 1 MET cc_start: 0.5279 (mmm) cc_final: 0.4279 (mmm) REVERT: M 17 GLU cc_start: 0.6027 (OUTLIER) cc_final: 0.5792 (tt0) REVERT: M 21 LYS cc_start: 0.8494 (mttp) cc_final: 0.8127 (mmtt) REVERT: M 69 VAL cc_start: 0.7322 (t) cc_final: 0.6783 (m) REVERT: M 116 MET cc_start: 0.6938 (tpp) cc_final: 0.6666 (tpp) REVERT: S 1 MET cc_start: 0.6562 (OUTLIER) cc_final: 0.6256 (tpt) REVERT: S 68 TYR cc_start: 0.7481 (m-80) cc_final: 0.7264 (m-80) REVERT: S 140 GLN cc_start: 0.7408 (tt0) cc_final: 0.6951 (tt0) outliers start: 46 outliers final: 31 residues processed: 397 average time/residue: 0.2847 time to fit residues: 158.2442 Evaluate side-chains 414 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 375 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 383 HIS Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 417 TRP Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 522 TYR Chi-restraints excluded: chain D residue 535 GLN Chi-restraints excluded: chain D residue 595 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 592 LYS Chi-restraints excluded: chain B residue 598 PHE Chi-restraints excluded: chain B residue 650 ASN Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 10 CYS Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 51 THR Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 97 CYS Chi-restraints excluded: chain M residue 110 TYR Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 13 LYS Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 132 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 129 optimal weight: 0.0060 chunk 8 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 111 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 102 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 500 HIS D 581 HIS D 583 GLN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 GLN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN B 426 GLN B 579 GLN B 601 GLN ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 ASN ** M 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.150953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.131760 restraints weight = 22691.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.136180 restraints weight = 13386.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.139265 restraints weight = 8686.299| |-----------------------------------------------------------------------------| r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11559 Z= 0.138 Angle : 0.660 12.030 15640 Z= 0.327 Chirality : 0.042 0.251 1850 Planarity : 0.004 0.047 1971 Dihedral : 4.433 19.459 1535 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.60 % Allowed : 23.10 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.22), residues: 1419 helix: 1.10 (0.16), residues: 999 sheet: 1.06 (0.85), residues: 45 loop : 0.55 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 236 HIS 0.007 0.001 HIS S 117 PHE 0.050 0.002 PHE D 226 TYR 0.015 0.001 TYR D 277 ARG 0.006 0.000 ARG B 649 Details of bonding type rmsd hydrogen bonds : bond 0.04139 ( 749) hydrogen bonds : angle 4.79321 ( 2175) covalent geometry : bond 0.00298 (11559) covalent geometry : angle 0.65961 (15640) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 385 time to evaluate : 1.210 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: D 67 MET cc_start: 0.6062 (ttt) cc_final: 0.5448 (tpt) REVERT: D 92 ARG cc_start: 0.7798 (ttt180) cc_final: 0.7093 (ttt180) REVERT: D 93 ILE cc_start: 0.8641 (mm) cc_final: 0.8098 (tp) REVERT: D 118 LYS cc_start: 0.8620 (ptpp) cc_final: 0.8264 (ptpp) REVERT: D 170 MET cc_start: 0.7390 (mmm) cc_final: 0.6953 (mmm) REVERT: D 177 TYR cc_start: 0.6885 (t80) cc_final: 0.6033 (t80) REVERT: D 207 ILE cc_start: 0.8169 (tt) cc_final: 0.7693 (mt) REVERT: D 242 ILE cc_start: 0.8714 (mm) cc_final: 0.8232 (tp) REVERT: D 245 PHE cc_start: 0.8127 (m-80) cc_final: 0.7746 (m-80) REVERT: D 257 LYS cc_start: 0.8507 (tppt) cc_final: 0.8208 (tppt) REVERT: D 306 GLN cc_start: 0.8578 (tp-100) cc_final: 0.8278 (tp-100) REVERT: D 307 LYS cc_start: 0.8667 (mmtm) cc_final: 0.8422 (mmtm) REVERT: D 314 ASP cc_start: 0.7090 (t0) cc_final: 0.6746 (t0) REVERT: D 345 ILE cc_start: 0.8923 (mt) cc_final: 0.8473 (tp) REVERT: D 346 LEU cc_start: 0.9016 (mt) cc_final: 0.8630 (mt) REVERT: D 351 ASP cc_start: 0.7972 (m-30) cc_final: 0.7576 (t0) REVERT: D 357 ARG cc_start: 0.7624 (mtm-85) cc_final: 0.6952 (mtm-85) REVERT: D 371 LYS cc_start: 0.8188 (ttpp) cc_final: 0.7745 (ttpp) REVERT: D 372 ASN cc_start: 0.8098 (p0) cc_final: 0.7706 (p0) REVERT: D 375 GLU cc_start: 0.8051 (mp0) cc_final: 0.7435 (mp0) REVERT: D 378 LYS cc_start: 0.8759 (mttp) cc_final: 0.8354 (mttp) REVERT: D 379 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7539 (mppt) REVERT: D 440 GLN cc_start: 0.8080 (mt0) cc_final: 0.7369 (tt0) REVERT: D 442 LEU cc_start: 0.8626 (mt) cc_final: 0.8377 (mt) REVERT: D 449 LYS cc_start: 0.8160 (tttt) cc_final: 0.7938 (tttt) REVERT: D 482 LEU cc_start: 0.8047 (mp) cc_final: 0.7844 (mt) REVERT: D 523 VAL cc_start: 0.7979 (t) cc_final: 0.7602 (p) REVERT: D 528 LYS cc_start: 0.7621 (mttt) cc_final: 0.7191 (mttp) REVERT: D 535 GLN cc_start: 0.7189 (tp-100) cc_final: 0.6718 (tp-100) REVERT: D 547 GLN cc_start: 0.8445 (tp-100) cc_final: 0.8054 (tp-100) REVERT: D 551 GLN cc_start: 0.7947 (mm110) cc_final: 0.7641 (mm-40) REVERT: D 577 GLN cc_start: 0.7277 (tp-100) cc_final: 0.6830 (tp40) REVERT: D 584 LYS cc_start: 0.8415 (mttt) cc_final: 0.8073 (mptt) REVERT: B 50 MET cc_start: 0.7028 (tpp) cc_final: 0.6539 (tpp) REVERT: B 63 MET cc_start: 0.7882 (mmm) cc_final: 0.7573 (mmm) REVERT: B 69 MET cc_start: 0.7653 (ppp) cc_final: 0.7364 (ppp) REVERT: B 90 LYS cc_start: 0.8398 (tptp) cc_final: 0.8028 (tptp) REVERT: B 97 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7477 (mm) REVERT: B 125 LYS cc_start: 0.8672 (mmtp) cc_final: 0.8038 (tptp) REVERT: B 130 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8397 (tt) REVERT: B 137 ARG cc_start: 0.7843 (mtm110) cc_final: 0.7419 (mtp85) REVERT: B 153 LEU cc_start: 0.8901 (tp) cc_final: 0.8651 (tt) REVERT: B 156 LYS cc_start: 0.9158 (mmtm) cc_final: 0.8919 (mmmm) REVERT: B 169 ASN cc_start: 0.8394 (m-40) cc_final: 0.7959 (m-40) REVERT: B 190 GLU cc_start: 0.8256 (tp30) cc_final: 0.7633 (tp30) REVERT: B 194 LYS cc_start: 0.8453 (mttt) cc_final: 0.7956 (mttt) REVERT: B 209 MET cc_start: 0.7904 (ttm) cc_final: 0.7302 (ttm) REVERT: B 243 VAL cc_start: 0.7126 (t) cc_final: 0.6818 (m) REVERT: B 255 GLN cc_start: 0.7736 (mm-40) cc_final: 0.7287 (mm-40) REVERT: B 311 ARG cc_start: 0.7573 (mtm-85) cc_final: 0.7306 (mtm-85) REVERT: B 346 ASN cc_start: 0.7110 (p0) cc_final: 0.6858 (p0) REVERT: B 391 GLU cc_start: 0.7838 (tp30) cc_final: 0.7534 (tp30) REVERT: B 402 ILE cc_start: 0.4480 (tp) cc_final: 0.4235 (tp) REVERT: B 420 PHE cc_start: 0.6416 (t80) cc_final: 0.6108 (t80) REVERT: B 469 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7270 (tt) REVERT: B 483 MET cc_start: 0.6610 (mmp) cc_final: 0.6386 (mmp) REVERT: B 503 ILE cc_start: 0.8283 (tt) cc_final: 0.7963 (tt) REVERT: B 523 LYS cc_start: 0.8566 (mttt) cc_final: 0.8027 (mptt) REVERT: B 531 LEU cc_start: 0.8275 (tp) cc_final: 0.8050 (mp) REVERT: B 556 GLN cc_start: 0.8236 (tm130) cc_final: 0.7949 (tm-30) REVERT: B 563 LYS cc_start: 0.7483 (tttp) cc_final: 0.7190 (ttpp) REVERT: B 564 TYR cc_start: 0.8194 (m-80) cc_final: 0.7497 (m-10) REVERT: B 565 ASP cc_start: 0.8092 (t70) cc_final: 0.7880 (t70) REVERT: B 572 ASP cc_start: 0.8038 (t0) cc_final: 0.7525 (t0) REVERT: B 573 ARG cc_start: 0.7855 (mmt90) cc_final: 0.7592 (tpp-160) REVERT: B 577 ILE cc_start: 0.8625 (mt) cc_final: 0.8410 (mm) REVERT: B 593 TYR cc_start: 0.7866 (m-80) cc_final: 0.7609 (m-80) REVERT: M 1 MET cc_start: 0.5183 (mmm) cc_final: 0.4505 (mmm) REVERT: M 17 GLU cc_start: 0.6031 (OUTLIER) cc_final: 0.5764 (tt0) REVERT: M 21 LYS cc_start: 0.8612 (mttp) cc_final: 0.8253 (mmtt) REVERT: M 69 VAL cc_start: 0.7438 (t) cc_final: 0.6897 (m) REVERT: M 116 MET cc_start: 0.6886 (tpp) cc_final: 0.6683 (tpp) REVERT: S 1 MET cc_start: 0.6276 (OUTLIER) cc_final: 0.5963 (tpt) REVERT: S 13 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7245 (tttp) outliers start: 46 outliers final: 30 residues processed: 401 average time/residue: 0.2545 time to fit residues: 140.3181 Evaluate side-chains 415 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 378 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 382 THR Chi-restraints excluded: chain D residue 383 HIS Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 417 TRP Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 522 TYR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 592 LYS Chi-restraints excluded: chain B residue 598 PHE Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 51 THR Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 97 CYS Chi-restraints excluded: chain M residue 110 TYR Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 13 LYS Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 132 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 40 optimal weight: 0.5980 chunk 118 optimal weight: 0.6980 chunk 128 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 32 optimal weight: 0.0770 chunk 109 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN B 426 GLN B 601 GLN ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 9 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.150156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.130904 restraints weight = 22777.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.135236 restraints weight = 13411.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.138367 restraints weight = 8775.102| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11559 Z= 0.145 Angle : 0.683 12.438 15640 Z= 0.337 Chirality : 0.042 0.226 1850 Planarity : 0.004 0.047 1971 Dihedral : 4.429 19.373 1535 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.07 % Allowed : 23.02 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.22), residues: 1419 helix: 1.10 (0.16), residues: 1000 sheet: 0.91 (0.84), residues: 46 loop : 0.47 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 236 HIS 0.007 0.001 HIS D 341 PHE 0.051 0.002 PHE D 226 TYR 0.017 0.001 TYR D 277 ARG 0.004 0.000 ARG B 250 Details of bonding type rmsd hydrogen bonds : bond 0.04155 ( 749) hydrogen bonds : angle 4.80843 ( 2175) covalent geometry : bond 0.00314 (11559) covalent geometry : angle 0.68330 (15640) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 384 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 67 MET cc_start: 0.6056 (ttt) cc_final: 0.5418 (tpt) REVERT: D 92 ARG cc_start: 0.7823 (ttt180) cc_final: 0.7129 (ttt180) REVERT: D 93 ILE cc_start: 0.8672 (mm) cc_final: 0.8157 (tp) REVERT: D 118 LYS cc_start: 0.8635 (ptpp) cc_final: 0.8373 (ptpp) REVERT: D 170 MET cc_start: 0.7403 (mmm) cc_final: 0.6941 (mmm) REVERT: D 177 TYR cc_start: 0.6949 (t80) cc_final: 0.6161 (t80) REVERT: D 207 ILE cc_start: 0.8160 (tt) cc_final: 0.7711 (mt) REVERT: D 242 ILE cc_start: 0.8699 (mm) cc_final: 0.8244 (tp) REVERT: D 245 PHE cc_start: 0.8125 (m-80) cc_final: 0.7746 (m-80) REVERT: D 257 LYS cc_start: 0.8521 (tppt) cc_final: 0.8110 (tppt) REVERT: D 306 GLN cc_start: 0.8589 (tp-100) cc_final: 0.8313 (tp-100) REVERT: D 307 LYS cc_start: 0.8690 (mmtm) cc_final: 0.8424 (mmtm) REVERT: D 314 ASP cc_start: 0.7105 (t0) cc_final: 0.6741 (t0) REVERT: D 345 ILE cc_start: 0.8906 (mt) cc_final: 0.8528 (tp) REVERT: D 346 LEU cc_start: 0.9020 (mt) cc_final: 0.8606 (mt) REVERT: D 351 ASP cc_start: 0.7930 (m-30) cc_final: 0.7540 (t0) REVERT: D 357 ARG cc_start: 0.7639 (mtm-85) cc_final: 0.6949 (mtm-85) REVERT: D 371 LYS cc_start: 0.8231 (ttpp) cc_final: 0.7847 (ttpp) REVERT: D 372 ASN cc_start: 0.8134 (p0) cc_final: 0.7582 (p0) REVERT: D 375 GLU cc_start: 0.8052 (mp0) cc_final: 0.7466 (mp0) REVERT: D 378 LYS cc_start: 0.8771 (mttp) cc_final: 0.8346 (mttm) REVERT: D 379 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7528 (mppt) REVERT: D 416 GLU cc_start: 0.7793 (tt0) cc_final: 0.7166 (mm-30) REVERT: D 440 GLN cc_start: 0.8015 (mt0) cc_final: 0.7327 (tt0) REVERT: D 442 LEU cc_start: 0.8603 (mt) cc_final: 0.8315 (mt) REVERT: D 449 LYS cc_start: 0.8215 (tttt) cc_final: 0.7877 (tttt) REVERT: D 452 ARG cc_start: 0.7612 (mtt180) cc_final: 0.7165 (mtp180) REVERT: D 528 LYS cc_start: 0.7588 (mttt) cc_final: 0.7192 (mttp) REVERT: D 535 GLN cc_start: 0.7157 (tp-100) cc_final: 0.6683 (tp-100) REVERT: D 547 GLN cc_start: 0.8496 (tp-100) cc_final: 0.8110 (tp-100) REVERT: D 551 GLN cc_start: 0.7996 (mm110) cc_final: 0.7702 (mm-40) REVERT: D 567 GLU cc_start: 0.7681 (tp30) cc_final: 0.7240 (mm-30) REVERT: D 570 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8132 (tm-30) REVERT: D 577 GLN cc_start: 0.7553 (tp-100) cc_final: 0.6667 (tm-30) REVERT: D 595 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7103 (tt0) REVERT: B 50 MET cc_start: 0.7129 (tpp) cc_final: 0.6568 (tpt) REVERT: B 69 MET cc_start: 0.7661 (ppp) cc_final: 0.7345 (ppp) REVERT: B 97 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7537 (mm) REVERT: B 101 TYR cc_start: 0.8378 (t80) cc_final: 0.8153 (t80) REVERT: B 125 LYS cc_start: 0.8704 (mmtp) cc_final: 0.8070 (tptp) REVERT: B 137 ARG cc_start: 0.7859 (mtm110) cc_final: 0.7441 (mtp85) REVERT: B 153 LEU cc_start: 0.8883 (tp) cc_final: 0.8636 (tt) REVERT: B 156 LYS cc_start: 0.9141 (mmtm) cc_final: 0.8909 (mmmm) REVERT: B 169 ASN cc_start: 0.8409 (m-40) cc_final: 0.7976 (m-40) REVERT: B 175 GLN cc_start: 0.8017 (mm110) cc_final: 0.7568 (tp40) REVERT: B 190 GLU cc_start: 0.8261 (tp30) cc_final: 0.7670 (tp30) REVERT: B 194 LYS cc_start: 0.8486 (mttt) cc_final: 0.7972 (mttt) REVERT: B 209 MET cc_start: 0.7902 (ttm) cc_final: 0.7245 (ttm) REVERT: B 243 VAL cc_start: 0.7154 (t) cc_final: 0.6849 (m) REVERT: B 255 GLN cc_start: 0.7686 (mm-40) cc_final: 0.7219 (mm-40) REVERT: B 346 ASN cc_start: 0.7130 (p0) cc_final: 0.6896 (p0) REVERT: B 391 GLU cc_start: 0.7923 (tp30) cc_final: 0.7578 (tp30) REVERT: B 420 PHE cc_start: 0.6402 (t80) cc_final: 0.6190 (t80) REVERT: B 469 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7236 (tt) REVERT: B 503 ILE cc_start: 0.8264 (tt) cc_final: 0.7954 (tt) REVERT: B 523 LYS cc_start: 0.8561 (mttt) cc_final: 0.8024 (mptt) REVERT: B 533 LYS cc_start: 0.8779 (mtpp) cc_final: 0.8341 (mmtp) REVERT: B 556 GLN cc_start: 0.8247 (tm130) cc_final: 0.7960 (tm-30) REVERT: B 563 LYS cc_start: 0.7499 (tttp) cc_final: 0.7227 (ttpp) REVERT: B 564 TYR cc_start: 0.8226 (m-80) cc_final: 0.7541 (m-10) REVERT: B 572 ASP cc_start: 0.8021 (t0) cc_final: 0.7446 (t0) REVERT: B 577 ILE cc_start: 0.8637 (mt) cc_final: 0.8429 (mm) REVERT: B 579 GLN cc_start: 0.7323 (OUTLIER) cc_final: 0.6328 (tp-100) REVERT: M 1 MET cc_start: 0.5086 (mmm) cc_final: 0.4422 (mmm) REVERT: M 17 GLU cc_start: 0.6057 (OUTLIER) cc_final: 0.5684 (tt0) REVERT: M 21 LYS cc_start: 0.8666 (mttp) cc_final: 0.8270 (mmtt) REVERT: M 69 VAL cc_start: 0.7497 (t) cc_final: 0.6955 (m) REVERT: M 93 TYR cc_start: 0.6877 (t80) cc_final: 0.6451 (t80) REVERT: S 1 MET cc_start: 0.6349 (tpt) cc_final: 0.5992 (tpt) REVERT: S 140 GLN cc_start: 0.7403 (tt0) cc_final: 0.7097 (tt0) outliers start: 52 outliers final: 34 residues processed: 408 average time/residue: 0.2703 time to fit residues: 152.5921 Evaluate side-chains 416 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 376 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 382 THR Chi-restraints excluded: chain D residue 383 HIS Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 417 TRP Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 522 TYR Chi-restraints excluded: chain D residue 595 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 579 GLN Chi-restraints excluded: chain B residue 592 LYS Chi-restraints excluded: chain B residue 598 PHE Chi-restraints excluded: chain B residue 601 GLN Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 10 CYS Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 51 THR Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 97 CYS Chi-restraints excluded: chain M residue 110 TYR Chi-restraints excluded: chain S residue 13 LYS Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 89 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 28 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 104 optimal weight: 0.4980 chunk 98 optimal weight: 0.5980 chunk 117 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN B 426 GLN B 601 GLN ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.150086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.130789 restraints weight = 22645.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.135207 restraints weight = 13398.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.138320 restraints weight = 8689.729| |-----------------------------------------------------------------------------| r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11559 Z= 0.153 Angle : 0.716 13.191 15640 Z= 0.351 Chirality : 0.043 0.383 1850 Planarity : 0.004 0.047 1971 Dihedral : 4.481 19.605 1535 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.60 % Allowed : 24.12 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.22), residues: 1419 helix: 1.13 (0.16), residues: 998 sheet: 0.92 (0.84), residues: 46 loop : 0.38 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.003 TRP D 236 HIS 0.008 0.001 HIS S 117 PHE 0.050 0.002 PHE D 226 TYR 0.017 0.001 TYR D 277 ARG 0.005 0.000 ARG B 250 Details of bonding type rmsd hydrogen bonds : bond 0.04195 ( 749) hydrogen bonds : angle 4.85818 ( 2175) covalent geometry : bond 0.00329 (11559) covalent geometry : angle 0.71582 (15640) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 384 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 67 MET cc_start: 0.6105 (ttt) cc_final: 0.5481 (tpt) REVERT: D 92 ARG cc_start: 0.7843 (ttt180) cc_final: 0.7171 (ttt180) REVERT: D 93 ILE cc_start: 0.8697 (mm) cc_final: 0.8192 (tp) REVERT: D 118 LYS cc_start: 0.8649 (ptpp) cc_final: 0.8388 (ptpp) REVERT: D 170 MET cc_start: 0.7462 (mmm) cc_final: 0.6967 (mmm) REVERT: D 177 TYR cc_start: 0.6977 (t80) cc_final: 0.5940 (t80) REVERT: D 207 ILE cc_start: 0.8222 (tt) cc_final: 0.7800 (mt) REVERT: D 209 GLU cc_start: 0.7784 (tp30) cc_final: 0.7500 (tp30) REVERT: D 242 ILE cc_start: 0.8699 (mm) cc_final: 0.8100 (mm) REVERT: D 245 PHE cc_start: 0.8078 (m-80) cc_final: 0.7606 (m-80) REVERT: D 257 LYS cc_start: 0.8527 (tppt) cc_final: 0.8040 (tppt) REVERT: D 306 GLN cc_start: 0.8600 (tp-100) cc_final: 0.8322 (tp-100) REVERT: D 307 LYS cc_start: 0.8682 (mmtm) cc_final: 0.8424 (mmtm) REVERT: D 314 ASP cc_start: 0.7099 (t0) cc_final: 0.6766 (t0) REVERT: D 342 LYS cc_start: 0.8079 (mttt) cc_final: 0.7829 (mttt) REVERT: D 345 ILE cc_start: 0.8909 (mt) cc_final: 0.8555 (tp) REVERT: D 346 LEU cc_start: 0.9026 (mt) cc_final: 0.8612 (mt) REVERT: D 351 ASP cc_start: 0.7864 (m-30) cc_final: 0.7488 (t0) REVERT: D 357 ARG cc_start: 0.7606 (mtm-85) cc_final: 0.6920 (mtm-85) REVERT: D 371 LYS cc_start: 0.8205 (ttpp) cc_final: 0.7732 (ttpp) REVERT: D 372 ASN cc_start: 0.8131 (p0) cc_final: 0.7673 (p0) REVERT: D 375 GLU cc_start: 0.8052 (mp0) cc_final: 0.7475 (mp0) REVERT: D 378 LYS cc_start: 0.8763 (mttp) cc_final: 0.8378 (mttp) REVERT: D 379 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7525 (mppt) REVERT: D 440 GLN cc_start: 0.8034 (mt0) cc_final: 0.7333 (tt0) REVERT: D 442 LEU cc_start: 0.8605 (mt) cc_final: 0.8326 (mt) REVERT: D 449 LYS cc_start: 0.8235 (tttt) cc_final: 0.7903 (tttt) REVERT: D 452 ARG cc_start: 0.7608 (mtt180) cc_final: 0.7189 (mtp180) REVERT: D 482 LEU cc_start: 0.8070 (mp) cc_final: 0.7852 (mt) REVERT: D 528 LYS cc_start: 0.7576 (mttt) cc_final: 0.7169 (mttp) REVERT: D 535 GLN cc_start: 0.7155 (tp-100) cc_final: 0.6668 (tp-100) REVERT: D 547 GLN cc_start: 0.8505 (tp-100) cc_final: 0.8114 (tp-100) REVERT: D 551 GLN cc_start: 0.7999 (mm110) cc_final: 0.7700 (mm-40) REVERT: D 567 GLU cc_start: 0.7653 (tp30) cc_final: 0.7396 (tp30) REVERT: D 577 GLN cc_start: 0.7465 (tp-100) cc_final: 0.6646 (tm-30) REVERT: D 595 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7001 (tt0) REVERT: B 50 MET cc_start: 0.7140 (tpp) cc_final: 0.6618 (tpt) REVERT: B 52 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7300 (mt-10) REVERT: B 69 MET cc_start: 0.7672 (ppp) cc_final: 0.7358 (ppp) REVERT: B 97 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7503 (mm) REVERT: B 125 LYS cc_start: 0.8719 (mmtp) cc_final: 0.8101 (tptp) REVERT: B 137 ARG cc_start: 0.7923 (mtm110) cc_final: 0.7511 (mtp85) REVERT: B 153 LEU cc_start: 0.8916 (tp) cc_final: 0.8680 (tt) REVERT: B 156 LYS cc_start: 0.9158 (mmtm) cc_final: 0.8930 (mmtm) REVERT: B 169 ASN cc_start: 0.8409 (m-40) cc_final: 0.8006 (m-40) REVERT: B 175 GLN cc_start: 0.8006 (mm110) cc_final: 0.7574 (tp40) REVERT: B 190 GLU cc_start: 0.8261 (tp30) cc_final: 0.7675 (tp30) REVERT: B 194 LYS cc_start: 0.8500 (mttt) cc_final: 0.7990 (mttt) REVERT: B 209 MET cc_start: 0.7949 (ttm) cc_final: 0.7284 (ttm) REVERT: B 243 VAL cc_start: 0.7177 (t) cc_final: 0.6876 (m) REVERT: B 255 GLN cc_start: 0.7698 (mm-40) cc_final: 0.7228 (mm-40) REVERT: B 346 ASN cc_start: 0.7138 (p0) cc_final: 0.6888 (p0) REVERT: B 391 GLU cc_start: 0.7899 (tp30) cc_final: 0.7522 (tp30) REVERT: B 420 PHE cc_start: 0.6465 (t80) cc_final: 0.6263 (t80) REVERT: B 469 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7252 (tt) REVERT: B 503 ILE cc_start: 0.8277 (tt) cc_final: 0.7963 (tt) REVERT: B 523 LYS cc_start: 0.8528 (mttt) cc_final: 0.8026 (mptt) REVERT: B 533 LYS cc_start: 0.8728 (mtpp) cc_final: 0.7815 (mmtp) REVERT: B 556 GLN cc_start: 0.8218 (tm130) cc_final: 0.7922 (tm-30) REVERT: B 563 LYS cc_start: 0.7532 (tttp) cc_final: 0.7245 (ttpp) REVERT: B 564 TYR cc_start: 0.8149 (m-80) cc_final: 0.7507 (m-10) REVERT: B 565 ASP cc_start: 0.8125 (t0) cc_final: 0.7916 (t0) REVERT: B 572 ASP cc_start: 0.7985 (t0) cc_final: 0.7428 (t0) REVERT: B 592 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8267 (ttpp) REVERT: M 1 MET cc_start: 0.5107 (mmm) cc_final: 0.4436 (mmm) REVERT: M 17 GLU cc_start: 0.6047 (OUTLIER) cc_final: 0.5667 (tt0) REVERT: M 21 LYS cc_start: 0.8662 (mttp) cc_final: 0.8246 (mmtt) REVERT: M 69 VAL cc_start: 0.7492 (t) cc_final: 0.6957 (m) REVERT: M 93 TYR cc_start: 0.6838 (t80) cc_final: 0.6435 (t80) REVERT: M 116 MET cc_start: 0.6839 (tpp) cc_final: 0.6315 (tpp) REVERT: S 1 MET cc_start: 0.6300 (tpt) cc_final: 0.5925 (tpt) REVERT: S 71 LEU cc_start: 0.7573 (mp) cc_final: 0.7306 (mp) REVERT: S 140 GLN cc_start: 0.7433 (tt0) cc_final: 0.7186 (tt0) outliers start: 46 outliers final: 37 residues processed: 402 average time/residue: 0.2729 time to fit residues: 151.1403 Evaluate side-chains 415 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 372 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 383 HIS Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 417 TRP Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 522 TYR Chi-restraints excluded: chain D residue 581 HIS Chi-restraints excluded: chain D residue 595 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 592 LYS Chi-restraints excluded: chain B residue 598 PHE Chi-restraints excluded: chain B residue 650 ASN Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 10 CYS Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 51 THR Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 97 CYS Chi-restraints excluded: chain M residue 110 TYR Chi-restraints excluded: chain S residue 13 LYS Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 89 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 17 optimal weight: 0.9980 chunk 102 optimal weight: 0.0370 chunk 2 optimal weight: 2.9990 chunk 110 optimal weight: 0.0050 chunk 133 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 123 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 overall best weight: 0.3872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN B 426 GLN B 601 GLN ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 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 = 0.4211 r_free = 0.4211 target = 0.151179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.131739 restraints weight = 22496.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.136202 restraints weight = 13340.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.139288 restraints weight = 8664.086| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11559 Z= 0.137 Angle : 0.723 13.676 15640 Z= 0.351 Chirality : 0.043 0.373 1850 Planarity : 0.004 0.046 1971 Dihedral : 4.444 18.911 1535 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.13 % Allowed : 24.98 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.22), residues: 1419 helix: 1.14 (0.16), residues: 995 sheet: 0.81 (0.83), residues: 46 loop : 0.32 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP D 236 HIS 0.008 0.001 HIS S 117 PHE 0.051 0.002 PHE D 226 TYR 0.019 0.001 TYR D 277 ARG 0.006 0.000 ARG D 359 Details of bonding type rmsd hydrogen bonds : bond 0.04088 ( 749) hydrogen bonds : angle 4.78874 ( 2175) covalent geometry : bond 0.00299 (11559) covalent geometry : angle 0.72336 (15640) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 385 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 32 GLU cc_start: 0.8040 (pm20) cc_final: 0.7002 (pm20) REVERT: D 67 MET cc_start: 0.6220 (ttt) cc_final: 0.5573 (tpt) REVERT: D 92 ARG cc_start: 0.7830 (ttt180) cc_final: 0.7099 (ttt180) REVERT: D 93 ILE cc_start: 0.8684 (mm) cc_final: 0.8166 (tp) REVERT: D 118 LYS cc_start: 0.8636 (ptpp) cc_final: 0.8357 (ptpp) REVERT: D 170 MET cc_start: 0.7348 (mmm) cc_final: 0.6817 (mmm) REVERT: D 177 TYR cc_start: 0.6923 (t80) cc_final: 0.5909 (t80) REVERT: D 207 ILE cc_start: 0.8198 (tt) cc_final: 0.7795 (mt) REVERT: D 209 GLU cc_start: 0.7671 (tp30) cc_final: 0.7367 (tp30) REVERT: D 242 ILE cc_start: 0.8688 (mm) cc_final: 0.8356 (tp) REVERT: D 245 PHE cc_start: 0.8094 (m-80) cc_final: 0.7826 (m-80) REVERT: D 257 LYS cc_start: 0.8541 (tppt) cc_final: 0.8049 (tppt) REVERT: D 306 GLN cc_start: 0.8579 (tp-100) cc_final: 0.8316 (tp-100) REVERT: D 307 LYS cc_start: 0.8684 (mmtm) cc_final: 0.8423 (mmtm) REVERT: D 314 ASP cc_start: 0.7021 (t0) cc_final: 0.6714 (t0) REVERT: D 342 LYS cc_start: 0.8102 (mttt) cc_final: 0.7872 (mttt) REVERT: D 345 ILE cc_start: 0.8874 (mt) cc_final: 0.8538 (tp) REVERT: D 346 LEU cc_start: 0.9009 (mt) cc_final: 0.8658 (mt) REVERT: D 351 ASP cc_start: 0.7810 (m-30) cc_final: 0.7440 (t0) REVERT: D 357 ARG cc_start: 0.7579 (mtm-85) cc_final: 0.6909 (mtm-85) REVERT: D 371 LYS cc_start: 0.8192 (ttpp) cc_final: 0.7737 (ttpp) REVERT: D 372 ASN cc_start: 0.8068 (p0) cc_final: 0.7443 (p0) REVERT: D 375 GLU cc_start: 0.8050 (mp0) cc_final: 0.7466 (mp0) REVERT: D 378 LYS cc_start: 0.8719 (mttp) cc_final: 0.8304 (mttm) REVERT: D 379 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7454 (mppt) REVERT: D 418 TYR cc_start: 0.7441 (t80) cc_final: 0.7002 (t80) REVERT: D 440 GLN cc_start: 0.7992 (mt0) cc_final: 0.7378 (tt0) REVERT: D 442 LEU cc_start: 0.8582 (mt) cc_final: 0.8310 (mt) REVERT: D 449 LYS cc_start: 0.8197 (tttt) cc_final: 0.7845 (tttt) REVERT: D 452 ARG cc_start: 0.7581 (mtt180) cc_final: 0.7171 (mtp180) REVERT: D 482 LEU cc_start: 0.8056 (mp) cc_final: 0.7850 (mt) REVERT: D 528 LYS cc_start: 0.7545 (mttt) cc_final: 0.7157 (mttp) REVERT: D 535 GLN cc_start: 0.7218 (tp-100) cc_final: 0.6711 (tp-100) REVERT: D 547 GLN cc_start: 0.8514 (tp-100) cc_final: 0.8136 (tp-100) REVERT: D 577 GLN cc_start: 0.7431 (tp-100) cc_final: 0.6641 (tm-30) REVERT: D 595 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7044 (tt0) REVERT: B 50 MET cc_start: 0.7138 (tpp) cc_final: 0.6610 (tpt) REVERT: B 69 MET cc_start: 0.7726 (ppp) cc_final: 0.7382 (ppp) REVERT: B 97 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7477 (mm) REVERT: B 101 TYR cc_start: 0.8372 (t80) cc_final: 0.8056 (t80) REVERT: B 125 LYS cc_start: 0.8679 (mmtp) cc_final: 0.8046 (tptp) REVERT: B 137 ARG cc_start: 0.7861 (mtm110) cc_final: 0.7437 (mtp85) REVERT: B 153 LEU cc_start: 0.8869 (tp) cc_final: 0.8627 (tt) REVERT: B 156 LYS cc_start: 0.9151 (mmtm) cc_final: 0.8827 (mmtm) REVERT: B 169 ASN cc_start: 0.8422 (m-40) cc_final: 0.7994 (m-40) REVERT: B 175 GLN cc_start: 0.8037 (mm110) cc_final: 0.7622 (tp40) REVERT: B 190 GLU cc_start: 0.8236 (tp30) cc_final: 0.7622 (tp30) REVERT: B 194 LYS cc_start: 0.8463 (mttt) cc_final: 0.7970 (mttt) REVERT: B 243 VAL cc_start: 0.7135 (t) cc_final: 0.6820 (m) REVERT: B 255 GLN cc_start: 0.7703 (mm-40) cc_final: 0.7227 (mm-40) REVERT: B 346 ASN cc_start: 0.7120 (p0) cc_final: 0.6867 (p0) REVERT: B 391 GLU cc_start: 0.7877 (tp30) cc_final: 0.7498 (tp30) REVERT: B 420 PHE cc_start: 0.6388 (t80) cc_final: 0.6170 (t80) REVERT: B 455 GLU cc_start: 0.7196 (pm20) cc_final: 0.6843 (pm20) REVERT: B 469 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7219 (tt) REVERT: B 483 MET cc_start: 0.6743 (mmp) cc_final: 0.6453 (mmp) REVERT: B 503 ILE cc_start: 0.8259 (tt) cc_final: 0.7943 (tt) REVERT: B 523 LYS cc_start: 0.8509 (mttt) cc_final: 0.7987 (mptt) REVERT: B 533 LYS cc_start: 0.8784 (mtpp) cc_final: 0.7963 (mmtp) REVERT: B 556 GLN cc_start: 0.8202 (tm130) cc_final: 0.7779 (tm-30) REVERT: B 563 LYS cc_start: 0.7494 (tttp) cc_final: 0.7204 (ttpp) REVERT: B 564 TYR cc_start: 0.8125 (m-80) cc_final: 0.7454 (m-10) REVERT: B 565 ASP cc_start: 0.8122 (t0) cc_final: 0.7917 (t0) REVERT: B 572 ASP cc_start: 0.7969 (t0) cc_final: 0.7449 (t0) REVERT: B 592 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8233 (pttp) REVERT: M 17 GLU cc_start: 0.6044 (OUTLIER) cc_final: 0.5680 (tt0) REVERT: M 21 LYS cc_start: 0.8628 (mttp) cc_final: 0.8241 (mmtt) REVERT: M 69 VAL cc_start: 0.7425 (t) cc_final: 0.6869 (m) REVERT: M 93 TYR cc_start: 0.6806 (t80) cc_final: 0.6440 (t80) REVERT: M 116 MET cc_start: 0.6754 (tpp) cc_final: 0.6259 (tpp) REVERT: S 1 MET cc_start: 0.6229 (tpt) cc_final: 0.5889 (tpt) REVERT: S 71 LEU cc_start: 0.7464 (mp) cc_final: 0.7217 (mp) outliers start: 40 outliers final: 30 residues processed: 401 average time/residue: 0.2933 time to fit residues: 165.5289 Evaluate side-chains 413 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 377 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 383 HIS Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 417 TRP Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 522 TYR Chi-restraints excluded: chain D residue 581 HIS Chi-restraints excluded: chain D residue 595 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 592 LYS Chi-restraints excluded: chain B residue 598 PHE Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 10 CYS Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 51 THR Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 97 CYS Chi-restraints excluded: chain M residue 110 TYR Chi-restraints excluded: chain S residue 13 LYS Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 89 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 43 optimal weight: 0.4980 chunk 132 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN B 426 GLN B 601 GLN ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.151001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.131399 restraints weight = 22540.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.135846 restraints weight = 13231.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.139039 restraints weight = 8627.355| |-----------------------------------------------------------------------------| r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11559 Z= 0.157 Angle : 0.743 12.866 15640 Z= 0.364 Chirality : 0.044 0.364 1850 Planarity : 0.005 0.077 1971 Dihedral : 4.504 19.675 1535 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.45 % Allowed : 25.22 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.22), residues: 1419 helix: 1.09 (0.16), residues: 1000 sheet: 0.82 (0.82), residues: 46 loop : 0.30 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP D 236 HIS 0.009 0.001 HIS S 117 PHE 0.053 0.002 PHE D 226 TYR 0.018 0.001 TYR D 277 ARG 0.009 0.000 ARG B 341 Details of bonding type rmsd hydrogen bonds : bond 0.04192 ( 749) hydrogen bonds : angle 4.85589 ( 2175) covalent geometry : bond 0.00341 (11559) covalent geometry : angle 0.74271 (15640) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 381 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 32 GLU cc_start: 0.8010 (pm20) cc_final: 0.6976 (pm20) REVERT: D 67 MET cc_start: 0.6191 (ttt) cc_final: 0.5496 (tpt) REVERT: D 92 ARG cc_start: 0.7890 (ttt180) cc_final: 0.7164 (ttt180) REVERT: D 93 ILE cc_start: 0.8691 (mm) cc_final: 0.8182 (tp) REVERT: D 118 LYS cc_start: 0.8668 (ptpp) cc_final: 0.8398 (ptpp) REVERT: D 170 MET cc_start: 0.7470 (mmm) cc_final: 0.6933 (mmm) REVERT: D 177 TYR cc_start: 0.6998 (t80) cc_final: 0.5955 (t80) REVERT: D 207 ILE cc_start: 0.8252 (tt) cc_final: 0.7883 (mt) REVERT: D 209 GLU cc_start: 0.7773 (tp30) cc_final: 0.7491 (tp30) REVERT: D 242 ILE cc_start: 0.8768 (mm) cc_final: 0.8371 (tp) REVERT: D 245 PHE cc_start: 0.8194 (m-80) cc_final: 0.7834 (m-80) REVERT: D 257 LYS cc_start: 0.8580 (tppt) cc_final: 0.8132 (tppt) REVERT: D 306 GLN cc_start: 0.8602 (tp-100) cc_final: 0.8353 (tp-100) REVERT: D 314 ASP cc_start: 0.7138 (t0) cc_final: 0.6794 (t0) REVERT: D 342 LYS cc_start: 0.8244 (mttt) cc_final: 0.7938 (mttt) REVERT: D 345 ILE cc_start: 0.8885 (mt) cc_final: 0.8572 (tp) REVERT: D 346 LEU cc_start: 0.9048 (mt) cc_final: 0.8665 (mt) REVERT: D 351 ASP cc_start: 0.7827 (m-30) cc_final: 0.7460 (t0) REVERT: D 357 ARG cc_start: 0.7646 (mtm-85) cc_final: 0.6989 (mtm-85) REVERT: D 371 LYS cc_start: 0.8245 (ttpp) cc_final: 0.7768 (ttpp) REVERT: D 372 ASN cc_start: 0.8157 (p0) cc_final: 0.7548 (p0) REVERT: D 375 GLU cc_start: 0.8115 (mp0) cc_final: 0.7491 (mp0) REVERT: D 378 LYS cc_start: 0.8732 (mttp) cc_final: 0.8347 (mttp) REVERT: D 379 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7515 (mppt) REVERT: D 440 GLN cc_start: 0.8057 (mt0) cc_final: 0.7379 (tt0) REVERT: D 442 LEU cc_start: 0.8600 (mt) cc_final: 0.8326 (mt) REVERT: D 449 LYS cc_start: 0.8246 (tttt) cc_final: 0.7883 (tttt) REVERT: D 452 ARG cc_start: 0.7651 (mtt180) cc_final: 0.7239 (mtp180) REVERT: D 482 LEU cc_start: 0.8092 (mp) cc_final: 0.7873 (mt) REVERT: D 528 LYS cc_start: 0.7627 (mttt) cc_final: 0.7204 (mttp) REVERT: D 535 GLN cc_start: 0.7222 (tp-100) cc_final: 0.6716 (tp-100) REVERT: D 547 GLN cc_start: 0.8520 (tp-100) cc_final: 0.8140 (tp-100) REVERT: D 567 GLU cc_start: 0.7779 (tp30) cc_final: 0.7393 (tp30) REVERT: D 577 GLN cc_start: 0.7417 (tp-100) cc_final: 0.6878 (tp40) REVERT: D 595 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7085 (tt0) REVERT: B 50 MET cc_start: 0.7283 (tpp) cc_final: 0.6703 (tpt) REVERT: B 69 MET cc_start: 0.7696 (ppp) cc_final: 0.7375 (ppp) REVERT: B 97 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7529 (mm) REVERT: B 101 TYR cc_start: 0.8466 (t80) cc_final: 0.8187 (t80) REVERT: B 125 LYS cc_start: 0.8700 (mmtp) cc_final: 0.8050 (tptp) REVERT: B 137 ARG cc_start: 0.7915 (mtm110) cc_final: 0.7505 (mtp85) REVERT: B 153 LEU cc_start: 0.8883 (tp) cc_final: 0.8651 (tt) REVERT: B 156 LYS cc_start: 0.9047 (mmtm) cc_final: 0.8830 (mmtm) REVERT: B 169 ASN cc_start: 0.8459 (m-40) cc_final: 0.8044 (m-40) REVERT: B 175 GLN cc_start: 0.8073 (mm110) cc_final: 0.7667 (tp40) REVERT: B 185 LYS cc_start: 0.8447 (ptmm) cc_final: 0.8198 (ptmm) REVERT: B 190 GLU cc_start: 0.8277 (tp30) cc_final: 0.7691 (tp30) REVERT: B 194 LYS cc_start: 0.8486 (mttt) cc_final: 0.8015 (mttt) REVERT: B 243 VAL cc_start: 0.7114 (t) cc_final: 0.6803 (m) REVERT: B 255 GLN cc_start: 0.7716 (mm-40) cc_final: 0.7212 (mm-40) REVERT: B 317 MET cc_start: 0.7538 (tpp) cc_final: 0.6880 (tmm) REVERT: B 346 ASN cc_start: 0.7072 (p0) cc_final: 0.6817 (p0) REVERT: B 391 GLU cc_start: 0.7855 (tp30) cc_final: 0.7491 (tp30) REVERT: B 420 PHE cc_start: 0.6448 (t80) cc_final: 0.6233 (t80) REVERT: B 455 GLU cc_start: 0.7151 (pm20) cc_final: 0.6844 (pm20) REVERT: B 469 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7251 (tt) REVERT: B 483 MET cc_start: 0.6672 (mmp) cc_final: 0.6357 (mmp) REVERT: B 503 ILE cc_start: 0.8268 (tt) cc_final: 0.7944 (tt) REVERT: B 523 LYS cc_start: 0.8531 (mttt) cc_final: 0.7988 (mptt) REVERT: B 533 LYS cc_start: 0.8856 (mtpp) cc_final: 0.8019 (mmtp) REVERT: B 556 GLN cc_start: 0.8189 (tm130) cc_final: 0.7765 (tm-30) REVERT: B 563 LYS cc_start: 0.7510 (tttp) cc_final: 0.7203 (ttpp) REVERT: B 564 TYR cc_start: 0.8151 (m-80) cc_final: 0.7447 (m-10) REVERT: B 565 ASP cc_start: 0.8185 (t70) cc_final: 0.7955 (t0) REVERT: B 572 ASP cc_start: 0.8053 (t0) cc_final: 0.7508 (t0) REVERT: B 592 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8245 (pttp) REVERT: M 1 MET cc_start: 0.5086 (mmm) cc_final: 0.4750 (mmm) REVERT: M 17 GLU cc_start: 0.6084 (OUTLIER) cc_final: 0.5772 (tt0) REVERT: M 21 LYS cc_start: 0.8688 (mttp) cc_final: 0.8264 (mmtt) REVERT: M 69 VAL cc_start: 0.7504 (t) cc_final: 0.6979 (m) REVERT: M 93 TYR cc_start: 0.6882 (t80) cc_final: 0.6518 (t80) REVERT: M 116 MET cc_start: 0.6794 (tpp) cc_final: 0.6315 (tpp) REVERT: S 1 MET cc_start: 0.6320 (tpt) cc_final: 0.5950 (tpt) REVERT: S 13 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7300 (tttp) REVERT: S 71 LEU cc_start: 0.7433 (mp) cc_final: 0.7200 (mp) REVERT: S 140 GLN cc_start: 0.7506 (tt0) cc_final: 0.7136 (tt0) outliers start: 44 outliers final: 30 residues processed: 399 average time/residue: 0.3212 time to fit residues: 176.3494 Evaluate side-chains 413 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 376 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 383 HIS Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 417 TRP Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 522 TYR Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 581 HIS Chi-restraints excluded: chain D residue 595 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 592 LYS Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 650 ASN Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 10 CYS Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 51 THR Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 97 CYS Chi-restraints excluded: chain M residue 110 TYR Chi-restraints excluded: chain S residue 13 LYS Chi-restraints excluded: chain S residue 24 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 95 optimal weight: 1.9990 chunk 113 optimal weight: 0.0000 chunk 123 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 119 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 57 optimal weight: 0.0570 chunk 15 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 73 optimal weight: 0.0570 chunk 130 optimal weight: 0.5980 overall best weight: 0.2820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN B 426 GLN B 601 GLN ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 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 = 0.4213 r_free = 0.4213 target = 0.151402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.131655 restraints weight = 22674.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.136142 restraints weight = 13441.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.139298 restraints weight = 8785.106| |-----------------------------------------------------------------------------| r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 11559 Z= 0.171 Angle : 0.958 59.176 15640 Z= 0.514 Chirality : 0.047 0.808 1850 Planarity : 0.005 0.071 1971 Dihedral : 4.571 29.209 1535 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.52 % Allowed : 25.76 % Favored : 70.71 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.22), residues: 1419 helix: 1.10 (0.16), residues: 1000 sheet: 0.81 (0.82), residues: 46 loop : 0.26 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP D 236 HIS 0.009 0.001 HIS S 117 PHE 0.051 0.002 PHE D 226 TYR 0.015 0.001 TYR B 99 ARG 0.005 0.000 ARG B 250 Details of bonding type rmsd hydrogen bonds : bond 0.04183 ( 749) hydrogen bonds : angle 4.85294 ( 2175) covalent geometry : bond 0.00370 (11559) covalent geometry : angle 0.95794 (15640) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6045.48 seconds wall clock time: 107 minutes 38.32 seconds (6458.32 seconds total)