Starting phenix.real_space_refine on Sat Aug 23 10:00:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c5c_45214/08_2025/9c5c_45214.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c5c_45214/08_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_45214/08_2025/9c5c_45214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c5c_45214/08_2025/9c5c_45214.map" model { file = "/net/cci-nas-00/data/ceres_data/9c5c_45214/08_2025/9c5c_45214.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c5c_45214/08_2025/9c5c_45214.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.95, per 1000 atoms: 0.17 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: 1.00 Conformation dependent library (CDL) restraints added in 486.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.38 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: 1.94 Time building geometry restraints manager: 1.25 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: 3.670 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.780 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.770 ------------------------------------------------------------------------------- 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 : 20.68 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.014 0.001 ARG D 475 TYR 0.023 0.002 TYR D 161 PHE 0.036 0.002 PHE M 32 TRP 0.018 0.002 TRP D 74 HIS 0.008 0.001 HIS S 117 Details of bonding type rmsd covalent geometry : bond 0.00365 (11559) covalent geometry : angle 0.73447 (15640) hydrogen bonds : bond 0.18433 ( 749) hydrogen bonds : angle 6.65637 ( 2175) *********************** 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 : 0.439 Fit side-chains 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 92 ARG cc_start: 0.6693 (ttt180) cc_final: 0.6240 (ttt180) REVERT: D 168 LEU cc_start: 0.6675 (mt) cc_final: 0.5962 (mt) REVERT: D 177 TYR cc_start: 0.5552 (t80) cc_final: 0.5225 (t80) REVERT: D 180 SER cc_start: 0.5130 (p) cc_final: 0.4861 (p) REVERT: D 194 ASP cc_start: 0.5509 (t70) cc_final: 0.4806 (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: 0.6528 (mt) REVERT: D 321 TYR cc_start: 0.5814 (t80) cc_final: 0.5435 (t80) REVERT: D 327 MET cc_start: 0.5209 (mtp) cc_final: 0.4994 (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: 0.7114 (mt) REVERT: D 443 ASP cc_start: 0.6298 (t70) cc_final: 0.5295 (t0) REVERT: D 475 ARG cc_start: 0.6986 (mmm160) cc_final: 0.6735 (mmm160) REVERT: D 480 GLU cc_start: 0.6293 (tp30) cc_final: 0.5702 (tp30) REVERT: D 567 GLU cc_start: 0.6795 (tp30) cc_final: 0.6073 (tp30) REVERT: D 584 LYS cc_start: 0.7467 (mttt) cc_final: 0.7210 (mttt) REVERT: B 59 LYS cc_start: 0.7795 (mtmt) cc_final: 0.7564 (mtmm) REVERT: B 64 LYS cc_start: 0.8490 (mttm) cc_final: 0.8262 (mttt) REVERT: B 83 VAL cc_start: 0.7239 (t) cc_final: 0.7036 (p) REVERT: B 153 LEU cc_start: 0.8345 (tp) cc_final: 0.8063 (tt) REVERT: B 194 LYS cc_start: 0.7713 (mttt) cc_final: 0.7497 (mtpp) REVERT: B 243 VAL cc_start: 0.7522 (t) cc_final: 0.7316 (m) REVERT: B 302 ARG cc_start: 0.7689 (tpt90) cc_final: 0.7167 (tpt90) REVERT: B 420 PHE cc_start: 0.7194 (t80) cc_final: 0.6633 (t80) REVERT: B 426 GLN cc_start: 0.8399 (mm-40) cc_final: 0.7968 (mm110) REVERT: B 523 LYS cc_start: 0.7966 (mttt) cc_final: 0.7631 (mmtm) REVERT: B 526 THR cc_start: 0.9012 (p) cc_final: 0.8576 (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: 0.7620 (mm) REVERT: B 564 TYR cc_start: 0.7669 (m-80) cc_final: 0.7419 (m-10) REVERT: B 577 ILE cc_start: 0.8607 (mt) cc_final: 0.8330 (mm) REVERT: B 593 TYR cc_start: 0.7487 (m-80) cc_final: 0.6242 (m-80) REVERT: B 618 GLN cc_start: 0.6457 (tt0) cc_final: 0.6098 (tt0) REVERT: B 650 ASN cc_start: 0.7195 (m110) cc_final: 0.6828 (p0) REVERT: S 115 LYS cc_start: 0.8445 (ttpt) cc_final: 0.8056 (ttpt) outliers start: 1 outliers final: 0 residues processed: 419 average time/residue: 0.1036 time to fit residues: 59.3842 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 : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 559 GLN D 586 GLN B 91 ASN ** 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** S 30 GLN ** S 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.149287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.130713 restraints weight = 22679.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.135109 restraints weight = 13259.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.138225 restraints weight = 8550.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.140534 restraints weight = 5813.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.142093 restraints weight = 4145.355| |-----------------------------------------------------------------------------| r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11559 Z= 0.204 Angle : 0.734 12.145 15640 Z= 0.379 Chirality : 0.044 0.229 1850 Planarity : 0.005 0.052 1971 Dihedral : 4.605 24.225 1535 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.76 % Allowed : 17.78 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.22), residues: 1419 helix: 0.78 (0.16), residues: 997 sheet: 0.66 (0.82), residues: 44 loop : 0.74 (0.35), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 447 TYR 0.022 0.002 TYR B 101 PHE 0.022 0.002 PHE M 66 TRP 0.021 0.002 TRP D 236 HIS 0.021 0.001 HIS S 117 Details of bonding type rmsd covalent geometry : bond 0.00433 (11559) covalent geometry : angle 0.73379 (15640) hydrogen bonds : bond 0.05504 ( 749) hydrogen bonds : angle 5.28390 ( 2175) *********************** 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 429 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 381 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 93 ILE cc_start: 0.8645 (mm) cc_final: 0.8055 (tp) REVERT: D 170 MET cc_start: 0.7650 (mmm) cc_final: 0.7406 (mmm) REVERT: D 177 TYR cc_start: 0.6954 (t80) cc_final: 0.6178 (t80) REVERT: D 191 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7591 (tppt) REVERT: D 207 ILE cc_start: 0.8206 (tt) cc_final: 0.7780 (mt) REVERT: D 209 GLU cc_start: 0.7688 (tp30) cc_final: 0.7278 (tp30) REVERT: D 242 ILE cc_start: 0.8823 (mm) cc_final: 0.8383 (mm) REVERT: D 245 PHE cc_start: 0.8261 (m-80) cc_final: 0.7686 (m-80) REVERT: D 257 LYS cc_start: 0.8531 (tppt) cc_final: 0.8205 (tppt) REVERT: D 306 GLN cc_start: 0.8613 (tp-100) cc_final: 0.8185 (tp-100) REVERT: D 307 LYS cc_start: 0.8688 (mmtm) cc_final: 0.8430 (mmtm) REVERT: D 308 LEU cc_start: 0.8613 (mt) cc_final: 0.8401 (mt) REVERT: D 314 ASP cc_start: 0.6947 (t0) cc_final: 0.6590 (t0) REVERT: D 341 HIS cc_start: 0.6910 (m-70) cc_final: 0.6477 (m-70) REVERT: D 374 MET cc_start: 0.8275 (mtt) cc_final: 0.7958 (mtt) REVERT: D 375 GLU cc_start: 0.8174 (mp0) cc_final: 0.7585 (pm20) REVERT: D 378 LYS cc_start: 0.8804 (mttp) cc_final: 0.8397 (mtmm) REVERT: D 379 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7510 (mppt) REVERT: D 416 GLU cc_start: 0.7914 (tt0) cc_final: 0.7646 (mm-30) REVERT: D 440 GLN cc_start: 0.8327 (mm-40) cc_final: 0.7329 (mm110) REVERT: D 442 LEU cc_start: 0.8787 (mt) cc_final: 0.8519 (mt) REVERT: D 443 ASP cc_start: 0.8272 (t70) cc_final: 0.8034 (t0) REVERT: D 449 LYS cc_start: 0.8087 (tttt) cc_final: 0.7833 (tttt) REVERT: D 535 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.6935 (tp-100) REVERT: D 547 GLN cc_start: 0.8587 (tp-100) cc_final: 0.7999 (tp-100) REVERT: B 50 MET cc_start: 0.6948 (tpp) cc_final: 0.6639 (tpp) REVERT: B 59 LYS cc_start: 0.8438 (mtmt) cc_final: 0.7607 (mmmt) REVERT: B 83 VAL cc_start: 0.7819 (t) cc_final: 0.7551 (p) REVERT: B 87 VAL cc_start: 0.8755 (m) cc_final: 0.8402 (t) REVERT: B 97 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7442 (mm) REVERT: B 125 LYS cc_start: 0.8705 (mmtp) cc_final: 0.8285 (mmtm) REVERT: B 169 ASN cc_start: 0.8401 (m-40) cc_final: 0.7868 (m110) REVERT: B 190 GLU cc_start: 0.8235 (tp30) cc_final: 0.7978 (tp30) REVERT: B 194 LYS cc_start: 0.8624 (mttt) cc_final: 0.8160 (mtpp) REVERT: B 243 VAL cc_start: 0.7164 (t) cc_final: 0.6849 (m) REVERT: B 255 GLN cc_start: 0.7795 (mm110) cc_final: 0.7516 (mm110) REVERT: B 302 ARG cc_start: 0.8372 (tpt90) cc_final: 0.8068 (tpp80) REVERT: B 312 ASN cc_start: 0.8039 (t0) cc_final: 0.7660 (t0) REVERT: B 317 MET cc_start: 0.7332 (tpp) cc_final: 0.6996 (tpp) REVERT: B 346 ASN cc_start: 0.7270 (p0) cc_final: 0.7028 (p0) REVERT: B 418 LYS cc_start: 0.7466 (mmtt) cc_final: 0.7074 (mmmt) REVERT: B 424 THR cc_start: 0.8387 (m) cc_final: 0.8132 (m) REVERT: B 503 ILE cc_start: 0.8306 (tt) cc_final: 0.8061 (tt) REVERT: B 523 LYS cc_start: 0.8576 (mttt) cc_final: 0.7960 (mmtm) REVERT: B 556 GLN cc_start: 0.8180 (tm130) cc_final: 0.7692 (tm-30) REVERT: B 564 TYR cc_start: 0.8283 (m-80) cc_final: 0.7901 (m-10) REVERT: B 573 ARG cc_start: 0.7916 (mmt90) cc_final: 0.7690 (tpp-160) REVERT: B 579 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.6858 (tp-100) REVERT: B 601 GLN cc_start: 0.8287 (tm-30) cc_final: 0.8061 (tm-30) REVERT: B 624 HIS cc_start: 0.8347 (t-90) cc_final: 0.8075 (t70) REVERT: M 1 MET cc_start: 0.5337 (mmm) cc_final: 0.4910 (mmm) REVERT: M 17 GLU cc_start: 0.5724 (OUTLIER) cc_final: 0.5404 (tt0) REVERT: M 43 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8172 (mm-30) REVERT: M 61 ARG cc_start: 0.7043 (ptm160) cc_final: 0.6559 (ptm160) REVERT: M 116 MET cc_start: 0.7064 (tpp) cc_final: 0.6676 (tpp) REVERT: S 1 MET cc_start: 0.6907 (OUTLIER) cc_final: 0.6686 (tpt) REVERT: S 93 PHE cc_start: 0.7423 (t80) cc_final: 0.7167 (t80) REVERT: S 96 THR cc_start: 0.8972 (m) cc_final: 0.8664 (p) REVERT: S 115 LYS cc_start: 0.8680 (ttpt) cc_final: 0.8082 (ttpt) REVERT: S 144 GLN cc_start: 0.8039 (mt0) cc_final: 0.7775 (mt0) outliers start: 48 outliers final: 23 residues processed: 404 average time/residue: 0.0970 time to fit residues: 55.0706 Evaluate side-chains 398 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 368 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 191 LYS 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 219 ILE 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 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 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 13 LYS 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 21 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 500 HIS D 577 GLN D 583 GLN D 586 GLN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** M 119 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.148508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.129985 restraints weight = 22752.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.134321 restraints weight = 13320.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.137427 restraints weight = 8621.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.139675 restraints weight = 5868.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.141220 restraints weight = 4187.263| |-----------------------------------------------------------------------------| r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11559 Z= 0.172 Angle : 0.686 12.568 15640 Z= 0.349 Chirality : 0.044 0.199 1850 Planarity : 0.005 0.049 1971 Dihedral : 4.621 25.451 1535 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.39 % Allowed : 19.26 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.22), residues: 1419 helix: 0.88 (0.16), residues: 1006 sheet: 0.54 (0.81), residues: 48 loop : 0.54 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 250 TYR 0.028 0.002 TYR B 101 PHE 0.021 0.002 PHE B 420 TRP 0.015 0.002 TRP D 236 HIS 0.006 0.001 HIS B 223 Details of bonding type rmsd covalent geometry : bond 0.00364 (11559) covalent geometry : angle 0.68632 (15640) hydrogen bonds : bond 0.04765 ( 749) hydrogen bonds : angle 5.06273 ( 2175) *********************** 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 438 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 382 time to evaluate : 0.319 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 59 VAL cc_start: 0.6574 (OUTLIER) cc_final: 0.6198 (m) REVERT: D 93 ILE cc_start: 0.8677 (mm) cc_final: 0.8156 (tp) REVERT: D 170 MET cc_start: 0.7663 (mmm) cc_final: 0.7278 (mmm) REVERT: D 177 TYR cc_start: 0.6974 (t80) cc_final: 0.5906 (t80) REVERT: D 182 ARG cc_start: 0.7654 (mmm160) cc_final: 0.7394 (mmm160) REVERT: D 207 ILE cc_start: 0.8273 (tt) cc_final: 0.7802 (mt) REVERT: D 242 ILE cc_start: 0.8723 (mm) cc_final: 0.8291 (mm) REVERT: D 245 PHE cc_start: 0.8187 (m-80) cc_final: 0.7729 (m-80) REVERT: D 257 LYS cc_start: 0.8449 (tppt) cc_final: 0.8197 (tppt) REVERT: D 306 GLN cc_start: 0.8642 (tp-100) cc_final: 0.8416 (tp-100) REVERT: D 307 LYS cc_start: 0.8679 (mmtm) cc_final: 0.8413 (mmtm) REVERT: D 314 ASP cc_start: 0.7048 (t0) cc_final: 0.6616 (t0) REVERT: D 345 ILE cc_start: 0.8998 (mt) cc_final: 0.8482 (tp) REVERT: D 346 LEU cc_start: 0.9022 (mt) cc_final: 0.8671 (mt) REVERT: D 357 ARG cc_start: 0.7608 (mtm-85) cc_final: 0.6954 (mtm-85) REVERT: D 359 ARG cc_start: 0.7639 (tpp80) cc_final: 0.7377 (tpp80) REVERT: D 374 MET cc_start: 0.8296 (mtt) cc_final: 0.8018 (mtt) REVERT: D 375 GLU cc_start: 0.8072 (mp0) cc_final: 0.7491 (pm20) REVERT: D 378 LYS cc_start: 0.8737 (mttp) cc_final: 0.8436 (mttp) REVERT: D 379 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7536 (mppt) REVERT: D 442 LEU cc_start: 0.8720 (mt) cc_final: 0.8455 (mt) REVERT: D 449 LYS cc_start: 0.8198 (tttt) cc_final: 0.7965 (tttt) REVERT: D 464 ASP cc_start: 0.7846 (m-30) cc_final: 0.7643 (m-30) REVERT: D 528 LYS cc_start: 0.7605 (mttp) cc_final: 0.7123 (ptpt) REVERT: D 535 GLN cc_start: 0.7308 (OUTLIER) cc_final: 0.6854 (tp-100) REVERT: D 547 GLN cc_start: 0.8439 (tp-100) cc_final: 0.8115 (tp-100) REVERT: D 567 GLU cc_start: 0.7550 (tp30) cc_final: 0.6715 (mm-30) REVERT: B 50 MET cc_start: 0.6901 (tpp) cc_final: 0.6539 (tpp) REVERT: B 52 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7301 (mt-10) REVERT: B 59 LYS cc_start: 0.8402 (mtmt) cc_final: 0.7670 (mmmt) REVERT: B 87 VAL cc_start: 0.8809 (m) cc_final: 0.8496 (t) REVERT: B 97 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7409 (mm) REVERT: B 130 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8391 (tt) REVERT: B 156 LYS cc_start: 0.9140 (mmtm) cc_final: 0.8858 (mmtm) REVERT: B 169 ASN cc_start: 0.8332 (m-40) cc_final: 0.7952 (m-40) REVERT: B 190 GLU cc_start: 0.8222 (tp30) cc_final: 0.7856 (tp30) REVERT: B 194 LYS cc_start: 0.8590 (mttt) cc_final: 0.8099 (mtpp) REVERT: B 209 MET cc_start: 0.7919 (ttm) cc_final: 0.7045 (ttm) REVERT: B 243 VAL cc_start: 0.7192 (t) cc_final: 0.6867 (m) REVERT: B 255 GLN cc_start: 0.7715 (mm110) cc_final: 0.7466 (mm110) REVERT: B 302 ARG cc_start: 0.8343 (tpt90) cc_final: 0.8091 (tpp80) REVERT: B 312 ASN cc_start: 0.8052 (t0) cc_final: 0.7654 (t0) REVERT: B 346 ASN cc_start: 0.7221 (p0) cc_final: 0.6986 (p0) REVERT: B 390 LEU cc_start: 0.8209 (tp) cc_final: 0.7965 (tp) REVERT: B 402 ILE cc_start: 0.4612 (tp) cc_final: 0.4245 (tp) REVERT: B 418 LYS cc_start: 0.7580 (mmtt) cc_final: 0.7268 (mmmt) REVERT: B 455 GLU cc_start: 0.7428 (pm20) cc_final: 0.6852 (pm20) REVERT: B 503 ILE cc_start: 0.8251 (tt) cc_final: 0.7978 (tt) REVERT: B 531 LEU cc_start: 0.8311 (tp) cc_final: 0.8066 (mp) REVERT: B 533 LYS cc_start: 0.8745 (mtpp) cc_final: 0.7953 (mttp) REVERT: B 554 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.6951 (tp) REVERT: B 563 LYS cc_start: 0.7542 (tttp) cc_final: 0.7198 (ttpp) REVERT: B 564 TYR cc_start: 0.8288 (m-80) cc_final: 0.7766 (m-10) REVERT: B 566 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7462 (tm-30) REVERT: M 1 MET cc_start: 0.5280 (mmm) cc_final: 0.4546 (mmm) REVERT: M 116 MET cc_start: 0.6998 (tpp) cc_final: 0.6649 (tpp) outliers start: 56 outliers final: 33 residues processed: 403 average time/residue: 0.1005 time to fit residues: 56.6307 Evaluate side-chains 417 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 377 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 192 LEU Chi-restraints excluded: chain D residue 219 LEU 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 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 219 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 355 GLN Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 566 GLN 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 49 ILE Chi-restraints excluded: chain M residue 51 THR Chi-restraints excluded: chain M residue 70 ILE 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 57 optimal weight: 0.4980 chunk 116 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 128 optimal weight: 0.4980 chunk 76 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 D 583 GLN B 121 GLN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 579 GLN ** B 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 638 ASN B 650 ASN M 26 GLN ** M 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 144 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.149912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.131093 restraints weight = 22928.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.135592 restraints weight = 13434.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.138701 restraints weight = 8606.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.140933 restraints weight = 5894.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.142453 restraints weight = 4229.755| |-----------------------------------------------------------------------------| r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.3321 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 : 0.675 11.393 15640 Z= 0.337 Chirality : 0.042 0.210 1850 Planarity : 0.004 0.048 1971 Dihedral : 4.560 24.878 1535 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.31 % Allowed : 20.91 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.22), residues: 1419 helix: 0.96 (0.16), residues: 999 sheet: 0.90 (0.82), residues: 46 loop : 0.56 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 250 TYR 0.014 0.001 TYR D 522 PHE 0.018 0.002 PHE M 66 TRP 0.034 0.003 TRP D 236 HIS 0.007 0.001 HIS S 117 Details of bonding type rmsd covalent geometry : bond 0.00336 (11559) covalent geometry : angle 0.67485 (15640) hydrogen bonds : bond 0.04498 ( 749) hydrogen bonds : angle 4.92894 ( 2175) *********************** 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 432 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 377 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 59 VAL cc_start: 0.6567 (OUTLIER) cc_final: 0.6176 (m) REVERT: D 92 ARG cc_start: 0.7821 (ttt180) cc_final: 0.7290 (ttt180) REVERT: D 93 ILE cc_start: 0.8676 (mm) cc_final: 0.8148 (tp) REVERT: D 170 MET cc_start: 0.7579 (mmm) cc_final: 0.7063 (mmm) REVERT: D 177 TYR cc_start: 0.6927 (t80) cc_final: 0.6103 (t80) REVERT: D 207 ILE cc_start: 0.8252 (tt) cc_final: 0.7768 (mt) REVERT: D 242 ILE cc_start: 0.8721 (mm) cc_final: 0.8243 (mm) REVERT: D 245 PHE cc_start: 0.8205 (m-80) cc_final: 0.7709 (m-80) REVERT: D 263 LEU cc_start: 0.8916 (mt) cc_final: 0.8700 (mt) REVERT: D 306 GLN cc_start: 0.8589 (tp-100) cc_final: 0.8359 (tp-100) REVERT: D 307 LYS cc_start: 0.8683 (mmtm) cc_final: 0.8399 (mmtm) REVERT: D 314 ASP cc_start: 0.7048 (t0) cc_final: 0.6680 (t0) REVERT: D 345 ILE cc_start: 0.8960 (mt) cc_final: 0.8451 (tp) REVERT: D 346 LEU cc_start: 0.8988 (mt) cc_final: 0.8610 (mt) REVERT: D 357 ARG cc_start: 0.7586 (mtm-85) cc_final: 0.6876 (mtm-85) REVERT: D 359 ARG cc_start: 0.7562 (tpp80) cc_final: 0.7276 (tpp80) REVERT: D 371 LYS cc_start: 0.8067 (ttpp) cc_final: 0.7638 (ttpp) REVERT: D 372 ASN cc_start: 0.8080 (p0) cc_final: 0.7764 (p0) REVERT: D 374 MET cc_start: 0.8207 (mtt) cc_final: 0.7562 (mtt) REVERT: D 375 GLU cc_start: 0.8003 (mp0) cc_final: 0.7556 (mp0) REVERT: D 378 LYS cc_start: 0.8720 (mttp) cc_final: 0.8225 (mttp) REVERT: D 379 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7471 (mppt) REVERT: D 442 LEU cc_start: 0.8710 (mt) cc_final: 0.8457 (mt) REVERT: D 449 LYS cc_start: 0.8196 (tttt) cc_final: 0.7970 (tttt) REVERT: D 489 CYS cc_start: 0.7144 (p) cc_final: 0.6930 (p) REVERT: D 547 GLN cc_start: 0.8437 (tp-100) cc_final: 0.8068 (tp-100) REVERT: D 567 GLU cc_start: 0.7533 (tp30) cc_final: 0.7312 (tp30) REVERT: D 577 GLN cc_start: 0.7275 (tp-100) cc_final: 0.6727 (tm-30) REVERT: B 50 MET cc_start: 0.6938 (tpp) cc_final: 0.6514 (tpp) REVERT: B 63 MET cc_start: 0.7878 (mmm) cc_final: 0.7537 (mmm) REVERT: B 69 MET cc_start: 0.7555 (ppp) cc_final: 0.7270 (ppp) REVERT: B 87 VAL cc_start: 0.8832 (m) cc_final: 0.8539 (t) REVERT: B 97 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7413 (mm) REVERT: B 101 TYR cc_start: 0.8334 (t80) cc_final: 0.7985 (t80) REVERT: B 125 LYS cc_start: 0.8731 (mmtp) cc_final: 0.8071 (tptp) REVERT: B 130 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8380 (tt) REVERT: B 156 LYS cc_start: 0.9145 (mmtm) cc_final: 0.8788 (mmtm) REVERT: B 169 ASN cc_start: 0.8410 (m-40) cc_final: 0.8008 (m-40) REVERT: B 190 GLU cc_start: 0.8254 (tp30) cc_final: 0.7795 (tp30) REVERT: B 194 LYS cc_start: 0.8526 (mttt) cc_final: 0.7969 (mtpp) REVERT: B 209 MET cc_start: 0.7915 (ttm) cc_final: 0.6823 (ttm) REVERT: B 243 VAL cc_start: 0.7197 (t) cc_final: 0.6869 (m) REVERT: B 255 GLN cc_start: 0.7656 (mm110) cc_final: 0.7438 (mm110) REVERT: B 301 ILE cc_start: 0.7664 (mm) cc_final: 0.7433 (mm) REVERT: B 311 ARG cc_start: 0.7453 (mtm-85) cc_final: 0.7209 (mtm-85) REVERT: B 346 ASN cc_start: 0.7188 (p0) cc_final: 0.6922 (p0) REVERT: B 503 ILE cc_start: 0.8264 (tt) cc_final: 0.7990 (tt) REVERT: B 531 LEU cc_start: 0.8289 (tp) cc_final: 0.8046 (mp) REVERT: B 556 GLN cc_start: 0.8242 (tm130) cc_final: 0.8034 (tm-30) REVERT: B 563 LYS cc_start: 0.7523 (tttp) cc_final: 0.7255 (ttpp) REVERT: B 564 TYR cc_start: 0.8202 (m-80) cc_final: 0.7646 (m-10) REVERT: B 566 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7699 (pp30) REVERT: B 577 ILE cc_start: 0.8579 (mt) cc_final: 0.8354 (mm) REVERT: B 579 GLN cc_start: 0.7450 (OUTLIER) cc_final: 0.6604 (tp-100) REVERT: B 602 LYS cc_start: 0.8971 (mmmm) cc_final: 0.8498 (mmmt) REVERT: M 1 MET cc_start: 0.5135 (mmm) cc_final: 0.4141 (mmm) REVERT: M 21 LYS cc_start: 0.8602 (mttp) cc_final: 0.8167 (mmtt) REVERT: M 116 MET cc_start: 0.6937 (tpp) cc_final: 0.6648 (tpp) REVERT: S 1 MET cc_start: 0.6661 (OUTLIER) cc_final: 0.6332 (tpt) REVERT: S 71 LEU cc_start: 0.7852 (mp) cc_final: 0.7640 (mp) REVERT: S 96 THR cc_start: 0.8913 (m) cc_final: 0.8671 (p) REVERT: S 128 MET cc_start: 0.7452 (mmm) cc_final: 0.7171 (mmp) outliers start: 55 outliers final: 33 residues processed: 395 average time/residue: 0.1000 time to fit residues: 55.3160 Evaluate side-chains 405 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 365 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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 192 LEU Chi-restraints excluded: chain D residue 219 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 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 355 GLN Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 566 GLN 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 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 89 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 91 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 23 optimal weight: 0.0470 chunk 119 optimal weight: 3.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 78 ASN ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 GLN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 638 ASN B 650 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.149316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.130443 restraints weight = 22442.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.134873 restraints weight = 13162.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.138022 restraints weight = 8497.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.140200 restraints weight = 5795.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.141825 restraints weight = 4180.944| |-----------------------------------------------------------------------------| r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11559 Z= 0.154 Angle : 0.663 11.576 15640 Z= 0.334 Chirality : 0.042 0.225 1850 Planarity : 0.004 0.048 1971 Dihedral : 4.508 23.648 1535 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.15 % Allowed : 22.00 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.22), residues: 1419 helix: 0.95 (0.16), residues: 1005 sheet: 0.64 (0.81), residues: 48 loop : 0.52 (0.35), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 250 TYR 0.015 0.001 TYR D 522 PHE 0.022 0.002 PHE D 454 TRP 0.048 0.003 TRP D 236 HIS 0.007 0.001 HIS S 117 Details of bonding type rmsd covalent geometry : bond 0.00332 (11559) covalent geometry : angle 0.66316 (15640) hydrogen bonds : bond 0.04372 ( 749) hydrogen bonds : angle 4.87621 ( 2175) *********************** 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 430 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 377 time to evaluate : 0.262 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 59 VAL cc_start: 0.6621 (OUTLIER) cc_final: 0.6137 (m) REVERT: D 92 ARG cc_start: 0.7940 (ttt180) cc_final: 0.7409 (ttt180) REVERT: D 93 ILE cc_start: 0.8704 (mm) cc_final: 0.8184 (tp) REVERT: D 170 MET cc_start: 0.7595 (mmm) cc_final: 0.7011 (mmm) REVERT: D 177 TYR cc_start: 0.6983 (t80) cc_final: 0.6180 (t80) REVERT: D 207 ILE cc_start: 0.8239 (tt) cc_final: 0.7754 (mt) REVERT: D 242 ILE cc_start: 0.8764 (mm) cc_final: 0.8262 (mm) REVERT: D 245 PHE cc_start: 0.8221 (m-80) cc_final: 0.7775 (m-80) REVERT: D 257 LYS cc_start: 0.8484 (tppt) cc_final: 0.8216 (tppt) REVERT: D 306 GLN cc_start: 0.8539 (tp-100) cc_final: 0.8314 (tp-100) REVERT: D 307 LYS cc_start: 0.8702 (mmtm) cc_final: 0.8412 (mmtm) REVERT: D 314 ASP cc_start: 0.7104 (t0) cc_final: 0.6732 (t0) REVERT: D 345 ILE cc_start: 0.8935 (mt) cc_final: 0.8445 (tp) REVERT: D 346 LEU cc_start: 0.9017 (mt) cc_final: 0.8636 (mt) REVERT: D 357 ARG cc_start: 0.7622 (mtm-85) cc_final: 0.6904 (mtm-85) REVERT: D 371 LYS cc_start: 0.8134 (ttpp) cc_final: 0.7675 (ttpp) REVERT: D 372 ASN cc_start: 0.8172 (p0) cc_final: 0.7835 (p0) REVERT: D 374 MET cc_start: 0.8216 (mtt) cc_final: 0.7568 (mtt) REVERT: D 375 GLU cc_start: 0.8030 (mp0) cc_final: 0.7545 (mp0) REVERT: D 378 LYS cc_start: 0.8777 (mttp) cc_final: 0.8280 (mptp) REVERT: D 379 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7513 (mppt) REVERT: D 442 LEU cc_start: 0.8677 (mt) cc_final: 0.8415 (mt) REVERT: D 449 LYS cc_start: 0.8276 (tttt) cc_final: 0.7912 (tttt) REVERT: D 452 ARG cc_start: 0.7628 (mtt180) cc_final: 0.7197 (mtp180) REVERT: D 489 CYS cc_start: 0.7162 (p) cc_final: 0.6921 (p) REVERT: D 535 GLN cc_start: 0.7227 (tp-100) cc_final: 0.6774 (tp-100) REVERT: D 547 GLN cc_start: 0.8421 (tp-100) cc_final: 0.8036 (tp-100) REVERT: D 584 LYS cc_start: 0.8389 (mttt) cc_final: 0.8013 (mptt) REVERT: B 50 MET cc_start: 0.6947 (tpp) cc_final: 0.6472 (tpp) REVERT: B 59 LYS cc_start: 0.8425 (mtmt) cc_final: 0.7487 (mmmt) REVERT: B 63 MET cc_start: 0.7782 (mmm) cc_final: 0.7534 (mmm) REVERT: B 69 MET cc_start: 0.7619 (ppp) cc_final: 0.7338 (ppp) REVERT: B 87 VAL cc_start: 0.8791 (m) cc_final: 0.8521 (t) REVERT: B 97 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7456 (mm) REVERT: B 101 TYR cc_start: 0.8455 (t80) cc_final: 0.8162 (t80) REVERT: B 125 LYS cc_start: 0.8728 (mmtp) cc_final: 0.8079 (tptp) REVERT: B 130 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8355 (tt) REVERT: B 152 MET cc_start: 0.7820 (mtm) cc_final: 0.7604 (mtt) REVERT: B 156 LYS cc_start: 0.9028 (mmtm) cc_final: 0.8785 (mmtm) REVERT: B 169 ASN cc_start: 0.8369 (m-40) cc_final: 0.8008 (m-40) REVERT: B 190 GLU cc_start: 0.8254 (tp30) cc_final: 0.7781 (tp30) REVERT: B 194 LYS cc_start: 0.8528 (mttt) cc_final: 0.8176 (mttt) REVERT: B 209 MET cc_start: 0.7921 (ttm) cc_final: 0.6940 (ttm) REVERT: B 243 VAL cc_start: 0.7175 (t) cc_final: 0.6859 (m) REVERT: B 301 ILE cc_start: 0.7564 (mm) cc_final: 0.7316 (mm) REVERT: B 311 ARG cc_start: 0.7494 (mtm-85) cc_final: 0.7231 (mtm-85) REVERT: B 346 ASN cc_start: 0.7135 (p0) cc_final: 0.6870 (p0) REVERT: B 420 PHE cc_start: 0.6422 (t80) cc_final: 0.6149 (t80) REVERT: B 469 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7245 (tt) REVERT: B 483 MET cc_start: 0.6611 (mmp) cc_final: 0.6367 (mmp) REVERT: B 503 ILE cc_start: 0.8247 (tt) cc_final: 0.7952 (tt) REVERT: B 531 LEU cc_start: 0.8314 (tp) cc_final: 0.8064 (mp) REVERT: B 556 GLN cc_start: 0.8212 (tm130) cc_final: 0.7811 (tm-30) REVERT: B 563 LYS cc_start: 0.7529 (tttp) cc_final: 0.7241 (ttpp) REVERT: B 564 TYR cc_start: 0.8212 (m-80) cc_final: 0.7634 (m-10) REVERT: B 573 ARG cc_start: 0.7712 (tpp-160) cc_final: 0.7493 (tpp80) REVERT: B 602 LYS cc_start: 0.9010 (mmmm) cc_final: 0.8636 (mmmm) REVERT: B 639 TRP cc_start: 0.5315 (m-10) cc_final: 0.5036 (m100) REVERT: B 644 PRO cc_start: 0.8551 (Cg_endo) cc_final: 0.7654 (Cg_exo) REVERT: M 1 MET cc_start: 0.5098 (mmm) cc_final: 0.4135 (mmm) REVERT: M 21 LYS cc_start: 0.8650 (mttp) cc_final: 0.8199 (mmtt) REVERT: M 116 MET cc_start: 0.6942 (tpp) cc_final: 0.6672 (tpp) REVERT: S 1 MET cc_start: 0.6745 (OUTLIER) cc_final: 0.6421 (tpt) REVERT: S 13 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.7175 (tttp) REVERT: S 96 THR cc_start: 0.8940 (m) cc_final: 0.8736 (p) REVERT: S 128 MET cc_start: 0.7540 (mmm) cc_final: 0.7253 (mmp) outliers start: 53 outliers final: 38 residues processed: 399 average time/residue: 0.1048 time to fit residues: 58.1464 Evaluate side-chains 423 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 378 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 192 LEU Chi-restraints excluded: chain D residue 219 LEU 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 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 488 ILE Chi-restraints excluded: chain D residue 522 TYR Chi-restraints excluded: chain B residue 95 LYS 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 355 GLN 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 49 ILE Chi-restraints excluded: chain M residue 51 THR Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 70 ILE 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 79 SER Chi-restraints excluded: chain S residue 89 LEU 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 119 optimal weight: 0.3980 chunk 139 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 135 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 111 optimal weight: 0.2980 chunk 57 optimal weight: 3.9990 chunk 118 optimal weight: 0.1980 chunk 54 optimal weight: 0.9980 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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** D 577 GLN D 583 GLN B 121 GLN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 GLN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 GLN ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 GLN B 579 GLN ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 HIS B 650 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.151254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.131823 restraints weight = 22676.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.136357 restraints weight = 13174.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.139571 restraints weight = 8505.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.141856 restraints weight = 5802.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.143525 restraints weight = 4177.750| |-----------------------------------------------------------------------------| r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11559 Z= 0.136 Angle : 0.685 12.951 15640 Z= 0.334 Chirality : 0.042 0.239 1850 Planarity : 0.004 0.047 1971 Dihedral : 4.436 21.853 1535 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.23 % Allowed : 23.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.22), residues: 1419 helix: 1.05 (0.16), residues: 1004 sheet: 0.67 (0.82), residues: 49 loop : 0.56 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 341 TYR 0.014 0.001 TYR D 277 PHE 0.022 0.002 PHE D 454 TRP 0.033 0.002 TRP D 236 HIS 0.007 0.001 HIS S 117 Details of bonding type rmsd covalent geometry : bond 0.00294 (11559) covalent geometry : angle 0.68536 (15640) hydrogen bonds : bond 0.04184 ( 749) hydrogen bonds : angle 4.77403 ( 2175) *********************** 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 428 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 374 time to evaluate : 0.436 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 59 VAL cc_start: 0.6536 (OUTLIER) cc_final: 0.6176 (m) REVERT: D 92 ARG cc_start: 0.7989 (ttt180) cc_final: 0.7428 (ttt180) REVERT: D 93 ILE cc_start: 0.8709 (mm) cc_final: 0.8179 (tp) REVERT: D 170 MET cc_start: 0.7594 (mmm) cc_final: 0.6977 (mmm) REVERT: D 177 TYR cc_start: 0.6895 (t80) cc_final: 0.6054 (t80) REVERT: D 193 GLU cc_start: 0.8317 (mp0) cc_final: 0.8037 (mm-30) REVERT: D 207 ILE cc_start: 0.8261 (tt) cc_final: 0.7668 (mm) REVERT: D 242 ILE cc_start: 0.8813 (mm) cc_final: 0.8340 (tp) REVERT: D 245 PHE cc_start: 0.8267 (m-80) cc_final: 0.7810 (m-80) REVERT: D 257 LYS cc_start: 0.8500 (tppt) cc_final: 0.8171 (tppt) REVERT: D 306 GLN cc_start: 0.8511 (tp-100) cc_final: 0.8289 (tp-100) REVERT: D 307 LYS cc_start: 0.8705 (mmtm) cc_final: 0.8432 (mmtm) REVERT: D 314 ASP cc_start: 0.7126 (t0) cc_final: 0.6757 (t0) REVERT: D 345 ILE cc_start: 0.8942 (mt) cc_final: 0.8471 (tp) REVERT: D 346 LEU cc_start: 0.9027 (mt) cc_final: 0.8649 (mt) REVERT: D 357 ARG cc_start: 0.7616 (mtm-85) cc_final: 0.6935 (mtm-85) REVERT: D 359 ARG cc_start: 0.7766 (tpp80) cc_final: 0.7485 (mmm-85) REVERT: D 371 LYS cc_start: 0.8184 (ttpp) cc_final: 0.7749 (ttpp) REVERT: D 372 ASN cc_start: 0.8201 (p0) cc_final: 0.7867 (p0) REVERT: D 375 GLU cc_start: 0.8020 (mp0) cc_final: 0.7550 (mp0) REVERT: D 379 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7517 (mppt) REVERT: D 442 LEU cc_start: 0.8658 (mt) cc_final: 0.8399 (mt) REVERT: D 449 LYS cc_start: 0.8208 (tttt) cc_final: 0.7820 (tttt) REVERT: D 452 ARG cc_start: 0.7663 (mtt180) cc_final: 0.7224 (mtp180) REVERT: D 489 CYS cc_start: 0.7186 (p) cc_final: 0.6906 (p) REVERT: D 535 GLN cc_start: 0.7190 (tp-100) cc_final: 0.6702 (tp-100) REVERT: D 547 GLN cc_start: 0.8455 (tp-100) cc_final: 0.8067 (tp-100) REVERT: D 584 LYS cc_start: 0.8373 (mttt) cc_final: 0.7995 (mptt) REVERT: D 595 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7003 (tt0) REVERT: B 50 MET cc_start: 0.7020 (tpp) cc_final: 0.6466 (tpt) REVERT: B 59 LYS cc_start: 0.8413 (mtmt) cc_final: 0.7477 (mmmt) REVERT: B 63 MET cc_start: 0.7828 (mmm) cc_final: 0.7583 (mmm) REVERT: B 69 MET cc_start: 0.7732 (ppp) cc_final: 0.7433 (ppp) REVERT: B 87 VAL cc_start: 0.8779 (m) cc_final: 0.8519 (t) REVERT: B 97 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7484 (mm) REVERT: B 101 TYR cc_start: 0.8493 (t80) cc_final: 0.8258 (t80) REVERT: B 125 LYS cc_start: 0.8712 (mmtp) cc_final: 0.8038 (tptp) REVERT: B 130 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8397 (tt) REVERT: B 151 MET cc_start: 0.7675 (ttp) cc_final: 0.7441 (ttp) REVERT: B 156 LYS cc_start: 0.9051 (mmtm) cc_final: 0.8848 (mmmm) REVERT: B 169 ASN cc_start: 0.8367 (m-40) cc_final: 0.7993 (m-40) REVERT: B 190 GLU cc_start: 0.8252 (tp30) cc_final: 0.7745 (tp30) REVERT: B 194 LYS cc_start: 0.8525 (mttt) cc_final: 0.8062 (mttt) REVERT: B 209 MET cc_start: 0.7948 (ttm) cc_final: 0.7227 (ttm) REVERT: B 243 VAL cc_start: 0.7093 (t) cc_final: 0.6793 (m) REVERT: B 255 GLN cc_start: 0.7734 (mm-40) cc_final: 0.7251 (mm-40) REVERT: B 311 ARG cc_start: 0.7540 (mtm-85) cc_final: 0.7287 (mtm-85) REVERT: B 317 MET cc_start: 0.7419 (tpp) cc_final: 0.7209 (tpp) REVERT: B 346 ASN cc_start: 0.7011 (p0) cc_final: 0.6745 (p0) REVERT: B 381 ASP cc_start: 0.6414 (m-30) cc_final: 0.6150 (m-30) REVERT: B 420 PHE cc_start: 0.6373 (t80) cc_final: 0.6113 (t80) REVERT: B 469 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7200 (tt) REVERT: B 503 ILE cc_start: 0.8199 (tt) cc_final: 0.7894 (tt) REVERT: B 556 GLN cc_start: 0.8211 (tm-30) cc_final: 0.7930 (tm-30) REVERT: B 563 LYS cc_start: 0.7465 (tttp) cc_final: 0.7202 (ttpp) REVERT: B 564 TYR cc_start: 0.8295 (m-80) cc_final: 0.7703 (m-10) REVERT: B 593 TYR cc_start: 0.7939 (m-80) cc_final: 0.7727 (m-80) REVERT: B 602 LYS cc_start: 0.9054 (mmmm) cc_final: 0.8838 (mmmt) REVERT: M 1 MET cc_start: 0.4912 (mmm) cc_final: 0.4262 (mmm) REVERT: M 21 LYS cc_start: 0.8616 (mttp) cc_final: 0.8171 (mmtt) REVERT: M 69 VAL cc_start: 0.7372 (t) cc_final: 0.6816 (m) REVERT: M 116 MET cc_start: 0.6939 (tpp) cc_final: 0.6683 (tpp) REVERT: S 1 MET cc_start: 0.6718 (OUTLIER) cc_final: 0.6452 (tpt) REVERT: S 13 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.7218 (tttp) REVERT: S 96 THR cc_start: 0.8974 (m) cc_final: 0.8761 (p) REVERT: S 140 GLN cc_start: 0.7519 (tt0) cc_final: 0.7206 (tt0) outliers start: 54 outliers final: 37 residues processed: 394 average time/residue: 0.1062 time to fit residues: 57.8942 Evaluate side-chains 410 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 365 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 168 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 271 SER 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 D residue 588 LYS Chi-restraints excluded: chain D residue 595 GLU Chi-restraints excluded: chain B residue 95 LYS 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 355 GLN Chi-restraints excluded: chain B residue 360 MET 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 566 GLN 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 49 ILE 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 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 79 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 79 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 140 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 58 optimal weight: 0.0040 chunk 44 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 19 optimal weight: 0.0980 chunk 100 optimal weight: 0.9990 overall best weight: 0.4192 ------------------------------------------------------------------------------- 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 577 GLN D 581 HIS D 583 GLN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.151896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.132292 restraints weight = 22983.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.136822 restraints weight = 13481.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.140055 restraints weight = 8750.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.142363 restraints weight = 5996.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.143891 restraints weight = 4328.446| |-----------------------------------------------------------------------------| r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.3981 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= 0.135 Angle : 0.687 12.946 15640 Z= 0.335 Chirality : 0.042 0.208 1850 Planarity : 0.004 0.047 1971 Dihedral : 4.364 19.334 1535 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.99 % Allowed : 23.96 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.22), residues: 1419 helix: 1.13 (0.16), residues: 1004 sheet: 0.61 (0.81), residues: 49 loop : 0.44 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 250 TYR 0.017 0.001 TYR D 277 PHE 0.040 0.002 PHE D 226 TRP 0.062 0.003 TRP D 236 HIS 0.008 0.001 HIS S 117 Details of bonding type rmsd covalent geometry : bond 0.00292 (11559) covalent geometry : angle 0.68730 (15640) hydrogen bonds : bond 0.04081 ( 749) hydrogen bonds : angle 4.71674 ( 2175) *********************** 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 429 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 378 time to evaluate : 0.363 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 59 VAL cc_start: 0.6420 (OUTLIER) cc_final: 0.5989 (m) REVERT: D 92 ARG cc_start: 0.8006 (ttt180) cc_final: 0.7449 (ttt180) REVERT: D 93 ILE cc_start: 0.8722 (mm) cc_final: 0.8199 (tp) REVERT: D 170 MET cc_start: 0.7577 (mmm) cc_final: 0.7071 (mmm) REVERT: D 177 TYR cc_start: 0.6883 (t80) cc_final: 0.6077 (t80) REVERT: D 207 ILE cc_start: 0.8210 (tt) cc_final: 0.7743 (mt) REVERT: D 209 GLU cc_start: 0.7802 (tp30) cc_final: 0.7474 (tp30) REVERT: D 242 ILE cc_start: 0.8752 (mm) cc_final: 0.8116 (mm) REVERT: D 245 PHE cc_start: 0.8202 (m-80) cc_final: 0.7672 (m-80) REVERT: D 257 LYS cc_start: 0.8523 (tppt) cc_final: 0.8077 (tppt) REVERT: D 306 GLN cc_start: 0.8502 (tp-100) cc_final: 0.8287 (tp-100) REVERT: D 307 LYS cc_start: 0.8687 (mmtm) cc_final: 0.8432 (mmtm) REVERT: D 314 ASP cc_start: 0.7088 (t0) cc_final: 0.6732 (t0) REVERT: D 345 ILE cc_start: 0.8932 (mt) cc_final: 0.8511 (tp) REVERT: D 346 LEU cc_start: 0.9020 (mt) cc_final: 0.8605 (mt) REVERT: D 351 ASP cc_start: 0.7925 (m-30) cc_final: 0.7707 (m-30) REVERT: D 357 ARG cc_start: 0.7611 (mtm-85) cc_final: 0.6905 (mtm-85) REVERT: D 371 LYS cc_start: 0.8193 (ttpp) cc_final: 0.7817 (ttpp) REVERT: D 372 ASN cc_start: 0.8191 (p0) cc_final: 0.7890 (p0) REVERT: D 374 MET cc_start: 0.8292 (mtt) cc_final: 0.7676 (mtt) REVERT: D 375 GLU cc_start: 0.8023 (mp0) cc_final: 0.7468 (mp0) REVERT: D 378 LYS cc_start: 0.8767 (mttp) cc_final: 0.8305 (mptp) REVERT: D 379 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7491 (mppt) REVERT: D 442 LEU cc_start: 0.8646 (mt) cc_final: 0.8362 (mt) REVERT: D 449 LYS cc_start: 0.8183 (tttt) cc_final: 0.7813 (tttt) REVERT: D 452 ARG cc_start: 0.7652 (mtt180) cc_final: 0.7233 (mtp180) REVERT: D 489 CYS cc_start: 0.7179 (p) cc_final: 0.6899 (p) REVERT: D 535 GLN cc_start: 0.7177 (tp-100) cc_final: 0.6673 (tp-100) REVERT: D 547 GLN cc_start: 0.8471 (tp-100) cc_final: 0.8083 (tp-100) REVERT: D 595 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7004 (tt0) REVERT: B 50 MET cc_start: 0.7042 (tpp) cc_final: 0.6488 (tpt) REVERT: B 59 LYS cc_start: 0.8420 (mtmt) cc_final: 0.7485 (mmmt) REVERT: B 63 MET cc_start: 0.7839 (mmm) cc_final: 0.7588 (mmm) REVERT: B 69 MET cc_start: 0.7758 (ppp) cc_final: 0.7450 (ppp) REVERT: B 87 VAL cc_start: 0.8781 (m) cc_final: 0.8535 (t) REVERT: B 97 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7479 (mm) REVERT: B 101 TYR cc_start: 0.8507 (t80) cc_final: 0.8273 (t80) REVERT: B 125 LYS cc_start: 0.8710 (mmtp) cc_final: 0.8027 (tptp) REVERT: B 130 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8418 (tt) REVERT: B 153 LEU cc_start: 0.8913 (tp) cc_final: 0.8662 (tt) REVERT: B 156 LYS cc_start: 0.9060 (mmtm) cc_final: 0.8830 (mmmm) REVERT: B 169 ASN cc_start: 0.8345 (m-40) cc_final: 0.7949 (m-40) REVERT: B 190 GLU cc_start: 0.8242 (tp30) cc_final: 0.7661 (tp30) REVERT: B 194 LYS cc_start: 0.8498 (mttt) cc_final: 0.7990 (mttt) REVERT: B 209 MET cc_start: 0.7933 (ttm) cc_final: 0.7253 (ttm) REVERT: B 243 VAL cc_start: 0.7076 (t) cc_final: 0.6769 (m) REVERT: B 255 GLN cc_start: 0.7712 (mm-40) cc_final: 0.7224 (mm-40) REVERT: B 311 ARG cc_start: 0.7558 (mtm-85) cc_final: 0.7331 (mtm-85) REVERT: B 317 MET cc_start: 0.7375 (tpp) cc_final: 0.7117 (tpp) REVERT: B 346 ASN cc_start: 0.6992 (p0) cc_final: 0.6729 (p0) REVERT: B 391 GLU cc_start: 0.7655 (tp30) cc_final: 0.7378 (tp30) REVERT: B 426 GLN cc_start: 0.8557 (mm-40) cc_final: 0.8088 (mm110) REVERT: B 483 MET cc_start: 0.6564 (mmp) cc_final: 0.6304 (mmp) REVERT: B 503 ILE cc_start: 0.8207 (tt) cc_final: 0.7889 (tt) REVERT: B 556 GLN cc_start: 0.8210 (tm-30) cc_final: 0.7932 (tm-30) REVERT: B 563 LYS cc_start: 0.7493 (tttp) cc_final: 0.7235 (ttpp) REVERT: B 564 TYR cc_start: 0.8279 (m-80) cc_final: 0.7744 (m-10) REVERT: B 571 ARG cc_start: 0.7446 (ttt180) cc_final: 0.7147 (ttp-170) REVERT: B 572 ASP cc_start: 0.8174 (t0) cc_final: 0.7735 (t0) REVERT: B 593 TYR cc_start: 0.7891 (m-80) cc_final: 0.7659 (m-80) REVERT: B 602 LYS cc_start: 0.9142 (mmmm) cc_final: 0.8818 (mmmt) REVERT: M 1 MET cc_start: 0.4971 (mmm) cc_final: 0.4299 (mmm) REVERT: M 21 LYS cc_start: 0.8611 (mttp) cc_final: 0.8151 (mmtt) REVERT: M 69 VAL cc_start: 0.7349 (t) cc_final: 0.6809 (m) REVERT: M 116 MET cc_start: 0.6953 (tpp) cc_final: 0.6753 (tpp) REVERT: S 1 MET cc_start: 0.6731 (OUTLIER) cc_final: 0.6423 (tpt) REVERT: S 13 LYS cc_start: 0.7593 (OUTLIER) cc_final: 0.7254 (tttp) REVERT: S 71 LEU cc_start: 0.7547 (mp) cc_final: 0.7305 (mp) REVERT: S 96 THR cc_start: 0.8976 (m) cc_final: 0.8702 (p) REVERT: S 140 GLN cc_start: 0.7572 (tt0) cc_final: 0.7338 (tt0) outliers start: 51 outliers final: 35 residues processed: 397 average time/residue: 0.1017 time to fit residues: 56.3462 Evaluate side-chains 414 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 372 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 194 ASP 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 588 LYS Chi-restraints excluded: chain D residue 595 GLU Chi-restraints excluded: chain B residue 95 LYS 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 355 GLN Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 566 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 49 ILE 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 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 79 SER Chi-restraints excluded: chain S residue 132 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 32 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 54 optimal weight: 0.2980 chunk 66 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 577 GLN D 581 HIS ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4204 r_free = 0.4204 target = 0.151095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.131816 restraints weight = 22744.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.136295 restraints weight = 13274.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.139513 restraints weight = 8596.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.141703 restraints weight = 5888.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.143313 restraints weight = 4266.227| |-----------------------------------------------------------------------------| r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11559 Z= 0.151 Angle : 0.698 12.245 15640 Z= 0.346 Chirality : 0.043 0.187 1850 Planarity : 0.004 0.046 1971 Dihedral : 4.437 19.857 1535 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.84 % Allowed : 24.98 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.22), residues: 1419 helix: 1.09 (0.16), residues: 1002 sheet: 0.68 (0.81), residues: 49 loop : 0.41 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 250 TYR 0.015 0.001 TYR D 277 PHE 0.055 0.002 PHE D 226 TRP 0.054 0.003 TRP D 236 HIS 0.008 0.001 HIS S 117 Details of bonding type rmsd covalent geometry : bond 0.00327 (11559) covalent geometry : angle 0.69770 (15640) hydrogen bonds : bond 0.04218 ( 749) hydrogen bonds : angle 4.79755 ( 2175) *********************** 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 431 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 382 time to evaluate : 0.425 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 59 VAL cc_start: 0.6445 (OUTLIER) cc_final: 0.6002 (m) REVERT: D 92 ARG cc_start: 0.8048 (ttt180) cc_final: 0.7471 (ttt180) REVERT: D 93 ILE cc_start: 0.8734 (mm) cc_final: 0.8231 (tp) REVERT: D 170 MET cc_start: 0.7582 (mmm) cc_final: 0.7067 (mmm) REVERT: D 207 ILE cc_start: 0.8252 (tt) cc_final: 0.7800 (mt) REVERT: D 209 GLU cc_start: 0.7837 (tp30) cc_final: 0.7464 (tp30) REVERT: D 242 ILE cc_start: 0.8794 (mm) cc_final: 0.8149 (mm) REVERT: D 245 PHE cc_start: 0.8236 (m-80) cc_final: 0.7781 (m-80) REVERT: D 257 LYS cc_start: 0.8520 (tppt) cc_final: 0.8005 (tppt) REVERT: D 306 GLN cc_start: 0.8567 (tp-100) cc_final: 0.8360 (tp-100) REVERT: D 307 LYS cc_start: 0.8708 (mmtm) cc_final: 0.8447 (mmtm) REVERT: D 314 ASP cc_start: 0.7154 (t0) cc_final: 0.6781 (t0) REVERT: D 342 LYS cc_start: 0.8096 (mttt) cc_final: 0.7819 (mttt) REVERT: D 345 ILE cc_start: 0.8927 (mt) cc_final: 0.8573 (tp) REVERT: D 346 LEU cc_start: 0.9047 (mt) cc_final: 0.8646 (mt) REVERT: D 351 ASP cc_start: 0.7805 (m-30) cc_final: 0.7577 (m-30) REVERT: D 357 ARG cc_start: 0.7619 (mtm-85) cc_final: 0.6901 (mtm-85) REVERT: D 359 ARG cc_start: 0.7851 (tpp80) cc_final: 0.7555 (tpp80) REVERT: D 371 LYS cc_start: 0.8207 (ttpp) cc_final: 0.7747 (ttpp) REVERT: D 372 ASN cc_start: 0.8246 (p0) cc_final: 0.7879 (p0) REVERT: D 375 GLU cc_start: 0.8025 (mp0) cc_final: 0.7471 (mp0) REVERT: D 378 LYS cc_start: 0.8766 (mttp) cc_final: 0.8397 (mttp) REVERT: D 379 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7516 (mppt) REVERT: D 442 LEU cc_start: 0.8643 (mt) cc_final: 0.8359 (mt) REVERT: D 449 LYS cc_start: 0.8235 (tttt) cc_final: 0.7876 (tttt) REVERT: D 452 ARG cc_start: 0.7645 (mtt180) cc_final: 0.7238 (mtp180) REVERT: D 489 CYS cc_start: 0.7186 (p) cc_final: 0.6929 (p) REVERT: D 535 GLN cc_start: 0.7189 (tp-100) cc_final: 0.6688 (tp-100) REVERT: D 547 GLN cc_start: 0.8477 (tp-100) cc_final: 0.8088 (tp-100) REVERT: D 582 ILE cc_start: 0.8210 (mt) cc_final: 0.7674 (tp) REVERT: D 584 LYS cc_start: 0.8399 (mttt) cc_final: 0.7994 (mptt) REVERT: D 595 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7060 (tt0) REVERT: B 50 MET cc_start: 0.7040 (tpp) cc_final: 0.6485 (tpt) REVERT: B 59 LYS cc_start: 0.8425 (mtmt) cc_final: 0.7500 (mmmt) REVERT: B 63 MET cc_start: 0.7856 (mmm) cc_final: 0.7605 (mmm) REVERT: B 69 MET cc_start: 0.7747 (ppp) cc_final: 0.7425 (ppp) REVERT: B 87 VAL cc_start: 0.8784 (m) cc_final: 0.8541 (t) REVERT: B 97 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7508 (mm) REVERT: B 101 TYR cc_start: 0.8535 (t80) cc_final: 0.8324 (t80) REVERT: B 125 LYS cc_start: 0.8748 (mmtp) cc_final: 0.8075 (tptp) REVERT: B 151 MET cc_start: 0.7514 (ttt) cc_final: 0.7258 (ttt) REVERT: B 169 ASN cc_start: 0.8341 (m-40) cc_final: 0.7951 (m-40) REVERT: B 190 GLU cc_start: 0.8254 (tp30) cc_final: 0.7660 (tp30) REVERT: B 194 LYS cc_start: 0.8523 (mttt) cc_final: 0.8020 (mttt) REVERT: B 209 MET cc_start: 0.7956 (ttm) cc_final: 0.7370 (ttm) REVERT: B 243 VAL cc_start: 0.7107 (t) cc_final: 0.6801 (m) REVERT: B 255 GLN cc_start: 0.7700 (mm-40) cc_final: 0.7226 (mm-40) REVERT: B 346 ASN cc_start: 0.7025 (p0) cc_final: 0.6761 (p0) REVERT: B 381 ASP cc_start: 0.6411 (m-30) cc_final: 0.6133 (m-30) REVERT: B 391 GLU cc_start: 0.7717 (tp30) cc_final: 0.7427 (tp30) REVERT: B 469 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7182 (tt) REVERT: B 503 ILE cc_start: 0.8196 (tt) cc_final: 0.7888 (tt) REVERT: B 556 GLN cc_start: 0.8169 (tm-30) cc_final: 0.7931 (tm-30) REVERT: B 563 LYS cc_start: 0.7488 (tttp) cc_final: 0.7238 (ttpp) REVERT: B 564 TYR cc_start: 0.8278 (m-80) cc_final: 0.7760 (m-10) REVERT: B 565 ASP cc_start: 0.7879 (t0) cc_final: 0.7533 (t0) REVERT: B 572 ASP cc_start: 0.8181 (t0) cc_final: 0.7731 (t0) REVERT: B 573 ARG cc_start: 0.7644 (tpp-160) cc_final: 0.7330 (tpp80) REVERT: B 593 TYR cc_start: 0.7905 (m-80) cc_final: 0.7683 (m-80) REVERT: B 602 LYS cc_start: 0.9151 (mmmm) cc_final: 0.8854 (mmmt) REVERT: M 1 MET cc_start: 0.4982 (mmm) cc_final: 0.4322 (mmm) REVERT: M 21 LYS cc_start: 0.8675 (mttp) cc_final: 0.8211 (mmtt) REVERT: M 69 VAL cc_start: 0.7402 (t) cc_final: 0.6878 (m) REVERT: M 93 TYR cc_start: 0.6869 (t80) cc_final: 0.6410 (t80) REVERT: S 1 MET cc_start: 0.6796 (OUTLIER) cc_final: 0.6447 (tpt) REVERT: S 13 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7293 (tttp) REVERT: S 71 LEU cc_start: 0.7450 (mp) cc_final: 0.7214 (mp) REVERT: S 128 MET cc_start: 0.7483 (mmm) cc_final: 0.7225 (mmp) REVERT: S 137 ILE cc_start: 0.9024 (mt) cc_final: 0.8736 (mm) outliers start: 49 outliers final: 31 residues processed: 404 average time/residue: 0.1040 time to fit residues: 58.5323 Evaluate side-chains 416 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 378 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 194 ASP 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 379 LYS Chi-restraints excluded: chain D residue 382 THR 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 588 LYS Chi-restraints excluded: chain D residue 595 GLU Chi-restraints excluded: chain B residue 95 LYS 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 355 GLN 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 M residue 2 ILE Chi-restraints excluded: chain M residue 10 CYS Chi-restraints excluded: chain M residue 49 ILE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 91 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 63 optimal weight: 0.6980 chunk 102 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 48 optimal weight: 0.0970 chunk 64 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 577 GLN D 581 HIS B 121 GLN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.151296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.131801 restraints weight = 22462.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.136326 restraints weight = 13247.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.139517 restraints weight = 8551.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.141845 restraints weight = 5878.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.143356 restraints weight = 4240.886| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11559 Z= 0.148 Angle : 0.732 12.542 15640 Z= 0.358 Chirality : 0.043 0.210 1850 Planarity : 0.004 0.045 1971 Dihedral : 4.456 19.596 1535 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.60 % Allowed : 25.61 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.22), residues: 1419 helix: 1.10 (0.16), residues: 995 sheet: 0.57 (0.79), residues: 49 loop : 0.18 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 341 TYR 0.016 0.001 TYR D 277 PHE 0.054 0.002 PHE D 226 TRP 0.049 0.003 TRP D 236 HIS 0.010 0.001 HIS D 581 Details of bonding type rmsd covalent geometry : bond 0.00324 (11559) covalent geometry : angle 0.73226 (15640) hydrogen bonds : bond 0.04189 ( 749) hydrogen bonds : angle 4.77985 ( 2175) *********************** 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 424 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 378 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 59 VAL cc_start: 0.6431 (OUTLIER) cc_final: 0.5966 (m) REVERT: D 92 ARG cc_start: 0.8046 (ttt180) cc_final: 0.7468 (ttt180) REVERT: D 93 ILE cc_start: 0.8735 (mm) cc_final: 0.8247 (tp) REVERT: D 170 MET cc_start: 0.7555 (mmm) cc_final: 0.7007 (mmm) REVERT: D 177 TYR cc_start: 0.6926 (t80) cc_final: 0.5922 (t80) REVERT: D 207 ILE cc_start: 0.8240 (tt) cc_final: 0.7813 (mt) REVERT: D 209 GLU cc_start: 0.7810 (tp30) cc_final: 0.7419 (tp30) REVERT: D 242 ILE cc_start: 0.8789 (mm) cc_final: 0.8153 (mm) REVERT: D 245 PHE cc_start: 0.8213 (m-80) cc_final: 0.7757 (m-80) REVERT: D 257 LYS cc_start: 0.8499 (tppt) cc_final: 0.7982 (tppt) REVERT: D 306 GLN cc_start: 0.8551 (tp-100) cc_final: 0.8339 (tp-100) REVERT: D 307 LYS cc_start: 0.8717 (mmtm) cc_final: 0.8472 (mmtm) REVERT: D 314 ASP cc_start: 0.7137 (t0) cc_final: 0.6749 (t0) REVERT: D 342 LYS cc_start: 0.8159 (mttt) cc_final: 0.7880 (mttt) REVERT: D 345 ILE cc_start: 0.8881 (mt) cc_final: 0.8561 (tp) REVERT: D 346 LEU cc_start: 0.9010 (mt) cc_final: 0.8656 (mt) REVERT: D 357 ARG cc_start: 0.7559 (mtm-85) cc_final: 0.6891 (mtm-85) REVERT: D 359 ARG cc_start: 0.7838 (tpp80) cc_final: 0.7193 (mpp80) REVERT: D 371 LYS cc_start: 0.8196 (ttpp) cc_final: 0.7737 (ttpp) REVERT: D 372 ASN cc_start: 0.8230 (p0) cc_final: 0.7616 (p0) REVERT: D 375 GLU cc_start: 0.7993 (mp0) cc_final: 0.7444 (mp0) REVERT: D 378 LYS cc_start: 0.8753 (mttp) cc_final: 0.8381 (mttp) REVERT: D 379 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7539 (mppt) REVERT: D 442 LEU cc_start: 0.8637 (mt) cc_final: 0.8381 (mt) REVERT: D 449 LYS cc_start: 0.8256 (tttt) cc_final: 0.7864 (tttt) REVERT: D 452 ARG cc_start: 0.7638 (mtt180) cc_final: 0.7207 (mtp180) REVERT: D 464 ASP cc_start: 0.7973 (m-30) cc_final: 0.7761 (m-30) REVERT: D 535 GLN cc_start: 0.7148 (tp-100) cc_final: 0.6652 (tp-100) REVERT: D 547 GLN cc_start: 0.8479 (tp-100) cc_final: 0.8084 (tp-100) REVERT: D 582 ILE cc_start: 0.8259 (mt) cc_final: 0.7709 (tp) REVERT: D 584 LYS cc_start: 0.8365 (mttt) cc_final: 0.7929 (mptt) REVERT: D 595 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7079 (tt0) REVERT: B 50 MET cc_start: 0.7035 (tpp) cc_final: 0.6480 (tpt) REVERT: B 59 LYS cc_start: 0.8403 (mtmt) cc_final: 0.7515 (mmmt) REVERT: B 63 MET cc_start: 0.7847 (mmm) cc_final: 0.7597 (mmm) REVERT: B 69 MET cc_start: 0.7760 (ppp) cc_final: 0.7435 (ppp) REVERT: B 87 VAL cc_start: 0.8783 (m) cc_final: 0.8553 (t) REVERT: B 97 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7486 (mm) REVERT: B 125 LYS cc_start: 0.8741 (mmtp) cc_final: 0.8077 (tptp) REVERT: B 169 ASN cc_start: 0.8332 (m-40) cc_final: 0.7927 (m-40) REVERT: B 190 GLU cc_start: 0.8256 (tp30) cc_final: 0.7636 (tp30) REVERT: B 194 LYS cc_start: 0.8512 (mttt) cc_final: 0.8013 (mttt) REVERT: B 209 MET cc_start: 0.7952 (ttm) cc_final: 0.7391 (ttm) REVERT: B 243 VAL cc_start: 0.7109 (t) cc_final: 0.6815 (m) REVERT: B 255 GLN cc_start: 0.7734 (mm-40) cc_final: 0.7254 (mm-40) REVERT: B 346 ASN cc_start: 0.7017 (p0) cc_final: 0.6743 (p0) REVERT: B 381 ASP cc_start: 0.6418 (m-30) cc_final: 0.6143 (m-30) REVERT: B 391 GLU cc_start: 0.7719 (tp30) cc_final: 0.7424 (tp30) REVERT: B 452 ASN cc_start: 0.7405 (t0) cc_final: 0.7171 (t0) REVERT: B 469 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7148 (tt) REVERT: B 483 MET cc_start: 0.6640 (mmp) cc_final: 0.6328 (mmp) REVERT: B 503 ILE cc_start: 0.8185 (tt) cc_final: 0.7872 (tt) REVERT: B 556 GLN cc_start: 0.8155 (tm-30) cc_final: 0.7909 (tm-30) REVERT: B 563 LYS cc_start: 0.7483 (tttp) cc_final: 0.7220 (ttpp) REVERT: B 564 TYR cc_start: 0.8289 (m-80) cc_final: 0.7727 (m-10) REVERT: B 565 ASP cc_start: 0.7841 (t0) cc_final: 0.7480 (t0) REVERT: B 572 ASP cc_start: 0.8167 (t0) cc_final: 0.7713 (t0) REVERT: B 573 ARG cc_start: 0.7644 (tpp-160) cc_final: 0.7329 (tpp80) REVERT: B 593 TYR cc_start: 0.7908 (m-80) cc_final: 0.7636 (m-80) REVERT: B 602 LYS cc_start: 0.9149 (mmmm) cc_final: 0.8853 (mmmt) REVERT: M 1 MET cc_start: 0.4957 (mmm) cc_final: 0.4349 (mmm) REVERT: M 21 LYS cc_start: 0.8691 (mttp) cc_final: 0.8214 (mmtt) REVERT: M 93 TYR cc_start: 0.6832 (t80) cc_final: 0.6424 (t80) REVERT: M 116 MET cc_start: 0.6824 (tpp) cc_final: 0.6319 (tpp) REVERT: S 1 MET cc_start: 0.6816 (OUTLIER) cc_final: 0.6540 (tpt) REVERT: S 13 LYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7293 (tttp) REVERT: S 71 LEU cc_start: 0.7348 (mp) cc_final: 0.7114 (mp) REVERT: S 140 GLN cc_start: 0.7546 (tt0) cc_final: 0.7133 (tt0) outliers start: 46 outliers final: 34 residues processed: 396 average time/residue: 0.0993 time to fit residues: 54.7696 Evaluate side-chains 413 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 372 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 194 ASP Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 229 MET 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 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 460 SER Chi-restraints excluded: chain D residue 522 TYR Chi-restraints excluded: chain D residue 581 HIS Chi-restraints excluded: chain D residue 588 LYS Chi-restraints excluded: chain D residue 595 GLU Chi-restraints excluded: chain B residue 95 LYS 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 355 GLN 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 598 PHE Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 10 CYS Chi-restraints excluded: chain M residue 49 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 36 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 89 optimal weight: 0.2980 chunk 87 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 577 GLN D 581 HIS ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.150144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.130863 restraints weight = 22780.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.135255 restraints weight = 13496.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.138399 restraints weight = 8793.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.140534 restraints weight = 6070.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.142244 restraints weight = 4437.135| |-----------------------------------------------------------------------------| r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11559 Z= 0.160 Angle : 0.760 13.389 15640 Z= 0.369 Chirality : 0.044 0.344 1850 Planarity : 0.004 0.045 1971 Dihedral : 4.485 20.177 1535 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.45 % Allowed : 26.39 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.22), residues: 1419 helix: 1.03 (0.16), residues: 998 sheet: 0.58 (0.79), residues: 49 loop : 0.13 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 341 TYR 0.015 0.001 TYR B 99 PHE 0.054 0.002 PHE D 226 TRP 0.048 0.003 TRP D 236 HIS 0.010 0.001 HIS D 383 Details of bonding type rmsd covalent geometry : bond 0.00348 (11559) covalent geometry : angle 0.75971 (15640) hydrogen bonds : bond 0.04258 ( 749) hydrogen bonds : angle 4.85972 ( 2175) ********************** 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 418 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 374 time to evaluate : 0.359 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: 0.8029 (ttt180) cc_final: 0.7494 (ttt180) REVERT: D 93 ILE cc_start: 0.8722 (mm) cc_final: 0.8261 (tp) REVERT: D 170 MET cc_start: 0.7498 (mmm) cc_final: 0.6970 (mmm) REVERT: D 177 TYR cc_start: 0.6947 (t80) cc_final: 0.5949 (t80) REVERT: D 207 ILE cc_start: 0.8254 (tt) cc_final: 0.7849 (mt) REVERT: D 209 GLU cc_start: 0.7800 (tp30) cc_final: 0.7434 (tp30) REVERT: D 242 ILE cc_start: 0.8802 (mm) cc_final: 0.8175 (mm) REVERT: D 245 PHE cc_start: 0.8136 (m-80) cc_final: 0.7705 (m-80) REVERT: D 257 LYS cc_start: 0.8503 (tppt) cc_final: 0.8135 (tppt) REVERT: D 306 GLN cc_start: 0.8535 (tp-100) cc_final: 0.8322 (tp-100) REVERT: D 307 LYS cc_start: 0.8700 (mmtm) cc_final: 0.8448 (mmtm) REVERT: D 314 ASP cc_start: 0.7157 (t0) cc_final: 0.6765 (t0) REVERT: D 337 SER cc_start: 0.8231 (m) cc_final: 0.7992 (p) REVERT: D 342 LYS cc_start: 0.8211 (mttt) cc_final: 0.7929 (mttt) REVERT: D 345 ILE cc_start: 0.8809 (mt) cc_final: 0.8510 (tp) REVERT: D 346 LEU cc_start: 0.9034 (mt) cc_final: 0.8682 (mt) REVERT: D 351 ASP cc_start: 0.7779 (m-30) cc_final: 0.7425 (t0) REVERT: D 357 ARG cc_start: 0.7576 (mtm-85) cc_final: 0.6917 (mtm-85) REVERT: D 371 LYS cc_start: 0.8186 (ttpp) cc_final: 0.7718 (ttpp) REVERT: D 372 ASN cc_start: 0.8184 (p0) cc_final: 0.7567 (p0) REVERT: D 375 GLU cc_start: 0.7936 (mp0) cc_final: 0.7422 (mp0) REVERT: D 379 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7490 (mppt) REVERT: D 442 LEU cc_start: 0.8642 (mt) cc_final: 0.8380 (mt) REVERT: D 449 LYS cc_start: 0.8276 (tttt) cc_final: 0.7913 (tttt) REVERT: D 452 ARG cc_start: 0.7607 (mtt180) cc_final: 0.7204 (mtp180) REVERT: D 535 GLN cc_start: 0.7127 (tp-100) cc_final: 0.6629 (tp-100) REVERT: D 547 GLN cc_start: 0.8503 (tp-100) cc_final: 0.8115 (tp-100) REVERT: D 582 ILE cc_start: 0.8249 (mt) cc_final: 0.7716 (tp) REVERT: D 584 LYS cc_start: 0.8344 (mttt) cc_final: 0.7924 (mptt) REVERT: D 595 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7011 (tt0) REVERT: B 50 MET cc_start: 0.7006 (tpp) cc_final: 0.6494 (tpt) REVERT: B 59 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.7530 (mmmt) REVERT: B 63 MET cc_start: 0.7796 (mmm) cc_final: 0.7566 (mmm) REVERT: B 69 MET cc_start: 0.7709 (ppp) cc_final: 0.7365 (ppp) REVERT: B 87 VAL cc_start: 0.8797 (m) cc_final: 0.8570 (t) REVERT: B 97 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7471 (mm) REVERT: B 101 TYR cc_start: 0.8400 (t80) cc_final: 0.8049 (t80) REVERT: B 125 LYS cc_start: 0.8741 (mmtp) cc_final: 0.8093 (tptp) REVERT: B 152 MET cc_start: 0.7785 (mtm) cc_final: 0.7551 (mtm) REVERT: B 156 LYS cc_start: 0.9043 (mmmm) cc_final: 0.8677 (mmtm) REVERT: B 169 ASN cc_start: 0.8296 (m-40) cc_final: 0.7884 (m-40) REVERT: B 185 LYS cc_start: 0.8404 (ptmm) cc_final: 0.8179 (ptmm) REVERT: B 190 GLU cc_start: 0.8250 (tp30) cc_final: 0.7669 (tp30) REVERT: B 194 LYS cc_start: 0.8505 (mttt) cc_final: 0.8062 (mttt) REVERT: B 209 MET cc_start: 0.7882 (ttm) cc_final: 0.7312 (ttm) REVERT: B 243 VAL cc_start: 0.7167 (t) cc_final: 0.6863 (m) REVERT: B 255 GLN cc_start: 0.7700 (mm-40) cc_final: 0.7248 (mm-40) REVERT: B 346 ASN cc_start: 0.7124 (p0) cc_final: 0.6843 (p0) REVERT: B 381 ASP cc_start: 0.6424 (m-30) cc_final: 0.6135 (m-30) REVERT: B 391 GLU cc_start: 0.7776 (tp30) cc_final: 0.7481 (tp30) REVERT: B 452 ASN cc_start: 0.7213 (t0) cc_final: 0.7009 (t0) REVERT: B 469 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7146 (tt) REVERT: B 483 MET cc_start: 0.6765 (mmp) cc_final: 0.6511 (mmp) REVERT: B 503 ILE cc_start: 0.8202 (tt) cc_final: 0.7889 (tt) REVERT: B 533 LYS cc_start: 0.8661 (mtpp) cc_final: 0.7704 (mttp) REVERT: B 556 GLN cc_start: 0.8151 (tm-30) cc_final: 0.7910 (tm-30) REVERT: B 563 LYS cc_start: 0.7547 (tttp) cc_final: 0.7303 (ttpp) REVERT: B 564 TYR cc_start: 0.8276 (m-80) cc_final: 0.7818 (m-10) REVERT: B 565 ASP cc_start: 0.7848 (t0) cc_final: 0.7466 (t0) REVERT: B 572 ASP cc_start: 0.8110 (t0) cc_final: 0.7655 (t0) REVERT: B 573 ARG cc_start: 0.7731 (tpp-160) cc_final: 0.7515 (tpp-160) REVERT: B 593 TYR cc_start: 0.7904 (m-80) cc_final: 0.7613 (m-80) REVERT: B 602 LYS cc_start: 0.9133 (mmmm) cc_final: 0.8863 (mmmm) REVERT: M 1 MET cc_start: 0.4949 (mmm) cc_final: 0.4365 (mmm) REVERT: M 21 LYS cc_start: 0.8692 (mttp) cc_final: 0.8215 (mmtt) REVERT: M 93 TYR cc_start: 0.6812 (t80) cc_final: 0.6427 (t80) REVERT: M 116 MET cc_start: 0.6763 (tpp) cc_final: 0.6432 (tpp) REVERT: S 1 MET cc_start: 0.6744 (OUTLIER) cc_final: 0.6478 (tpt) REVERT: S 13 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7294 (tttp) REVERT: S 71 LEU cc_start: 0.7344 (mp) cc_final: 0.7110 (mp) REVERT: S 140 GLN cc_start: 0.7519 (tt0) cc_final: 0.7132 (tt0) outliers start: 44 outliers final: 34 residues processed: 391 average time/residue: 0.1019 time to fit residues: 55.2044 Evaluate side-chains 412 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 371 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 194 ASP Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 229 MET 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 379 LYS 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 460 SER 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 59 LYS 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 355 GLN 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 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 49 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 56 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** D 577 GLN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.149941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.130653 restraints weight = 22786.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.134948 restraints weight = 13562.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.138100 restraints weight = 8921.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.140359 restraints weight = 6161.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.141986 restraints weight = 4483.633| |-----------------------------------------------------------------------------| r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 11559 Z= 0.194 Angle : 0.986 59.150 15640 Z= 0.533 Chirality : 0.047 0.694 1850 Planarity : 0.005 0.139 1971 Dihedral : 4.534 27.820 1535 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.29 % Allowed : 26.39 % Favored : 70.32 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.22), residues: 1419 helix: 1.02 (0.16), residues: 998 sheet: 0.56 (0.79), residues: 49 loop : 0.10 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 359 TYR 0.014 0.001 TYR B 99 PHE 0.051 0.002 PHE D 226 TRP 0.042 0.003 TRP D 236 HIS 0.159 0.004 HIS D 581 Details of bonding type rmsd covalent geometry : bond 0.00410 (11559) covalent geometry : angle 0.98611 (15640) hydrogen bonds : bond 0.04273 ( 749) hydrogen bonds : angle 4.86107 ( 2175) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2345.42 seconds wall clock time: 41 minutes 9.92 seconds (2469.92 seconds total)