Starting phenix.real_space_refine on Sun Apr 5 14:52:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u9i_63965/04_2026/9u9i_63965.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u9i_63965/04_2026/9u9i_63965.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9u9i_63965/04_2026/9u9i_63965.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u9i_63965/04_2026/9u9i_63965.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9u9i_63965/04_2026/9u9i_63965.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u9i_63965/04_2026/9u9i_63965.map" } resolution = 4.0 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= 0.000 sd= 0.053 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 74 5.16 5 C 7047 2.51 5 N 1843 2.21 5 O 2012 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10976 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4372 Classifications: {'peptide': 554} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 26, 'TRANS': 527} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4405 Classifications: {'peptide': 547} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 17, 'TRANS': 529} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1124 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 1, 'TRANS': 133} Chain breaks: 1 Chain: "M" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1075 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Time building chain proxies: 2.52, per 1000 atoms: 0.23 Number of scatterers: 10976 At special positions: 0 Unit cell: (87.36, 120.64, 127.92, 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 74 16.00 O 2012 8.00 N 1843 7.00 C 7047 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: 0.98 Conformation dependent library (CDL) restraints added in 544.4 milliseconds 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2622 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 3 sheets defined 67.3% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'B' and resid 14 through 24 removed outlier: 4.303A pdb=" N ASN B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) Proline residue: B 20 - end of helix Processing helix chain 'B' and resid 27 through 42 removed outlier: 4.066A pdb=" N ILE B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN B 34 " --> pdb=" O ARG B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 57 removed outlier: 3.919A pdb=" N ALA B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 75 removed outlier: 3.628A pdb=" N LEU B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'B' and resid 98 through 112 Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 134 through 143 Processing helix chain 'B' and resid 144 through 147 Processing helix chain 'B' and resid 157 through 167 Processing helix chain 'B' and resid 168 through 170 No H-bonds generated for 'chain 'B' and resid 168 through 170' Processing helix chain 'B' and resid 174 through 188 Processing helix chain 'B' and resid 189 through 191 No H-bonds generated for 'chain 'B' and resid 189 through 191' Processing helix chain 'B' and resid 196 through 207 Processing helix chain 'B' and resid 211 through 222 Processing helix chain 'B' and resid 223 through 225 No H-bonds generated for 'chain 'B' and resid 223 through 225' Processing helix chain 'B' and resid 229 through 241 Processing helix chain 'B' and resid 242 through 246 removed outlier: 3.949A pdb=" N LYS B 245 " --> pdb=" O SER B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 263 removed outlier: 3.659A pdb=" N VAL B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 284 removed outlier: 3.990A pdb=" N GLN B 270 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLY B 279 " --> pdb=" O VAL B 275 " (cutoff:3.500A) Proline residue: B 280 - end of helix Processing helix chain 'B' and resid 289 through 305 Processing helix chain 'B' and resid 311 through 318 removed outlier: 4.944A pdb=" N LYS B 316 " --> pdb=" O SER B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 340 Processing helix chain 'B' and resid 345 through 358 removed outlier: 3.721A pdb=" N LEU B 349 " --> pdb=" O VAL B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 379 removed outlier: 4.164A pdb=" N THR B 377 " --> pdb=" O GLY B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 removed outlier: 4.176A pdb=" N ARG B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 410 removed outlier: 3.934A pdb=" N VAL B 401 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N GLN B 403 " --> pdb=" O THR B 399 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TRP B 410 " --> pdb=" O ARG B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 416 Processing helix chain 'B' and resid 422 through 426 removed outlier: 3.726A pdb=" N GLY B 425 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 446 removed outlier: 3.717A pdb=" N TRP B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 445 " --> pdb=" O TRP B 441 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 463 removed outlier: 3.570A pdb=" N ASN B 463 " --> pdb=" O ASP B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 487 removed outlier: 3.802A pdb=" N LYS B 473 " --> pdb=" O PHE B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 504 removed outlier: 3.772A pdb=" N LEU B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ARG B 497 " --> pdb=" O ASP B 493 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B 498 " --> pdb=" O MET B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 525 Processing helix chain 'B' and resid 525 through 532 Processing helix chain 'B' and resid 552 through 559 removed outlier: 4.344A pdb=" N TRP B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER B 558 " --> pdb=" O ASN B 554 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASP B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 66 Processing helix chain 'E' and resid 74 through 85 Processing helix chain 'E' and resid 92 through 99 removed outlier: 3.870A pdb=" N PHE E 96 " --> pdb=" O TYR E 92 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE E 99 " --> pdb=" O SER E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 123 Processing helix chain 'E' and resid 129 through 143 removed outlier: 3.736A pdb=" N LEU E 133 " --> pdb=" O GLU E 129 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN E 143 " --> pdb=" O VAL E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 158 removed outlier: 4.021A pdb=" N THR E 155 " --> pdb=" O CYS E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 175 Processing helix chain 'E' and resid 183 through 198 removed outlier: 4.056A pdb=" N LYS E 187 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU E 192 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS E 194 " --> pdb=" O LEU E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 215 removed outlier: 3.993A pdb=" N CYS E 215 " --> pdb=" O ARG E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 230 Processing helix chain 'E' and resid 231 through 235 removed outlier: 3.747A pdb=" N LYS E 234 " --> pdb=" O ARG E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 242 removed outlier: 3.516A pdb=" N LYS E 241 " --> pdb=" O SER E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 254 Processing helix chain 'E' and resid 271 through 285 removed outlier: 4.226A pdb=" N ILE E 275 " --> pdb=" O PRO E 271 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU E 281 " --> pdb=" O LEU E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 295 Processing helix chain 'E' and resid 295 through 301 removed outlier: 3.534A pdb=" N LEU E 299 " --> pdb=" O MET E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 323 Processing helix chain 'E' and resid 338 through 343 removed outlier: 3.818A pdb=" N GLY E 342 " --> pdb=" O ALA E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 365 Processing helix chain 'E' and resid 369 through 373 Processing helix chain 'E' and resid 374 through 382 removed outlier: 3.966A pdb=" N ILE E 379 " --> pdb=" O GLN E 375 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU E 380 " --> pdb=" O MET E 376 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N CYS E 381 " --> pdb=" O THR E 377 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU E 382 " --> pdb=" O ILE E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 400 removed outlier: 4.033A pdb=" N ARG E 391 " --> pdb=" O PRO E 387 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLU E 392 " --> pdb=" O ILE E 388 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR E 393 " --> pdb=" O ILE E 389 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU E 395 " --> pdb=" O ARG E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 420 removed outlier: 4.764A pdb=" N GLN E 411 " --> pdb=" O THR E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 440 removed outlier: 3.652A pdb=" N GLU E 435 " --> pdb=" O GLY E 431 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR E 440 " --> pdb=" O LEU E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 458 removed outlier: 4.032A pdb=" N ILE E 448 " --> pdb=" O ASN E 444 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ALA E 453 " --> pdb=" O GLN E 449 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL E 454 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 476 removed outlier: 3.626A pdb=" N GLU E 476 " --> pdb=" O ARG E 472 " (cutoff:3.500A) Processing helix chain 'E' and resid 481 through 501 removed outlier: 4.030A pdb=" N GLN E 485 " --> pdb=" O GLU E 481 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET E 501 " --> pdb=" O THR E 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 507 through 521 Processing helix chain 'E' and resid 529 through 543 removed outlier: 4.413A pdb=" N VAL E 533 " --> pdb=" O THR E 529 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN E 543 " --> pdb=" O LYS E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 562 Processing helix chain 'E' and resid 571 through 579 Processing helix chain 'E' and resid 585 through 599 removed outlier: 3.854A pdb=" N ASN E 599 " --> pdb=" O HIS E 595 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 607 removed outlier: 4.135A pdb=" N LYS E 604 " --> pdb=" O VAL E 600 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 40 removed outlier: 3.939A pdb=" N ARG S 28 " --> pdb=" O ASP S 24 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU S 40 " --> pdb=" O ILE S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 96 removed outlier: 3.764A pdb=" N HIS S 85 " --> pdb=" O TYR S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 101 through 106 Processing helix chain 'S' and resid 106 through 119 Processing helix chain 'S' and resid 127 through 131 removed outlier: 3.639A pdb=" N ILE S 131 " --> pdb=" O ARG S 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 39 Processing helix chain 'M' and resid 75 through 94 Processing helix chain 'M' and resid 98 through 105 removed outlier: 3.823A pdb=" N ASN M 105 " --> pdb=" O THR M 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 116 Processing helix chain 'M' and resid 126 through 134 Processing sheet with id=AA1, first strand: chain 'S' and resid 14 through 19 removed outlier: 3.663A pdb=" N LEU S 16 " --> pdb=" O MET S 7 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS S 18 " --> pdb=" O PHE S 5 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE S 5 " --> pdb=" O LYS S 18 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL S 8 " --> pdb=" O PHE S 66 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N PHE S 66 " --> pdb=" O VAL S 8 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE S 67 " --> pdb=" O ARG S 60 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG S 60 " --> pdb=" O ILE S 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 14 through 18 removed outlier: 7.047A pdb=" N ILE M 7 " --> pdb=" O LEU M 15 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TYR M 17 " --> pdb=" O PHE M 5 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE M 5 " --> pdb=" O TYR M 17 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 117 through 118 567 hydrogen bonds defined for protein. 1644 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: 1.53 Time building geometry restraints manager: 1.29 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: 3556 1.34 - 1.46: 2052 1.46 - 1.58: 5453 1.58 - 1.70: 0 1.70 - 1.81: 114 Bond restraints: 11175 Sorted by residual: bond pdb=" C ASN E 444 " pdb=" N ALA E 445 " ideal model delta sigma weight residual 1.335 1.279 0.056 1.25e-02 6.40e+03 1.98e+01 bond pdb=" N ASN M 73 " pdb=" CA ASN M 73 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.25e-02 6.40e+03 6.12e+00 bond pdb=" N LYS S 18 " pdb=" CA LYS S 18 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.01e+00 bond pdb=" N LYS E 390 " pdb=" CA LYS E 390 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 4.82e+00 bond pdb=" N ASN B 178 " pdb=" CA ASN B 178 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.23e-02 6.61e+03 4.78e+00 ... (remaining 11170 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.54: 15073 4.54 - 9.09: 45 9.09 - 13.63: 2 13.63 - 18.17: 0 18.17 - 22.71: 1 Bond angle restraints: 15121 Sorted by residual: angle pdb=" N ASN E 444 " pdb=" CA ASN E 444 " pdb=" C ASN E 444 " ideal model delta sigma weight residual 110.80 133.51 -22.71 2.13e+00 2.20e-01 1.14e+02 angle pdb=" N ALA E 445 " pdb=" CA ALA E 445 " pdb=" CB ALA E 445 " ideal model delta sigma weight residual 109.94 96.85 13.09 1.49e+00 4.50e-01 7.72e+01 angle pdb=" C ASN E 444 " pdb=" CA ASN E 444 " pdb=" CB ASN E 444 " ideal model delta sigma weight residual 110.42 99.74 10.68 1.99e+00 2.53e-01 2.88e+01 angle pdb=" N THR E 73 " pdb=" CA THR E 73 " pdb=" C THR E 73 " ideal model delta sigma weight residual 108.00 115.73 -7.73 1.48e+00 4.57e-01 2.73e+01 angle pdb=" C ALA B 361 " pdb=" CA ALA B 361 " pdb=" CB ALA B 361 " ideal model delta sigma weight residual 117.23 110.32 6.91 1.36e+00 5.41e-01 2.58e+01 ... (remaining 15116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 6067 17.98 - 35.97: 610 35.97 - 53.95: 88 53.95 - 71.94: 26 71.94 - 89.92: 12 Dihedral angle restraints: 6803 sinusoidal: 2765 harmonic: 4038 Sorted by residual: dihedral pdb=" N ALA E 445 " pdb=" C ALA E 445 " pdb=" CA ALA E 445 " pdb=" CB ALA E 445 " ideal model delta harmonic sigma weight residual 122.90 106.54 16.36 0 2.50e+00 1.60e-01 4.28e+01 dihedral pdb=" CA ASP S 24 " pdb=" C ASP S 24 " pdb=" N ILE S 25 " pdb=" CA ILE S 25 " ideal model delta harmonic sigma weight residual -180.00 -155.75 -24.25 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA MET B 114 " pdb=" C MET B 114 " pdb=" N PRO B 115 " pdb=" CA PRO B 115 " ideal model delta harmonic sigma weight residual 180.00 158.91 21.09 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 6800 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 1757 0.139 - 0.277: 8 0.277 - 0.416: 3 0.416 - 0.554: 0 0.554 - 0.693: 1 Chirality restraints: 1769 Sorted by residual: chirality pdb=" CA ASN E 444 " pdb=" N ASN E 444 " pdb=" C ASN E 444 " pdb=" CB ASN E 444 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.20e+01 chirality pdb=" CA ALA E 445 " pdb=" N ALA E 445 " pdb=" C ALA E 445 " pdb=" CB ALA E 445 " both_signs ideal model delta sigma weight residual False 2.48 2.85 -0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CA THR E 73 " pdb=" N THR E 73 " pdb=" C THR E 73 " pdb=" CB THR E 73 " both_signs ideal model delta sigma weight residual False 2.53 2.21 0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 1766 not shown) Planarity restraints: 1906 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN E 444 " -0.029 2.00e-02 2.50e+03 5.55e-02 3.08e+01 pdb=" C ASN E 444 " 0.096 2.00e-02 2.50e+03 pdb=" O ASN E 444 " -0.034 2.00e-02 2.50e+03 pdb=" N ALA E 445 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 114 " 0.044 5.00e-02 4.00e+02 6.59e-02 6.95e+00 pdb=" N PRO B 115 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 115 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 115 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 98 " -0.035 5.00e-02 4.00e+02 5.42e-02 4.70e+00 pdb=" N PRO B 99 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 99 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 99 " -0.030 5.00e-02 4.00e+02 ... (remaining 1903 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 490 2.72 - 3.27: 12947 3.27 - 3.81: 18054 3.81 - 4.36: 22217 4.36 - 4.90: 34322 Nonbonded interactions: 88030 Sorted by model distance: nonbonded pdb=" OH TYR E 98 " pdb=" O LEU E 124 " model vdw 2.177 3.040 nonbonded pdb=" O VAL E 156 " pdb=" ND2 ASN S 120 " model vdw 2.218 3.120 nonbonded pdb=" OH TYR B 225 " pdb=" OE2 GLU B 232 " model vdw 2.238 3.040 nonbonded pdb=" O LYS B 507 " pdb=" ND2 ASN E 468 " model vdw 2.268 3.120 nonbonded pdb=" OH TYR S 94 " pdb=" O ARG S 128 " model vdw 2.290 3.040 ... (remaining 88025 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: 1.370 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: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.190 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 : 0.003 0.056 11175 Z= 0.151 Angle : 0.771 22.713 15121 Z= 0.425 Chirality : 0.047 0.693 1769 Planarity : 0.004 0.066 1906 Dihedral : 14.968 89.922 4181 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.82 % Allowed : 10.91 % Favored : 88.28 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.08 % 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 are not related in a simple way. whole: -1.81 (0.23), residues: 1348 helix: -0.34 (0.19), residues: 790 sheet: -2.03 (0.82), residues: 44 loop : -2.45 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 206 TYR 0.020 0.001 TYR S 81 PHE 0.014 0.001 PHE E 505 TRP 0.006 0.001 TRP E 272 HIS 0.006 0.001 HIS E 196 Details of bonding type rmsd covalent geometry : bond 0.00285 (11175) covalent geometry : angle 0.77090 (15121) hydrogen bonds : bond 0.24980 ( 567) hydrogen bonds : angle 8.00493 ( 1644) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 MET cc_start: 0.8450 (mtm) cc_final: 0.8165 (mtm) REVERT: B 217 GLU cc_start: 0.8613 (tp30) cc_final: 0.8146 (tp30) REVERT: E 77 MET cc_start: 0.9278 (ppp) cc_final: 0.9019 (ppp) REVERT: E 193 TYR cc_start: 0.8564 (t80) cc_final: 0.8168 (t80) REVERT: E 438 GLU cc_start: 0.8247 (tp30) cc_final: 0.8047 (tp30) REVERT: S 59 TYR cc_start: 0.8082 (p90) cc_final: 0.7159 (p90) REVERT: S 117 MET cc_start: 0.9009 (mmp) cc_final: 0.8694 (mmm) REVERT: M 35 ARG cc_start: 0.8793 (ttp-110) cc_final: 0.8367 (ttp-110) REVERT: M 77 PHE cc_start: 0.8254 (m-80) cc_final: 0.7908 (m-80) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.1007 time to fit residues: 38.5280 Evaluate side-chains 204 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 20.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 365 GLN E 444 ASN E 468 ASN ** S 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 85 HIS S 86 ASN ** M 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.107098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.077764 restraints weight = 36673.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.080418 restraints weight = 21442.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.082194 restraints weight = 14943.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.083434 restraints weight = 11563.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.084284 restraints weight = 9581.321| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11175 Z= 0.163 Angle : 0.765 12.008 15121 Z= 0.390 Chirality : 0.045 0.252 1769 Planarity : 0.005 0.046 1906 Dihedral : 5.085 20.506 1483 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.74 % Allowed : 10.61 % Favored : 88.65 % Rotamer: Outliers : 2.11 % Allowed : 14.36 % Favored : 83.54 % 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 are not related in a simple way. whole: -1.45 (0.23), residues: 1348 helix: 0.04 (0.18), residues: 827 sheet: -1.46 (0.90), residues: 35 loop : -2.68 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 28 TYR 0.023 0.002 TYR B 69 PHE 0.044 0.002 PHE E 318 TRP 0.007 0.001 TRP B 441 HIS 0.011 0.001 HIS S 85 Details of bonding type rmsd covalent geometry : bond 0.00346 (11175) covalent geometry : angle 0.76467 (15121) hydrogen bonds : bond 0.04968 ( 567) hydrogen bonds : angle 5.41051 ( 1644) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 247 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 LYS cc_start: 0.9145 (ptpp) cc_final: 0.8782 (mttp) REVERT: B 69 TYR cc_start: 0.8878 (m-80) cc_final: 0.8523 (m-80) REVERT: B 109 MET cc_start: 0.8455 (mtm) cc_final: 0.8129 (mtm) REVERT: B 114 MET cc_start: 0.7992 (tpp) cc_final: 0.7784 (tpp) REVERT: B 217 GLU cc_start: 0.8543 (tp30) cc_final: 0.8204 (tp30) REVERT: B 301 ARG cc_start: 0.8656 (ttp-170) cc_final: 0.8340 (ttp-170) REVERT: E 77 MET cc_start: 0.9283 (ppp) cc_final: 0.8894 (ppp) REVERT: E 193 TYR cc_start: 0.8730 (t80) cc_final: 0.8204 (t80) REVERT: E 319 GLU cc_start: 0.9203 (mp0) cc_final: 0.8876 (mm-30) REVERT: E 438 GLU cc_start: 0.8269 (tp30) cc_final: 0.8033 (tp30) REVERT: E 592 GLU cc_start: 0.8613 (mp0) cc_final: 0.8332 (mp0) REVERT: S 31 LEU cc_start: 0.9090 (mm) cc_final: 0.8824 (pp) REVERT: S 59 TYR cc_start: 0.8213 (p90) cc_final: 0.7351 (p90) REVERT: S 95 PHE cc_start: 0.5310 (m-10) cc_final: 0.5083 (m-10) REVERT: S 117 MET cc_start: 0.9000 (mmp) cc_final: 0.8732 (mmm) REVERT: M 35 ARG cc_start: 0.8682 (ttp-110) cc_final: 0.8244 (ttp-110) REVERT: M 119 TYR cc_start: 0.7139 (t80) cc_final: 0.6851 (t80) outliers start: 26 outliers final: 14 residues processed: 261 average time/residue: 0.0968 time to fit residues: 36.3925 Evaluate side-chains 236 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 222 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 296 TYR Chi-restraints excluded: chain E residue 322 HIS Chi-restraints excluded: chain E residue 514 MET Chi-restraints excluded: chain S residue 5 PHE Chi-restraints excluded: chain S residue 73 ASP Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 80 ILE Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 125 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 23 optimal weight: 0.1980 chunk 27 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 82 optimal weight: 0.6980 chunk 58 optimal weight: 0.0010 chunk 42 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN B 305 HIS S 86 ASN ** M 135 GLN ** 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 = 0.3898 r_free = 0.3898 target = 0.106899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.077780 restraints weight = 36655.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.080447 restraints weight = 21460.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.082218 restraints weight = 14896.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.083481 restraints weight = 11514.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.084392 restraints weight = 9508.379| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11175 Z= 0.146 Angle : 0.729 10.799 15121 Z= 0.371 Chirality : 0.044 0.262 1769 Planarity : 0.004 0.047 1906 Dihedral : 4.999 21.020 1483 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.82 % Allowed : 10.39 % Favored : 88.80 % Rotamer: Outliers : 2.92 % Allowed : 17.27 % Favored : 79.81 % 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 are not related in a simple way. whole: -1.44 (0.23), residues: 1348 helix: 0.07 (0.19), residues: 820 sheet: -1.74 (0.92), residues: 38 loop : -2.66 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 28 TYR 0.017 0.001 TYR S 52 PHE 0.042 0.002 PHE E 318 TRP 0.006 0.001 TRP E 446 HIS 0.006 0.001 HIS E 125 Details of bonding type rmsd covalent geometry : bond 0.00315 (11175) covalent geometry : angle 0.72876 (15121) hydrogen bonds : bond 0.04347 ( 567) hydrogen bonds : angle 5.15017 ( 1644) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 246 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 LYS cc_start: 0.9179 (ptpp) cc_final: 0.8807 (mttp) REVERT: B 69 TYR cc_start: 0.8904 (m-80) cc_final: 0.8623 (m-80) REVERT: B 84 LEU cc_start: 0.9121 (pt) cc_final: 0.8506 (mm) REVERT: B 109 MET cc_start: 0.8363 (mtm) cc_final: 0.8123 (mtm) REVERT: B 114 MET cc_start: 0.8073 (tpp) cc_final: 0.7860 (tpp) REVERT: B 186 ILE cc_start: 0.8333 (mm) cc_final: 0.8132 (mm) REVERT: B 477 LEU cc_start: 0.9157 (tp) cc_final: 0.8825 (tp) REVERT: E 77 MET cc_start: 0.9302 (ppp) cc_final: 0.8929 (ppp) REVERT: E 193 TYR cc_start: 0.8706 (t80) cc_final: 0.8283 (t80) REVERT: E 319 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8911 (mm-30) REVERT: E 395 GLU cc_start: 0.8981 (pm20) cc_final: 0.8740 (pm20) REVERT: E 505 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7783 (m-80) REVERT: E 510 PHE cc_start: 0.8474 (t80) cc_final: 0.7910 (t80) REVERT: E 554 LEU cc_start: 0.9252 (mt) cc_final: 0.9025 (mt) REVERT: S 59 TYR cc_start: 0.8261 (p90) cc_final: 0.7322 (p90) REVERT: S 95 PHE cc_start: 0.5324 (m-10) cc_final: 0.5112 (m-10) REVERT: S 117 MET cc_start: 0.9002 (mmp) cc_final: 0.8713 (mmm) REVERT: M 35 ARG cc_start: 0.8688 (ttp-110) cc_final: 0.8272 (ttp-110) outliers start: 36 outliers final: 17 residues processed: 265 average time/residue: 0.0918 time to fit residues: 34.7977 Evaluate side-chains 243 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 224 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain E residue 322 HIS Chi-restraints excluded: chain E residue 505 PHE Chi-restraints excluded: chain E residue 514 MET Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain S residue 5 PHE Chi-restraints excluded: chain S residue 24 ASP Chi-restraints excluded: chain S residue 73 ASP Chi-restraints excluded: chain S residue 80 ILE Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain M residue 116 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 8 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 100 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 ASN E 449 GLN ** E 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 86 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.100847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.072251 restraints weight = 38575.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.074179 restraints weight = 26328.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.075772 restraints weight = 16334.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.076133 restraints weight = 13731.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.076280 restraints weight = 12462.451| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 11175 Z= 0.374 Angle : 0.879 11.716 15121 Z= 0.457 Chirality : 0.048 0.276 1769 Planarity : 0.006 0.051 1906 Dihedral : 5.498 23.122 1483 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 24.83 Ramachandran Plot: Outliers : 0.74 % Allowed : 12.09 % Favored : 87.17 % Rotamer: Outliers : 3.73 % Allowed : 20.28 % Favored : 75.99 % 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 are not related in a simple way. whole: -2.15 (0.22), residues: 1348 helix: -0.57 (0.17), residues: 851 sheet: -1.80 (1.01), residues: 27 loop : -2.95 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 60 TYR 0.026 0.002 TYR E 495 PHE 0.040 0.003 PHE E 318 TRP 0.012 0.002 TRP B 556 HIS 0.007 0.001 HIS M 58 Details of bonding type rmsd covalent geometry : bond 0.00776 (11175) covalent geometry : angle 0.87853 (15121) hydrogen bonds : bond 0.05042 ( 567) hydrogen bonds : angle 5.87850 ( 1644) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 220 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 TYR cc_start: 0.9084 (m-10) cc_final: 0.8780 (m-80) REVERT: B 109 MET cc_start: 0.8553 (mtm) cc_final: 0.8326 (mtm) REVERT: B 114 MET cc_start: 0.8330 (tpp) cc_final: 0.8047 (tpp) REVERT: B 130 ARG cc_start: 0.8825 (ptm160) cc_final: 0.8531 (ptm-80) REVERT: B 217 GLU cc_start: 0.8573 (tp30) cc_final: 0.8298 (tp30) REVERT: B 477 LEU cc_start: 0.9251 (tp) cc_final: 0.8941 (tp) REVERT: E 77 MET cc_start: 0.9339 (ppp) cc_final: 0.8946 (ppp) REVERT: E 84 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8502 (tt) REVERT: E 123 PHE cc_start: 0.8594 (m-80) cc_final: 0.8105 (m-80) REVERT: E 193 TYR cc_start: 0.8768 (t80) cc_final: 0.8406 (t80) REVERT: E 210 PHE cc_start: 0.7743 (t80) cc_final: 0.7424 (t80) REVERT: E 319 GLU cc_start: 0.9285 (OUTLIER) cc_final: 0.8920 (mm-30) REVERT: E 351 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8427 (m-40) REVERT: E 406 ILE cc_start: 0.9441 (OUTLIER) cc_final: 0.8967 (mp) REVERT: E 462 MET cc_start: 0.8675 (ppp) cc_final: 0.8412 (ppp) REVERT: S 31 LEU cc_start: 0.9213 (mm) cc_final: 0.8914 (pp) REVERT: S 59 TYR cc_start: 0.8181 (p90) cc_final: 0.7518 (p90) REVERT: S 95 PHE cc_start: 0.5557 (m-10) cc_final: 0.5330 (m-10) REVERT: S 117 MET cc_start: 0.9153 (mmp) cc_final: 0.8838 (mmm) REVERT: M 20 PHE cc_start: 0.7867 (m-10) cc_final: 0.7654 (m-80) REVERT: M 31 GLU cc_start: 0.8875 (mp0) cc_final: 0.7917 (pm20) REVERT: M 35 ARG cc_start: 0.8784 (ttp-110) cc_final: 0.8348 (ttp-110) REVERT: M 54 ARG cc_start: 0.6900 (ptp-170) cc_final: 0.6578 (ptp-170) REVERT: M 58 HIS cc_start: 0.7572 (t70) cc_final: 0.7334 (t70) REVERT: M 121 TYR cc_start: 0.8590 (m-10) cc_final: 0.8342 (m-10) outliers start: 46 outliers final: 29 residues processed: 241 average time/residue: 0.0986 time to fit residues: 33.5892 Evaluate side-chains 246 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 213 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 240 TYR Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain E residue 322 HIS Chi-restraints excluded: chain E residue 351 ASN Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain S residue 5 PHE Chi-restraints excluded: chain S residue 24 ASP Chi-restraints excluded: chain S residue 73 ASP Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 80 ILE Chi-restraints excluded: chain S residue 86 ASN Chi-restraints excluded: chain S residue 122 CYS Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 125 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 111 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 ASN E 444 ASN E 468 ASN ** S 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 55 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.105379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.077070 restraints weight = 37066.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.079285 restraints weight = 22297.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.081674 restraints weight = 14138.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.081899 restraints weight = 11355.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.082121 restraints weight = 9861.877| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11175 Z= 0.149 Angle : 0.771 12.144 15121 Z= 0.382 Chirality : 0.045 0.269 1769 Planarity : 0.004 0.054 1906 Dihedral : 5.197 21.353 1483 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.89 % Allowed : 10.31 % Favored : 88.80 % Rotamer: Outliers : 3.81 % Allowed : 21.90 % Favored : 74.29 % 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 are not related in a simple way. whole: -1.68 (0.23), residues: 1348 helix: -0.16 (0.18), residues: 835 sheet: -1.32 (0.96), residues: 33 loop : -2.82 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 28 TYR 0.019 0.001 TYR B 327 PHE 0.040 0.002 PHE E 318 TRP 0.011 0.002 TRP E 272 HIS 0.008 0.001 HIS E 125 Details of bonding type rmsd covalent geometry : bond 0.00324 (11175) covalent geometry : angle 0.77141 (15121) hydrogen bonds : bond 0.04184 ( 567) hydrogen bonds : angle 5.11510 ( 1644) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 236 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8501 (pm20) REVERT: B 69 TYR cc_start: 0.9132 (m-10) cc_final: 0.8795 (m-80) REVERT: B 84 LEU cc_start: 0.9248 (pt) cc_final: 0.8617 (mm) REVERT: B 217 GLU cc_start: 0.8544 (tp30) cc_final: 0.8212 (tp30) REVERT: B 237 LEU cc_start: 0.9263 (mt) cc_final: 0.8676 (pp) REVERT: B 477 LEU cc_start: 0.9149 (tp) cc_final: 0.8832 (tp) REVERT: E 77 MET cc_start: 0.9332 (ppp) cc_final: 0.8963 (ppp) REVERT: E 98 TYR cc_start: 0.5778 (m-10) cc_final: 0.5457 (m-10) REVERT: E 102 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.8947 (mm) REVERT: E 123 PHE cc_start: 0.8517 (m-80) cc_final: 0.8054 (m-80) REVERT: E 195 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.7776 (m-80) REVERT: E 210 PHE cc_start: 0.7662 (t80) cc_final: 0.7433 (t80) REVERT: E 319 GLU cc_start: 0.9235 (OUTLIER) cc_final: 0.8657 (mm-30) REVERT: E 370 LEU cc_start: 0.8458 (tt) cc_final: 0.7967 (mt) REVERT: E 395 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8782 (pm20) REVERT: E 419 GLN cc_start: 0.9002 (tp-100) cc_final: 0.8775 (tm-30) REVERT: E 462 MET cc_start: 0.8769 (ppp) cc_final: 0.7642 (ppp) REVERT: S 59 TYR cc_start: 0.8132 (p90) cc_final: 0.7515 (p90) REVERT: S 117 MET cc_start: 0.9139 (mmp) cc_final: 0.8865 (mmm) REVERT: M 35 ARG cc_start: 0.8716 (ttp-110) cc_final: 0.8344 (ttp-110) REVERT: M 60 ARG cc_start: 0.7895 (mmm160) cc_final: 0.7558 (mmm160) outliers start: 47 outliers final: 27 residues processed: 263 average time/residue: 0.0935 time to fit residues: 35.6133 Evaluate side-chains 254 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 222 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 GLN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 296 TYR Chi-restraints excluded: chain E residue 301 GLU Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain E residue 322 HIS Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 444 ASN Chi-restraints excluded: chain E residue 468 ASN Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain S residue 5 PHE Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 24 ASP Chi-restraints excluded: chain S residue 73 ASP Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 80 ILE Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain M residue 116 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 90 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 92 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 ASN ** E 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 468 ASN S 76 ASN S 86 ASN ** M 135 GLN ** 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 = 0.3887 r_free = 0.3887 target = 0.106218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.077048 restraints weight = 37168.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.079674 restraints weight = 21663.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.081441 restraints weight = 15096.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.082659 restraints weight = 11681.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.083526 restraints weight = 9687.303| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11175 Z= 0.143 Angle : 0.786 13.140 15121 Z= 0.386 Chirality : 0.045 0.271 1769 Planarity : 0.004 0.066 1906 Dihedral : 5.103 22.137 1483 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.74 % Allowed : 10.61 % Favored : 88.65 % Rotamer: Outliers : 4.06 % Allowed : 23.11 % Favored : 72.83 % 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 are not related in a simple way. whole: -1.50 (0.23), residues: 1348 helix: -0.03 (0.18), residues: 841 sheet: -1.05 (0.97), residues: 31 loop : -2.74 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 28 TYR 0.034 0.001 TYR M 17 PHE 0.033 0.002 PHE E 318 TRP 0.014 0.002 TRP E 272 HIS 0.006 0.001 HIS E 125 Details of bonding type rmsd covalent geometry : bond 0.00312 (11175) covalent geometry : angle 0.78579 (15121) hydrogen bonds : bond 0.03972 ( 567) hydrogen bonds : angle 5.00637 ( 1644) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 237 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 TYR cc_start: 0.9086 (m-10) cc_final: 0.8737 (m-80) REVERT: B 84 LEU cc_start: 0.9156 (pt) cc_final: 0.8558 (mm) REVERT: B 213 TRP cc_start: 0.8655 (OUTLIER) cc_final: 0.7767 (m100) REVERT: B 237 LEU cc_start: 0.9258 (mt) cc_final: 0.8758 (pp) REVERT: B 290 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8488 (mmm-85) REVERT: B 477 LEU cc_start: 0.9143 (tp) cc_final: 0.8834 (tp) REVERT: E 77 MET cc_start: 0.9326 (ppp) cc_final: 0.8900 (ppp) REVERT: E 98 TYR cc_start: 0.5650 (m-10) cc_final: 0.5321 (m-10) REVERT: E 102 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8896 (mm) REVERT: E 123 PHE cc_start: 0.8542 (m-80) cc_final: 0.8073 (m-80) REVERT: E 195 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7503 (m-80) REVERT: E 210 PHE cc_start: 0.7516 (t80) cc_final: 0.7292 (t80) REVERT: E 370 LEU cc_start: 0.8359 (tt) cc_final: 0.7885 (mt) REVERT: E 406 ILE cc_start: 0.9434 (OUTLIER) cc_final: 0.8954 (mp) REVERT: E 462 MET cc_start: 0.8761 (ppp) cc_final: 0.7613 (ppp) REVERT: E 510 PHE cc_start: 0.8493 (t80) cc_final: 0.8055 (t80) REVERT: S 31 LEU cc_start: 0.9138 (mm) cc_final: 0.8850 (pp) REVERT: S 42 ARG cc_start: 0.7149 (ttp80) cc_final: 0.6919 (ttp80) REVERT: S 59 TYR cc_start: 0.8134 (p90) cc_final: 0.7554 (p90) REVERT: S 95 PHE cc_start: 0.5644 (m-10) cc_final: 0.5418 (m-10) REVERT: S 117 MET cc_start: 0.9100 (mmp) cc_final: 0.8849 (mmm) REVERT: M 35 ARG cc_start: 0.8698 (ttp-110) cc_final: 0.8314 (ttp-110) REVERT: M 60 ARG cc_start: 0.7669 (mmm160) cc_final: 0.7317 (mmm160) outliers start: 50 outliers final: 29 residues processed: 262 average time/residue: 0.0985 time to fit residues: 36.6619 Evaluate side-chains 255 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 221 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 213 TRP Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 296 TYR Chi-restraints excluded: chain E residue 301 GLU Chi-restraints excluded: chain E residue 322 HIS Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 444 ASN Chi-restraints excluded: chain E residue 468 ASN Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain S residue 5 PHE Chi-restraints excluded: chain S residue 24 ASP Chi-restraints excluded: chain S residue 73 ASP Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 80 ILE Chi-restraints excluded: chain S residue 86 ASN Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain M residue 116 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 89 optimal weight: 0.0670 chunk 3 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 444 ASN E 468 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.106111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.076578 restraints weight = 37102.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.079176 restraints weight = 21787.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.080946 restraints weight = 15263.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.082146 restraints weight = 11843.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.082975 restraints weight = 9855.586| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11175 Z= 0.158 Angle : 0.817 14.542 15121 Z= 0.398 Chirality : 0.045 0.288 1769 Planarity : 0.004 0.061 1906 Dihedral : 5.057 22.064 1483 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.74 % Allowed : 10.68 % Favored : 88.58 % Rotamer: Outliers : 3.49 % Allowed : 25.22 % Favored : 71.29 % 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 are not related in a simple way. whole: -1.43 (0.23), residues: 1348 helix: 0.04 (0.18), residues: 838 sheet: -1.30 (0.93), residues: 32 loop : -2.73 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 28 TYR 0.033 0.002 TYR M 17 PHE 0.031 0.002 PHE E 318 TRP 0.012 0.001 TRP E 272 HIS 0.005 0.001 HIS E 597 Details of bonding type rmsd covalent geometry : bond 0.00348 (11175) covalent geometry : angle 0.81669 (15121) hydrogen bonds : bond 0.03861 ( 567) hydrogen bonds : angle 5.02322 ( 1644) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 222 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 TYR cc_start: 0.9112 (m-10) cc_final: 0.8744 (m-80) REVERT: B 84 LEU cc_start: 0.9143 (pt) cc_final: 0.8565 (mm) REVERT: B 213 TRP cc_start: 0.8697 (OUTLIER) cc_final: 0.7900 (m100) REVERT: B 290 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8461 (mmm-85) REVERT: E 77 MET cc_start: 0.9316 (ppp) cc_final: 0.8911 (ppp) REVERT: E 98 TYR cc_start: 0.5651 (m-10) cc_final: 0.5379 (m-10) REVERT: E 102 ILE cc_start: 0.9135 (mp) cc_final: 0.8823 (mm) REVERT: E 123 PHE cc_start: 0.8525 (m-80) cc_final: 0.8117 (m-80) REVERT: E 195 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.7524 (m-80) REVERT: E 210 PHE cc_start: 0.7573 (t80) cc_final: 0.7338 (t80) REVERT: E 370 LEU cc_start: 0.8446 (tt) cc_final: 0.8021 (mt) REVERT: E 406 ILE cc_start: 0.9432 (OUTLIER) cc_final: 0.8972 (mp) REVERT: E 462 MET cc_start: 0.8757 (ppp) cc_final: 0.7688 (ppp) REVERT: S 31 LEU cc_start: 0.9152 (mm) cc_final: 0.8871 (pp) REVERT: S 59 TYR cc_start: 0.8201 (p90) cc_final: 0.7631 (p90) REVERT: S 95 PHE cc_start: 0.5786 (m-10) cc_final: 0.5500 (m-10) REVERT: S 117 MET cc_start: 0.9152 (mmp) cc_final: 0.8893 (mmm) REVERT: M 35 ARG cc_start: 0.8680 (ttp-110) cc_final: 0.8292 (ttp-110) REVERT: M 60 ARG cc_start: 0.7845 (mmm160) cc_final: 0.7580 (mmm160) outliers start: 43 outliers final: 30 residues processed: 247 average time/residue: 0.0968 time to fit residues: 33.9938 Evaluate side-chains 250 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 216 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 213 TRP Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 296 TYR Chi-restraints excluded: chain E residue 301 GLU Chi-restraints excluded: chain E residue 322 HIS Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 444 ASN Chi-restraints excluded: chain E residue 468 ASN Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain S residue 5 PHE Chi-restraints excluded: chain S residue 24 ASP Chi-restraints excluded: chain S residue 73 ASP Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 80 ILE Chi-restraints excluded: chain S residue 122 CYS Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain M residue 116 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 83 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 108 optimal weight: 0.0980 chunk 71 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 119 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 69 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 29 optimal weight: 0.0670 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 276 GLN E 468 ASN S 86 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.107408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.079786 restraints weight = 36533.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.081558 restraints weight = 21608.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.083023 restraints weight = 13827.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.083350 restraints weight = 12032.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.083577 restraints weight = 10857.305| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11175 Z= 0.137 Angle : 0.807 12.548 15121 Z= 0.392 Chirality : 0.045 0.321 1769 Planarity : 0.004 0.062 1906 Dihedral : 4.978 21.309 1483 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.59 % Allowed : 10.24 % Favored : 89.17 % Rotamer: Outliers : 3.41 % Allowed : 25.47 % Favored : 71.13 % 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 are not related in a simple way. whole: -1.28 (0.24), residues: 1348 helix: 0.13 (0.18), residues: 836 sheet: -1.27 (0.94), residues: 31 loop : -2.58 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 28 TYR 0.033 0.001 TYR M 17 PHE 0.027 0.002 PHE E 318 TRP 0.016 0.001 TRP E 272 HIS 0.005 0.001 HIS E 597 Details of bonding type rmsd covalent geometry : bond 0.00295 (11175) covalent geometry : angle 0.80709 (15121) hydrogen bonds : bond 0.03731 ( 567) hydrogen bonds : angle 4.85429 ( 1644) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 244 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 TYR cc_start: 0.9134 (m-10) cc_final: 0.8761 (m-80) REVERT: B 84 LEU cc_start: 0.9179 (pt) cc_final: 0.8614 (mm) REVERT: B 207 MET cc_start: 0.8468 (mmm) cc_final: 0.8111 (mmm) REVERT: B 213 TRP cc_start: 0.8683 (OUTLIER) cc_final: 0.7689 (m100) REVERT: B 290 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8464 (mmm-85) REVERT: B 475 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7647 (mt-10) REVERT: E 77 MET cc_start: 0.9319 (ppp) cc_final: 0.8937 (ppp) REVERT: E 98 TYR cc_start: 0.5654 (m-10) cc_final: 0.5387 (m-10) REVERT: E 102 ILE cc_start: 0.9173 (mp) cc_final: 0.8883 (mm) REVERT: E 123 PHE cc_start: 0.8464 (m-80) cc_final: 0.8132 (m-80) REVERT: E 195 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7630 (m-10) REVERT: E 210 PHE cc_start: 0.7595 (t80) cc_final: 0.7358 (t80) REVERT: E 370 LEU cc_start: 0.8618 (tt) cc_final: 0.8225 (mt) REVERT: E 462 MET cc_start: 0.8742 (ppp) cc_final: 0.7469 (ppp) REVERT: E 510 PHE cc_start: 0.8546 (t80) cc_final: 0.8034 (t80) REVERT: S 31 LEU cc_start: 0.9223 (mm) cc_final: 0.8934 (pp) REVERT: S 59 TYR cc_start: 0.8199 (p90) cc_final: 0.7665 (p90) REVERT: S 95 PHE cc_start: 0.5641 (m-10) cc_final: 0.5363 (m-10) REVERT: S 117 MET cc_start: 0.9157 (mmp) cc_final: 0.8887 (mmm) REVERT: M 35 ARG cc_start: 0.8697 (ttp-110) cc_final: 0.8307 (ttp-110) REVERT: M 60 ARG cc_start: 0.7606 (mmm160) cc_final: 0.7216 (mmm160) REVERT: M 105 ASN cc_start: 0.8478 (t0) cc_final: 0.8069 (t0) REVERT: M 108 LEU cc_start: 0.9083 (tp) cc_final: 0.8744 (tp) outliers start: 42 outliers final: 27 residues processed: 268 average time/residue: 0.1001 time to fit residues: 38.3672 Evaluate side-chains 261 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 231 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 213 TRP Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 240 TYR Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 296 TYR Chi-restraints excluded: chain E residue 301 GLU Chi-restraints excluded: chain E residue 322 HIS Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 444 ASN Chi-restraints excluded: chain E residue 468 ASN Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain S residue 5 PHE Chi-restraints excluded: chain S residue 73 ASP Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 80 ILE Chi-restraints excluded: chain S residue 86 ASN Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain M residue 116 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 15 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 121 optimal weight: 9.9990 chunk 113 optimal weight: 0.0470 chunk 88 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 ASN E 444 ASN E 468 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.107480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.078819 restraints weight = 36256.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.081490 restraints weight = 21079.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.083274 restraints weight = 14493.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.084509 restraints weight = 11098.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.085354 restraints weight = 9122.025| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11175 Z= 0.142 Angle : 0.845 14.766 15121 Z= 0.406 Chirality : 0.046 0.308 1769 Planarity : 0.004 0.054 1906 Dihedral : 4.980 21.015 1483 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.59 % Allowed : 10.16 % Favored : 89.24 % Rotamer: Outliers : 3.41 % Allowed : 26.36 % Favored : 70.24 % 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 are not related in a simple way. whole: -1.23 (0.24), residues: 1348 helix: 0.16 (0.18), residues: 842 sheet: -1.17 (0.97), residues: 31 loop : -2.59 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 28 TYR 0.031 0.001 TYR M 17 PHE 0.026 0.001 PHE E 318 TRP 0.012 0.002 TRP E 272 HIS 0.004 0.000 HIS E 597 Details of bonding type rmsd covalent geometry : bond 0.00310 (11175) covalent geometry : angle 0.84507 (15121) hydrogen bonds : bond 0.03763 ( 567) hydrogen bonds : angle 4.85875 ( 1644) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 238 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 TYR cc_start: 0.9119 (m-10) cc_final: 0.8802 (m-80) REVERT: B 84 LEU cc_start: 0.9113 (pt) cc_final: 0.8570 (mm) REVERT: B 213 TRP cc_start: 0.8688 (OUTLIER) cc_final: 0.7731 (m100) REVERT: B 220 ASN cc_start: 0.9424 (OUTLIER) cc_final: 0.9043 (p0) REVERT: B 290 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8384 (mmm-85) REVERT: B 475 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7683 (mt-10) REVERT: E 77 MET cc_start: 0.9304 (ppp) cc_final: 0.8934 (ppp) REVERT: E 98 TYR cc_start: 0.5530 (m-80) cc_final: 0.5288 (m-10) REVERT: E 102 ILE cc_start: 0.9134 (mp) cc_final: 0.8826 (mm) REVERT: E 123 PHE cc_start: 0.8470 (m-80) cc_final: 0.8157 (m-80) REVERT: E 195 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.7480 (m-10) REVERT: E 210 PHE cc_start: 0.7429 (t80) cc_final: 0.7183 (t80) REVERT: E 462 MET cc_start: 0.8794 (ppp) cc_final: 0.7656 (ppp) REVERT: E 510 PHE cc_start: 0.8510 (t80) cc_final: 0.7984 (t80) REVERT: S 31 LEU cc_start: 0.9231 (mm) cc_final: 0.8947 (pp) REVERT: S 59 TYR cc_start: 0.8121 (p90) cc_final: 0.7553 (p90) REVERT: S 62 TYR cc_start: 0.7610 (t80) cc_final: 0.7300 (t80) REVERT: S 95 PHE cc_start: 0.5556 (m-10) cc_final: 0.5293 (m-10) REVERT: M 20 PHE cc_start: 0.7629 (m-80) cc_final: 0.7004 (m-80) REVERT: M 35 ARG cc_start: 0.8657 (ttp-110) cc_final: 0.8245 (ttp-110) REVERT: M 105 ASN cc_start: 0.8301 (t0) cc_final: 0.7993 (t0) REVERT: M 108 LEU cc_start: 0.9031 (tp) cc_final: 0.8682 (tp) outliers start: 42 outliers final: 25 residues processed: 262 average time/residue: 0.0986 time to fit residues: 37.0188 Evaluate side-chains 262 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 233 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 213 TRP Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 296 TYR Chi-restraints excluded: chain E residue 301 GLU Chi-restraints excluded: chain E residue 322 HIS Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 444 ASN Chi-restraints excluded: chain E residue 468 ASN Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain S residue 5 PHE Chi-restraints excluded: chain S residue 73 ASP Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 80 ILE Chi-restraints excluded: chain S residue 86 ASN Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain M residue 116 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 26 optimal weight: 0.1980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 468 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.106920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.079915 restraints weight = 36460.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.081709 restraints weight = 21095.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.083601 restraints weight = 13564.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.083867 restraints weight = 11149.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.084086 restraints weight = 10121.931| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11175 Z= 0.152 Angle : 0.877 15.470 15121 Z= 0.421 Chirality : 0.047 0.329 1769 Planarity : 0.004 0.063 1906 Dihedral : 5.005 21.281 1483 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.59 % Allowed : 10.53 % Favored : 88.87 % Rotamer: Outliers : 2.60 % Allowed : 27.09 % Favored : 70.32 % 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 are not related in a simple way. whole: -1.26 (0.24), residues: 1348 helix: 0.11 (0.18), residues: 845 sheet: -1.30 (1.00), residues: 27 loop : -2.53 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 28 TYR 0.027 0.002 TYR M 17 PHE 0.026 0.001 PHE E 318 TRP 0.014 0.002 TRP E 272 HIS 0.004 0.001 HIS S 85 Details of bonding type rmsd covalent geometry : bond 0.00336 (11175) covalent geometry : angle 0.87673 (15121) hydrogen bonds : bond 0.03830 ( 567) hydrogen bonds : angle 4.97086 ( 1644) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 231 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 TYR cc_start: 0.9166 (m-10) cc_final: 0.8716 (m-80) REVERT: B 84 LEU cc_start: 0.9180 (pt) cc_final: 0.8642 (mm) REVERT: B 207 MET cc_start: 0.8259 (mmm) cc_final: 0.8013 (mmm) REVERT: B 213 TRP cc_start: 0.8679 (OUTLIER) cc_final: 0.7785 (m100) REVERT: B 290 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8410 (mmm-85) REVERT: B 475 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7686 (mt-10) REVERT: E 77 MET cc_start: 0.9314 (ppp) cc_final: 0.8891 (ppp) REVERT: E 98 TYR cc_start: 0.5662 (m-80) cc_final: 0.5392 (m-10) REVERT: E 102 ILE cc_start: 0.9132 (mp) cc_final: 0.8827 (mm) REVERT: E 123 PHE cc_start: 0.8462 (m-80) cc_final: 0.8163 (m-80) REVERT: E 154 LEU cc_start: 0.9458 (tt) cc_final: 0.9239 (tt) REVERT: E 193 TYR cc_start: 0.8765 (t80) cc_final: 0.8175 (t80) REVERT: E 195 PHE cc_start: 0.8047 (OUTLIER) cc_final: 0.7477 (m-80) REVERT: E 210 PHE cc_start: 0.7496 (t80) cc_final: 0.7247 (t80) REVERT: E 272 TRP cc_start: 0.8157 (p90) cc_final: 0.7652 (p90) REVERT: E 406 ILE cc_start: 0.9460 (OUTLIER) cc_final: 0.9034 (mp) REVERT: E 462 MET cc_start: 0.8818 (ppp) cc_final: 0.7674 (ppp) REVERT: E 510 PHE cc_start: 0.8486 (t80) cc_final: 0.7973 (t80) REVERT: S 31 LEU cc_start: 0.9221 (mm) cc_final: 0.8945 (pp) REVERT: S 59 TYR cc_start: 0.8192 (p90) cc_final: 0.7584 (p90) REVERT: S 62 TYR cc_start: 0.7590 (t80) cc_final: 0.7279 (t80) REVERT: S 95 PHE cc_start: 0.5502 (m-10) cc_final: 0.5261 (m-10) REVERT: M 35 ARG cc_start: 0.8684 (ttp-110) cc_final: 0.8286 (ttp-110) REVERT: M 60 ARG cc_start: 0.7660 (mmm160) cc_final: 0.7322 (mmm160) REVERT: M 105 ASN cc_start: 0.8445 (t0) cc_final: 0.8076 (t0) REVERT: M 108 LEU cc_start: 0.9066 (tp) cc_final: 0.8723 (tp) outliers start: 32 outliers final: 25 residues processed: 249 average time/residue: 0.1038 time to fit residues: 36.6592 Evaluate side-chains 256 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 227 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 213 TRP Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 296 TYR Chi-restraints excluded: chain E residue 301 GLU Chi-restraints excluded: chain E residue 322 HIS Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 444 ASN Chi-restraints excluded: chain E residue 468 ASN Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain S residue 5 PHE Chi-restraints excluded: chain S residue 73 ASP Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 80 ILE Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain M residue 116 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 4 optimal weight: 7.9990 chunk 45 optimal weight: 0.0770 chunk 97 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 1 optimal weight: 0.3980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 444 ASN E 468 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.108241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.080577 restraints weight = 36540.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.082466 restraints weight = 21585.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.084187 restraints weight = 13716.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.084561 restraints weight = 11593.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.084758 restraints weight = 10301.487| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 11175 Z= 0.148 Angle : 0.896 16.177 15121 Z= 0.425 Chirality : 0.049 0.498 1769 Planarity : 0.004 0.053 1906 Dihedral : 4.951 21.754 1483 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.52 % Allowed : 10.31 % Favored : 89.17 % Rotamer: Outliers : 2.35 % Allowed : 27.33 % Favored : 70.32 % 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 are not related in a simple way. whole: -1.24 (0.24), residues: 1348 helix: 0.10 (0.18), residues: 845 sheet: -1.20 (1.01), residues: 27 loop : -2.46 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 42 TYR 0.031 0.001 TYR M 17 PHE 0.028 0.001 PHE E 318 TRP 0.016 0.002 TRP E 272 HIS 0.004 0.001 HIS S 85 Details of bonding type rmsd covalent geometry : bond 0.00333 (11175) covalent geometry : angle 0.89565 (15121) hydrogen bonds : bond 0.03774 ( 567) hydrogen bonds : angle 4.91258 ( 1644) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1850.09 seconds wall clock time: 32 minutes 49.58 seconds (1969.58 seconds total)