Starting phenix.real_space_refine on Fri Sep 11 16:30:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xbk_22118/09_2026/6xbk_22118.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xbk_22118/09_2026/6xbk_22118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6xbk_22118/09_2026/6xbk_22118.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xbk_22118/09_2026/6xbk_22118.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xbk_22118/09_2026/6xbk_22118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xbk_22118/09_2026/6xbk_22118.map" model { file = "/net/cci-nas-00/data/ceres_data/6xbk_22118/09_2026/6xbk_22118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xbk_22118/09_2026/6xbk_22118.cif" } resolution = 3.24 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= 0.002 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 78 5.16 5 C 6489 2.51 5 N 1735 2.21 5 O 1912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10214 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 3674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3674 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 21, 'TRANS': 446} Chain breaks: 1 Chain: "A" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1736 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 212} Chain breaks: 2 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "S" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1785 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.03, per 1000 atoms: 0.20 Number of scatterers: 10214 At special positions: 0 Unit cell: (108.29, 119.952, 165.767, 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 78 16.00 O 1912 8.00 N 1735 7.00 C 6489 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS R 64 " - pdb=" SG CYS R 178 " distance=2.03 Simple disulfide: pdb=" SG CYS R 70 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 78 " - pdb=" SG CYS R 127 " distance=2.03 Simple disulfide: pdb=" SG CYS R 111 " - pdb=" SG CYS R 496 " distance=2.03 Simple disulfide: pdb=" SG CYS R 118 " - pdb=" SG CYS R 154 " distance=2.03 Simple disulfide: pdb=" SG CYS R 147 " - pdb=" SG CYS R 169 " distance=2.03 Simple disulfide: pdb=" SG CYS R 193 " - pdb=" SG CYS R 213 " distance=2.03 Simple disulfide: pdb=" SG CYS R 217 " - pdb=" SG CYS R 295 " distance=2.03 Simple disulfide: pdb=" SG CYS R 314 " - pdb=" SG CYS R 390 " distance=2.03 Simple disulfide: pdb=" SG CYS R 490 " - pdb=" SG CYS R 507 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.05 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.02 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: 0.87 Conformation dependent library (CDL) restraints added in 371.6 milliseconds 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2414 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 17 sheets defined 35.8% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'R' and resid 98 through 110 Processing helix chain 'R' and resid 111 through 114 removed outlier: 4.326A pdb=" N ASN R 114 " --> pdb=" O CYS R 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 111 through 114' Processing helix chain 'R' and resid 115 through 130 removed outlier: 5.028A pdb=" N VAL R 121 " --> pdb=" O ARG R 117 " (cutoff:3.500A) Proline residue: R 124 - end of helix Processing helix chain 'R' and resid 144 through 149 Processing helix chain 'R' and resid 155 through 161 Processing helix chain 'R' and resid 223 through 255 removed outlier: 3.958A pdb=" N ASP R 255 " --> pdb=" O THR R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 282 Processing helix chain 'R' and resid 288 through 295 removed outlier: 3.735A pdb=" N GLU R 292 " --> pdb=" O GLY R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 314 through 345 removed outlier: 3.596A pdb=" N VAL R 321 " --> pdb=" O ILE R 317 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA R 345 " --> pdb=" O THR R 341 " (cutoff:3.500A) Processing helix chain 'R' and resid 356 through 378 Proline residue: R 368 - end of helix removed outlier: 3.702A pdb=" N VAL R 378 " --> pdb=" O ALA R 374 " (cutoff:3.500A) Processing helix chain 'R' and resid 396 through 433 removed outlier: 3.958A pdb=" N ARG R 400 " --> pdb=" O ASN R 396 " (cutoff:3.500A) Proline residue: R 407 - end of helix removed outlier: 5.313A pdb=" N LYS R 430 " --> pdb=" O LEU R 426 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N SER R 431 " --> pdb=" O PHE R 427 " (cutoff:3.500A) Processing helix chain 'R' and resid 438 through 497 removed outlier: 3.916A pdb=" N LYS R 444 " --> pdb=" O LYS R 440 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG R 482 " --> pdb=" O ALA R 478 " (cutoff:3.500A) Processing helix chain 'R' and resid 514 through 532 removed outlier: 4.307A pdb=" N GLU R 518 " --> pdb=" O SER R 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.774A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.742A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.486A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.391A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 removed outlier: 4.154A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 removed outlier: 3.560A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 25 removed outlier: 3.800A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.889A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.710A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.250A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 62 through 65 removed outlier: 3.838A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing sheet with id=AA1, first strand: chain 'R' and resid 65 through 66 removed outlier: 3.719A pdb=" N ARG R 66 " --> pdb=" O VAL R 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 198 through 199 Processing sheet with id=AA3, first strand: chain 'R' and resid 382 through 384 removed outlier: 3.517A pdb=" N ILE R 389 " --> pdb=" O ASP R 384 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.895A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 38 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.895A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 38 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 49 through 52 removed outlier: 3.659A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.977A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 111 through 113 Processing sheet with id=AA9, first strand: chain 'B' and resid 120 through 121 removed outlier: 3.862A pdb=" N LEU B 139 " --> pdb=" O CYS B 121 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.893A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 187 through 191 removed outlier: 3.545A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.586A pdb=" N CYS B 233 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.646A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.779A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.815A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.859A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 143 through 146 471 hydrogen bonds defined for protein. 1326 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: 1.44 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1973 1.33 - 1.45: 2615 1.45 - 1.58: 5748 1.58 - 1.70: 0 1.70 - 1.82: 107 Bond restraints: 10443 Sorted by residual: bond pdb=" CD GLU A 8 " pdb=" OE1 GLU A 8 " ideal model delta sigma weight residual 1.249 1.345 -0.096 1.90e-02 2.77e+03 2.58e+01 bond pdb=" N ILE B 93 " pdb=" CA ILE B 93 " ideal model delta sigma weight residual 1.460 1.495 -0.035 7.30e-03 1.88e+04 2.24e+01 bond pdb=" N ILE B 270 " pdb=" CA ILE B 270 " ideal model delta sigma weight residual 1.460 1.498 -0.038 8.60e-03 1.35e+04 1.91e+01 bond pdb=" N GLY B 185 " pdb=" CA GLY B 185 " ideal model delta sigma weight residual 1.443 1.479 -0.035 8.60e-03 1.35e+04 1.70e+01 bond pdb=" N VAL S 64 " pdb=" CA VAL S 64 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.09e-02 8.42e+03 1.52e+01 ... (remaining 10438 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 12087 2.54 - 5.07: 2042 5.07 - 7.61: 27 7.61 - 10.14: 0 10.14 - 12.68: 1 Bond angle restraints: 14157 Sorted by residual: angle pdb=" C TYR S 223 " pdb=" CA TYR S 223 " pdb=" CB TYR S 223 " ideal model delta sigma weight residual 110.17 122.85 -12.68 1.97e+00 2.58e-01 4.14e+01 angle pdb=" C GLU R 194 " pdb=" N VAL R 195 " pdb=" CA VAL R 195 " ideal model delta sigma weight residual 120.33 125.11 -4.78 8.00e-01 1.56e+00 3.56e+01 angle pdb=" C THR R 170 " pdb=" CA THR R 170 " pdb=" CB THR R 170 " ideal model delta sigma weight residual 108.63 115.87 -7.24 1.54e+00 4.22e-01 2.21e+01 angle pdb=" C PHE R 526 " pdb=" N GLY R 527 " pdb=" CA GLY R 527 " ideal model delta sigma weight residual 119.98 125.01 -5.03 1.11e+00 8.12e-01 2.05e+01 angle pdb=" CA ALA B 28 " pdb=" C ALA B 28 " pdb=" O ALA B 28 " ideal model delta sigma weight residual 120.80 116.06 4.74 1.05e+00 9.07e-01 2.04e+01 ... (remaining 14152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.09: 5878 25.09 - 50.18: 278 50.18 - 75.27: 19 75.27 - 100.35: 5 100.35 - 125.44: 2 Dihedral angle restraints: 6182 sinusoidal: 2426 harmonic: 3756 Sorted by residual: dihedral pdb=" CA GLU R 305 " pdb=" C GLU R 305 " pdb=" N PRO R 306 " pdb=" CA PRO R 306 " ideal model delta harmonic sigma weight residual -180.00 -54.56 -125.44 0 5.00e+00 4.00e-02 6.29e+02 dihedral pdb=" CA TYR S 223 " pdb=" C TYR S 223 " pdb=" N PRO S 224 " pdb=" CA PRO S 224 " ideal model delta harmonic sigma weight residual -180.00 -62.75 -117.25 0 5.00e+00 4.00e-02 5.50e+02 dihedral pdb=" CB CYS R 147 " pdb=" SG CYS R 147 " pdb=" SG CYS R 169 " pdb=" CB CYS R 169 " ideal model delta sinusoidal sigma weight residual -86.00 -170.68 84.68 1 1.00e+01 1.00e-02 8.71e+01 ... (remaining 6179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 844 0.064 - 0.128: 581 0.128 - 0.191: 145 0.191 - 0.255: 4 0.255 - 0.319: 2 Chirality restraints: 1576 Sorted by residual: chirality pdb=" CA TYR S 223 " pdb=" N TYR S 223 " pdb=" C TYR S 223 " pdb=" CB TYR S 223 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" C13 CLR R 701 " pdb=" C12 CLR R 701 " pdb=" C14 CLR R 701 " pdb=" C17 CLR R 701 " both_signs ideal model delta sigma weight residual False -2.93 -2.65 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C14 CLR R 701 " pdb=" C13 CLR R 701 " pdb=" C15 CLR R 701 " pdb=" C8 CLR R 701 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 1573 not shown) Planarity restraints: 1804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU R 305 " 0.068 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO R 306 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO R 306 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO R 306 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU R 305 " -0.020 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" C GLU R 305 " 0.068 2.00e-02 2.50e+03 pdb=" O GLU R 305 " -0.025 2.00e-02 2.50e+03 pdb=" N PRO R 306 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR S 223 " -0.053 5.00e-02 4.00e+02 8.02e-02 1.03e+01 pdb=" N PRO S 224 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO S 224 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO S 224 " -0.045 5.00e-02 4.00e+02 ... (remaining 1801 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 647 2.75 - 3.29: 10233 3.29 - 3.83: 15563 3.83 - 4.36: 19951 4.36 - 4.90: 34013 Nonbonded interactions: 80407 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.219 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.245 3.040 nonbonded pdb=" OH TYR R 85 " pdb=" O MET R 131 " model vdw 2.319 3.040 nonbonded pdb=" O THR B 29 " pdb=" N GLN B 32 " model vdw 2.327 3.120 nonbonded pdb=" NH1 ARG S 168 " pdb=" O GLU S 210 " model vdw 2.329 3.120 ... (remaining 80402 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.040 Find NCS groups from input model: 0.050 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 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 : 0.014 0.096 10456 Z= 1.062 Angle : 1.701 12.680 14183 Z= 1.258 Chirality : 0.079 0.319 1576 Planarity : 0.005 0.103 1804 Dihedral : 13.500 125.443 3729 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.52 % Favored : 94.40 % Rotamer: Outliers : 0.09 % Allowed : 3.17 % Favored : 96.74 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -3.09 (0.20), residues: 1286 helix: -0.92 (0.22), residues: 419 sheet: -2.40 (0.32), residues: 232 loop : -2.73 (0.21), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG S 179 TYR 0.026 0.002 TYR S 103 PHE 0.022 0.002 PHE R 318 TRP 0.019 0.003 TRP B 99 HIS 0.008 0.001 HIS R 340 Details of bonding type rmsd/Z covalent geometry : bond 0.01382 / 1.06 (10443) covalent geometry : angle 1.70202 / 1.26 (14157) SS BOND : bond 0.00564 / 0.50 ( 13) SS BOND : angle 1.21820 / 0.80 ( 26) hydrogen bonds : bond 0.19614 / 13.14 ( 458) hydrogen bonds : angle 7.57156 / 5.37 ( 1326) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 203 time to evaluate : 0.399 Fit side-chains REVERT: R 119 TRP cc_start: 0.7799 (t60) cc_final: 0.7430 (t60) REVERT: R 230 MET cc_start: 0.7130 (tpp) cc_final: 0.6708 (tpp) REVERT: R 457 PHE cc_start: 0.7218 (t80) cc_final: 0.6925 (m-10) REVERT: R 491 GLN cc_start: 0.8429 (tp40) cc_final: 0.8090 (tt0) REVERT: R 525 MET cc_start: 0.7993 (ttt) cc_final: 0.7601 (ttt) REVERT: A 345 LYS cc_start: 0.7294 (tmmt) cc_final: 0.6930 (mtpp) REVERT: B 6 GLN cc_start: 0.7332 (pp30) cc_final: 0.7013 (pp30) REVERT: B 19 ARG cc_start: 0.7253 (tmm160) cc_final: 0.6680 (ttp-110) REVERT: B 42 ARG cc_start: 0.7693 (ttt-90) cc_final: 0.7176 (ttm-80) REVERT: B 44 GLN cc_start: 0.7451 (tt0) cc_final: 0.6631 (pp30) REVERT: B 46 ARG cc_start: 0.7298 (ttt-90) cc_final: 0.7020 (mtp85) REVERT: B 99 TRP cc_start: 0.8300 (m100) cc_final: 0.8055 (m100) REVERT: B 127 LYS cc_start: 0.8369 (mmtm) cc_final: 0.7834 (mmtp) REVERT: B 175 GLN cc_start: 0.7844 (pt0) cc_final: 0.7393 (mm110) REVERT: B 215 GLU cc_start: 0.8541 (mp0) cc_final: 0.8124 (mp0) REVERT: B 217 MET cc_start: 0.7494 (ptp) cc_final: 0.7243 (ptt) REVERT: B 254 ASP cc_start: 0.7514 (t70) cc_final: 0.6969 (t0) REVERT: B 316 SER cc_start: 0.7965 (OUTLIER) cc_final: 0.7559 (p) REVERT: G 47 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7704 (mp0) REVERT: S 13 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8122 (mm-40) REVERT: S 46 GLU cc_start: 0.7330 (mt-10) cc_final: 0.7064 (tt0) REVERT: S 62 ASP cc_start: 0.8051 (m-30) cc_final: 0.7831 (m-30) REVERT: S 113 GLN cc_start: 0.8461 (mm110) cc_final: 0.7891 (mm-40) REVERT: S 148 ARG cc_start: 0.7918 (ttp80) cc_final: 0.6923 (ttm-80) REVERT: S 180 MET cc_start: 0.8046 (ptm) cc_final: 0.7546 (ptm) REVERT: S 190 ARG cc_start: 0.8231 (mtm-85) cc_final: 0.7932 (mtm-85) REVERT: S 208 GLU cc_start: 0.8366 (pt0) cc_final: 0.8021 (pt0) REVERT: S 234 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7688 (tm-30) outliers start: 1 outliers final: 0 residues processed: 204 average time/residue: 0.1143 time to fit residues: 32.0386 Evaluate side-chains 147 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 316 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 180 ASN R 340 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 119 ASN B 295 ASN S 113 GLN S 130 GLN S 155 HIS S 174 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.146922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.100826 restraints weight = 13574.131| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.59 r_work: 0.3136 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10456 Z= 0.137 Angle : 0.615 9.919 14183 Z= 0.316 Chirality : 0.042 0.211 1576 Planarity : 0.006 0.135 1804 Dihedral : 5.470 83.368 1422 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.03 % Favored : 96.66 % Rotamer: Outliers : 2.26 % Allowed : 9.50 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -1.73 (0.23), residues: 1286 helix: 1.01 (0.25), residues: 431 sheet: -2.23 (0.29), residues: 271 loop : -2.29 (0.23), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 27 TYR 0.023 0.001 TYR S 223 PHE 0.017 0.001 PHE R 474 TRP 0.011 0.001 TRP R 119 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (10443) covalent geometry : angle 0.61215 / 0.31 (14157) SS BOND : bond 0.00346 / 0.33 ( 13) SS BOND : angle 1.47305 / 1.03 ( 26) hydrogen bonds : bond 0.04577 / 3.09 ( 458) hydrogen bonds : angle 4.75467 / 3.42 ( 1326) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: R 119 TRP cc_start: 0.7830 (t60) cc_final: 0.7438 (t60) REVERT: R 144 ARG cc_start: 0.5522 (mmm-85) cc_final: 0.5196 (mmm160) REVERT: R 230 MET cc_start: 0.7318 (tpp) cc_final: 0.6917 (tpp) REVERT: R 457 PHE cc_start: 0.7546 (t80) cc_final: 0.7085 (m-10) REVERT: A 18 MET cc_start: 0.7537 (ttp) cc_final: 0.7267 (ttm) REVERT: A 52 GLN cc_start: 0.8212 (tp40) cc_final: 0.7213 (mt0) REVERT: A 345 LYS cc_start: 0.7679 (tmmt) cc_final: 0.7290 (mtpp) REVERT: B 19 ARG cc_start: 0.7481 (tmm160) cc_final: 0.6916 (ttp-110) REVERT: B 42 ARG cc_start: 0.8185 (ttt-90) cc_final: 0.7413 (ttm-80) REVERT: B 44 GLN cc_start: 0.7759 (tt0) cc_final: 0.6764 (pp30) REVERT: B 46 ARG cc_start: 0.7828 (ttt-90) cc_final: 0.7311 (mtp85) REVERT: B 127 LYS cc_start: 0.8469 (mmtm) cc_final: 0.8019 (mmtp) REVERT: B 175 GLN cc_start: 0.8027 (pt0) cc_final: 0.7349 (mm110) REVERT: B 215 GLU cc_start: 0.8698 (mp0) cc_final: 0.8311 (mp0) REVERT: B 217 MET cc_start: 0.8119 (ptp) cc_final: 0.7828 (ptt) REVERT: B 254 ASP cc_start: 0.8181 (t70) cc_final: 0.7820 (t0) REVERT: B 292 PHE cc_start: 0.8697 (m-10) cc_final: 0.8258 (m-10) REVERT: G 46 LYS cc_start: 0.8979 (mtmm) cc_final: 0.8556 (mtmm) REVERT: G 47 GLU cc_start: 0.8518 (mt-10) cc_final: 0.7845 (mp0) REVERT: G 48 ASP cc_start: 0.8680 (t0) cc_final: 0.8395 (t0) REVERT: G 58 GLU cc_start: 0.8299 (mp0) cc_final: 0.7946 (mp0) REVERT: S 13 GLN cc_start: 0.8350 (mm-40) cc_final: 0.8006 (mm-40) REVERT: S 46 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7834 (tt0) REVERT: S 148 ARG cc_start: 0.8148 (ttp80) cc_final: 0.7011 (ttm-80) REVERT: S 174 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.8006 (pt0) REVERT: S 180 MET cc_start: 0.8580 (ptm) cc_final: 0.8071 (ptm) REVERT: S 208 GLU cc_start: 0.8603 (pt0) cc_final: 0.8273 (pt0) REVERT: S 219 GLN cc_start: 0.9433 (pp30) cc_final: 0.8829 (pp30) REVERT: S 234 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7808 (tm-30) outliers start: 25 outliers final: 12 residues processed: 178 average time/residue: 0.1053 time to fit residues: 25.5192 Evaluate side-chains 156 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 279 ILE Chi-restraints excluded: chain R residue 381 VAL Chi-restraints excluded: chain R residue 465 ILE Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 78 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 16 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.144948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.098366 restraints weight = 13712.908| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.61 r_work: 0.3100 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10456 Z= 0.159 Angle : 0.598 8.416 14183 Z= 0.306 Chirality : 0.043 0.201 1576 Planarity : 0.005 0.090 1804 Dihedral : 5.287 77.885 1421 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.04 % Favored : 95.65 % Rotamer: Outliers : 2.71 % Allowed : 10.23 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -1.36 (0.23), residues: 1286 helix: 1.37 (0.26), residues: 425 sheet: -2.01 (0.30), residues: 278 loop : -2.08 (0.24), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 27 TYR 0.027 0.001 TYR S 223 PHE 0.013 0.001 PHE R 474 TRP 0.008 0.001 TRP R 331 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (10443) covalent geometry : angle 0.59695 / 0.31 (14157) SS BOND : bond 0.00340 / 0.32 ( 13) SS BOND : angle 1.13111 / 0.76 ( 26) hydrogen bonds : bond 0.04213 / 2.86 ( 458) hydrogen bonds : angle 4.38400 / 3.13 ( 1326) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: R 119 TRP cc_start: 0.7749 (t60) cc_final: 0.7393 (t60) REVERT: R 230 MET cc_start: 0.7401 (tpp) cc_final: 0.7006 (tpp) REVERT: R 424 MET cc_start: 0.6790 (mmt) cc_final: 0.6391 (mtt) REVERT: R 457 PHE cc_start: 0.7588 (t80) cc_final: 0.7123 (m-10) REVERT: A 9 ASP cc_start: 0.8294 (t0) cc_final: 0.7929 (m-30) REVERT: A 18 MET cc_start: 0.7607 (ttp) cc_final: 0.7332 (ttm) REVERT: A 52 GLN cc_start: 0.8083 (tp40) cc_final: 0.7201 (mt0) REVERT: A 197 LYS cc_start: 0.8308 (mttt) cc_final: 0.7995 (mttp) REVERT: A 345 LYS cc_start: 0.7647 (tmmt) cc_final: 0.7260 (mtpp) REVERT: B 19 ARG cc_start: 0.7459 (tmm160) cc_final: 0.6894 (ttp-110) REVERT: B 42 ARG cc_start: 0.8266 (ttt-90) cc_final: 0.7478 (ttm-80) REVERT: B 44 GLN cc_start: 0.7726 (tt0) cc_final: 0.6883 (pp30) REVERT: B 46 ARG cc_start: 0.7855 (ttt-90) cc_final: 0.7510 (mtp85) REVERT: B 127 LYS cc_start: 0.8523 (mmtm) cc_final: 0.8081 (mmtp) REVERT: B 175 GLN cc_start: 0.8060 (pt0) cc_final: 0.7359 (mm110) REVERT: B 215 GLU cc_start: 0.8694 (mp0) cc_final: 0.8296 (mp0) REVERT: B 217 MET cc_start: 0.8146 (ptp) cc_final: 0.7871 (ptt) REVERT: B 228 ASP cc_start: 0.7951 (m-30) cc_final: 0.7723 (m-30) REVERT: B 254 ASP cc_start: 0.8285 (t70) cc_final: 0.7866 (t0) REVERT: B 267 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8266 (t0) REVERT: B 292 PHE cc_start: 0.8778 (m-10) cc_final: 0.8430 (m-10) REVERT: G 46 LYS cc_start: 0.8948 (mtmm) cc_final: 0.8507 (mtmm) REVERT: G 47 GLU cc_start: 0.8509 (mt-10) cc_final: 0.7855 (mp0) REVERT: G 58 GLU cc_start: 0.8391 (mp0) cc_final: 0.7968 (mp0) REVERT: S 13 GLN cc_start: 0.8339 (mm-40) cc_final: 0.8070 (mm-40) REVERT: S 46 GLU cc_start: 0.8416 (mt-10) cc_final: 0.7841 (tt0) REVERT: S 113 GLN cc_start: 0.8740 (mm-40) cc_final: 0.8320 (mm-40) REVERT: S 148 ARG cc_start: 0.8116 (ttp80) cc_final: 0.6974 (ttm-80) REVERT: S 174 GLN cc_start: 0.8478 (pt0) cc_final: 0.8237 (pt0) REVERT: S 180 MET cc_start: 0.8593 (ptm) cc_final: 0.8079 (ptm) REVERT: S 208 GLU cc_start: 0.8615 (pt0) cc_final: 0.8303 (pt0) REVERT: S 219 GLN cc_start: 0.9373 (pp30) cc_final: 0.8715 (pp30) REVERT: S 234 GLU cc_start: 0.8393 (tm-30) cc_final: 0.7748 (tm-30) outliers start: 30 outliers final: 19 residues processed: 177 average time/residue: 0.1164 time to fit residues: 28.2356 Evaluate side-chains 166 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 279 ILE Chi-restraints excluded: chain R residue 378 VAL Chi-restraints excluded: chain R residue 381 VAL Chi-restraints excluded: chain R residue 465 ILE Chi-restraints excluded: chain R residue 489 LEU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 17 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 75 optimal weight: 0.0170 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 overall best weight: 1.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 491 GLN B 75 GLN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.144585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.097794 restraints weight = 13644.292| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.61 r_work: 0.3089 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10456 Z= 0.159 Angle : 0.579 9.004 14183 Z= 0.297 Chirality : 0.042 0.186 1576 Planarity : 0.005 0.084 1804 Dihedral : 5.166 74.806 1421 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.04 % Favored : 95.72 % Rotamer: Outliers : 3.80 % Allowed : 11.13 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -1.21 (0.23), residues: 1286 helix: 1.47 (0.26), residues: 427 sheet: -1.83 (0.29), residues: 278 loop : -2.04 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 190 TYR 0.032 0.001 TYR S 223 PHE 0.013 0.001 PHE A 189 TRP 0.009 0.001 TRP B 99 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (10443) covalent geometry : angle 0.57826 / 0.30 (14157) SS BOND : bond 0.00297 / 0.28 ( 13) SS BOND : angle 0.97492 / 0.65 ( 26) hydrogen bonds : bond 0.04019 / 2.74 ( 458) hydrogen bonds : angle 4.20565 / 2.99 ( 1326) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 157 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 424 MET cc_start: 0.6729 (mmt) cc_final: 0.6340 (mtt) REVERT: R 457 PHE cc_start: 0.7557 (t80) cc_final: 0.7218 (m-10) REVERT: A 9 ASP cc_start: 0.8324 (t0) cc_final: 0.7822 (m-30) REVERT: A 18 MET cc_start: 0.7624 (ttp) cc_final: 0.7355 (ttm) REVERT: A 52 GLN cc_start: 0.8124 (tp40) cc_final: 0.7257 (mt0) REVERT: A 53 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7385 (mtt) REVERT: A 197 LYS cc_start: 0.8254 (mttt) cc_final: 0.7968 (mttp) REVERT: A 345 LYS cc_start: 0.7621 (tmmt) cc_final: 0.7256 (mtpp) REVERT: B 19 ARG cc_start: 0.7442 (tmm160) cc_final: 0.6887 (ttp-110) REVERT: B 42 ARG cc_start: 0.8197 (ttt-90) cc_final: 0.7400 (ttm-80) REVERT: B 44 GLN cc_start: 0.7816 (tt0) cc_final: 0.6863 (pp30) REVERT: B 46 ARG cc_start: 0.7884 (ttt-90) cc_final: 0.7544 (mtp85) REVERT: B 99 TRP cc_start: 0.8434 (m100) cc_final: 0.8126 (m100) REVERT: B 127 LYS cc_start: 0.8552 (mmtm) cc_final: 0.8134 (mmtp) REVERT: B 175 GLN cc_start: 0.8077 (pt0) cc_final: 0.7348 (mm110) REVERT: B 215 GLU cc_start: 0.8683 (mp0) cc_final: 0.8283 (mp0) REVERT: B 217 MET cc_start: 0.8136 (ptp) cc_final: 0.7844 (ptt) REVERT: B 228 ASP cc_start: 0.7981 (m-30) cc_final: 0.7431 (p0) REVERT: B 254 ASP cc_start: 0.8358 (t70) cc_final: 0.8007 (t0) REVERT: B 267 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8232 (t0) REVERT: B 292 PHE cc_start: 0.8813 (m-10) cc_final: 0.8496 (m-10) REVERT: G 47 GLU cc_start: 0.8473 (mt-10) cc_final: 0.7829 (mp0) REVERT: G 58 GLU cc_start: 0.8386 (mp0) cc_final: 0.8111 (mp0) REVERT: S 7 SER cc_start: 0.8929 (t) cc_final: 0.8645 (p) REVERT: S 13 GLN cc_start: 0.8330 (mm-40) cc_final: 0.8062 (mm-40) REVERT: S 46 GLU cc_start: 0.8424 (mt-10) cc_final: 0.7857 (tt0) REVERT: S 93 MET cc_start: 0.8112 (mtp) cc_final: 0.7730 (ttt) REVERT: S 113 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8332 (mm-40) REVERT: S 148 ARG cc_start: 0.8051 (ttp80) cc_final: 0.6924 (ttm-80) REVERT: S 174 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8117 (pt0) REVERT: S 180 MET cc_start: 0.8598 (ptm) cc_final: 0.8096 (ptm) REVERT: S 208 GLU cc_start: 0.8573 (pt0) cc_final: 0.8280 (pt0) REVERT: S 219 GLN cc_start: 0.9383 (pp30) cc_final: 0.8665 (pp30) REVERT: S 234 GLU cc_start: 0.8413 (tm-30) cc_final: 0.7711 (tm-30) outliers start: 42 outliers final: 23 residues processed: 182 average time/residue: 0.1058 time to fit residues: 26.6544 Evaluate side-chains 170 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 279 ILE Chi-restraints excluded: chain R residue 378 VAL Chi-restraints excluded: chain R residue 381 VAL Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 411 VAL Chi-restraints excluded: chain R residue 465 ILE Chi-restraints excluded: chain R residue 489 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 56 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 122 optimal weight: 0.6980 chunk 68 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.144120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.097261 restraints weight = 13644.831| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.61 r_work: 0.3076 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10456 Z= 0.167 Angle : 0.597 13.945 14183 Z= 0.301 Chirality : 0.042 0.181 1576 Planarity : 0.005 0.079 1804 Dihedral : 5.157 74.233 1421 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.20 % Favored : 95.57 % Rotamer: Outliers : 3.80 % Allowed : 12.76 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -1.15 (0.23), residues: 1286 helix: 1.45 (0.26), residues: 427 sheet: -1.76 (0.30), residues: 282 loop : -1.97 (0.24), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 190 TYR 0.030 0.001 TYR S 223 PHE 0.012 0.001 PHE A 189 TRP 0.011 0.001 TRP B 99 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (10443) covalent geometry : angle 0.59637 / 0.30 (14157) SS BOND : bond 0.00300 / 0.28 ( 13) SS BOND : angle 0.91832 / 0.61 ( 26) hydrogen bonds : bond 0.03996 / 2.72 ( 458) hydrogen bonds : angle 4.16325 / 2.96 ( 1326) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 230 MET cc_start: 0.7605 (tpp) cc_final: 0.7014 (tpp) REVERT: R 317 ILE cc_start: 0.7739 (OUTLIER) cc_final: 0.7479 (tp) REVERT: R 399 TYR cc_start: 0.7952 (m-80) cc_final: 0.7661 (m-80) REVERT: R 424 MET cc_start: 0.6728 (mmt) cc_final: 0.6329 (mtt) REVERT: R 457 PHE cc_start: 0.7577 (t80) cc_final: 0.7198 (m-10) REVERT: A 9 ASP cc_start: 0.8326 (t0) cc_final: 0.7912 (m-30) REVERT: A 18 MET cc_start: 0.7617 (ttp) cc_final: 0.7357 (ttm) REVERT: A 52 GLN cc_start: 0.8106 (tp40) cc_final: 0.7194 (mt0) REVERT: A 53 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.7353 (mtm) REVERT: A 197 LYS cc_start: 0.8269 (mttt) cc_final: 0.7982 (mttp) REVERT: A 345 LYS cc_start: 0.7626 (tmmt) cc_final: 0.7214 (mtpp) REVERT: B 19 ARG cc_start: 0.7412 (tmm160) cc_final: 0.6863 (ttp-110) REVERT: B 42 ARG cc_start: 0.8242 (ttt-90) cc_final: 0.7457 (ttm-80) REVERT: B 44 GLN cc_start: 0.7819 (tt0) cc_final: 0.6882 (pp30) REVERT: B 46 ARG cc_start: 0.7896 (ttt-90) cc_final: 0.7570 (mtp85) REVERT: B 127 LYS cc_start: 0.8577 (mmtm) cc_final: 0.8178 (mmtp) REVERT: B 175 GLN cc_start: 0.8069 (pt0) cc_final: 0.7367 (mm110) REVERT: B 215 GLU cc_start: 0.8652 (mp0) cc_final: 0.8257 (mp0) REVERT: B 217 MET cc_start: 0.8218 (ptp) cc_final: 0.7944 (ptt) REVERT: B 228 ASP cc_start: 0.7985 (m-30) cc_final: 0.7460 (p0) REVERT: B 254 ASP cc_start: 0.8386 (t70) cc_final: 0.8018 (t0) REVERT: B 267 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.8354 (t0) REVERT: B 292 PHE cc_start: 0.8839 (m-10) cc_final: 0.8519 (m-10) REVERT: G 47 GLU cc_start: 0.8481 (mt-10) cc_final: 0.7804 (mp0) REVERT: G 58 GLU cc_start: 0.8448 (mp0) cc_final: 0.8143 (mp0) REVERT: S 7 SER cc_start: 0.8947 (t) cc_final: 0.8662 (p) REVERT: S 13 GLN cc_start: 0.8342 (mm-40) cc_final: 0.8070 (mm-40) REVERT: S 46 GLU cc_start: 0.8402 (mt-10) cc_final: 0.7798 (tt0) REVERT: S 93 MET cc_start: 0.8124 (mtp) cc_final: 0.7741 (ttt) REVERT: S 113 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8398 (mm-40) REVERT: S 148 ARG cc_start: 0.8073 (ttp80) cc_final: 0.6970 (ttm-80) REVERT: S 180 MET cc_start: 0.8596 (ptm) cc_final: 0.8080 (ptm) REVERT: S 208 GLU cc_start: 0.8582 (pt0) cc_final: 0.8301 (pt0) REVERT: S 219 GLN cc_start: 0.9383 (pp30) cc_final: 0.8660 (pp30) REVERT: S 234 GLU cc_start: 0.8457 (tm-30) cc_final: 0.7782 (tm-30) outliers start: 42 outliers final: 29 residues processed: 181 average time/residue: 0.1069 time to fit residues: 26.9201 Evaluate side-chains 172 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 279 ILE Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 378 VAL Chi-restraints excluded: chain R residue 381 VAL Chi-restraints excluded: chain R residue 411 VAL Chi-restraints excluded: chain R residue 465 ILE Chi-restraints excluded: chain R residue 489 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 127 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.144469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.097549 restraints weight = 13762.913| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.61 r_work: 0.3078 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10456 Z= 0.156 Angle : 0.588 13.317 14183 Z= 0.296 Chirality : 0.042 0.183 1576 Planarity : 0.005 0.078 1804 Dihedral : 5.089 73.252 1421 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.82 % Favored : 94.95 % Rotamer: Outliers : 3.71 % Allowed : 14.57 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -1.06 (0.23), residues: 1286 helix: 1.50 (0.26), residues: 427 sheet: -1.72 (0.29), residues: 291 loop : -1.88 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 190 TYR 0.029 0.001 TYR S 223 PHE 0.011 0.001 PHE A 189 TRP 0.009 0.001 TRP B 99 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (10443) covalent geometry : angle 0.58724 / 0.30 (14157) SS BOND : bond 0.00279 / 0.26 ( 13) SS BOND : angle 0.85635 / 0.57 ( 26) hydrogen bonds : bond 0.03908 / 2.67 ( 458) hydrogen bonds : angle 4.09743 / 2.90 ( 1326) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 149 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 230 MET cc_start: 0.7604 (tpp) cc_final: 0.6996 (tpp) REVERT: R 317 ILE cc_start: 0.7667 (OUTLIER) cc_final: 0.7412 (tp) REVERT: R 399 TYR cc_start: 0.7936 (m-80) cc_final: 0.7675 (m-80) REVERT: R 424 MET cc_start: 0.6603 (mmt) cc_final: 0.6204 (mtt) REVERT: R 457 PHE cc_start: 0.7522 (t80) cc_final: 0.7159 (m-10) REVERT: A 9 ASP cc_start: 0.8352 (t0) cc_final: 0.7828 (m-30) REVERT: A 18 MET cc_start: 0.7603 (ttp) cc_final: 0.7338 (ttm) REVERT: A 52 GLN cc_start: 0.8047 (tp40) cc_final: 0.7172 (mt0) REVERT: A 53 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7451 (mtt) REVERT: A 197 LYS cc_start: 0.8291 (mttt) cc_final: 0.8011 (mttp) REVERT: A 345 LYS cc_start: 0.7623 (tmmt) cc_final: 0.7208 (mtpp) REVERT: B 19 ARG cc_start: 0.7390 (tmm160) cc_final: 0.6818 (ttp-110) REVERT: B 42 ARG cc_start: 0.8229 (ttt-90) cc_final: 0.7469 (ttm-80) REVERT: B 44 GLN cc_start: 0.7783 (tt0) cc_final: 0.6965 (pp30) REVERT: B 46 ARG cc_start: 0.7887 (ttt-90) cc_final: 0.7572 (mtp85) REVERT: B 127 LYS cc_start: 0.8573 (mmtm) cc_final: 0.8168 (mmtp) REVERT: B 175 GLN cc_start: 0.8075 (pt0) cc_final: 0.7360 (mm110) REVERT: B 215 GLU cc_start: 0.8642 (mp0) cc_final: 0.8251 (mp0) REVERT: B 217 MET cc_start: 0.8221 (ptp) cc_final: 0.7928 (ptt) REVERT: B 218 CYS cc_start: 0.8505 (p) cc_final: 0.8233 (p) REVERT: B 228 ASP cc_start: 0.7935 (m-30) cc_final: 0.7469 (p0) REVERT: B 254 ASP cc_start: 0.8408 (t70) cc_final: 0.8031 (t0) REVERT: B 292 PHE cc_start: 0.8857 (m-10) cc_final: 0.8551 (m-10) REVERT: G 47 GLU cc_start: 0.8440 (mt-10) cc_final: 0.7762 (mp0) REVERT: G 48 ASP cc_start: 0.8665 (t0) cc_final: 0.8112 (t0) REVERT: G 58 GLU cc_start: 0.8450 (mp0) cc_final: 0.8123 (mp0) REVERT: S 7 SER cc_start: 0.8926 (t) cc_final: 0.8640 (p) REVERT: S 13 GLN cc_start: 0.8346 (mm-40) cc_final: 0.8065 (mm-40) REVERT: S 46 GLU cc_start: 0.8419 (mt-10) cc_final: 0.7784 (tt0) REVERT: S 93 MET cc_start: 0.8105 (mtp) cc_final: 0.7745 (ttt) REVERT: S 113 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8428 (mm-40) REVERT: S 148 ARG cc_start: 0.8062 (ttp80) cc_final: 0.6970 (ttm-80) REVERT: S 180 MET cc_start: 0.8560 (ptm) cc_final: 0.8029 (ptm) REVERT: S 208 GLU cc_start: 0.8575 (pt0) cc_final: 0.8178 (pt0) REVERT: S 219 GLN cc_start: 0.9376 (pp30) cc_final: 0.8656 (pp30) REVERT: S 234 GLU cc_start: 0.8535 (tm-30) cc_final: 0.7863 (tm-30) outliers start: 41 outliers final: 33 residues processed: 177 average time/residue: 0.1225 time to fit residues: 29.5944 Evaluate side-chains 175 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 140 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 279 ILE Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 381 VAL Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 411 VAL Chi-restraints excluded: chain R residue 465 ILE Chi-restraints excluded: chain R residue 489 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 42 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 14 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 9 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 chunk 19 optimal weight: 0.0270 chunk 47 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.146489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.099739 restraints weight = 13543.445| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.60 r_work: 0.3113 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10456 Z= 0.122 Angle : 0.570 12.348 14183 Z= 0.287 Chirality : 0.041 0.176 1576 Planarity : 0.004 0.076 1804 Dihedral : 4.968 71.725 1421 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.51 % Favored : 95.26 % Rotamer: Outliers : 3.44 % Allowed : 15.29 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -0.93 (0.24), residues: 1286 helix: 1.61 (0.26), residues: 428 sheet: -1.69 (0.28), residues: 301 loop : -1.76 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 13 TYR 0.028 0.001 TYR S 223 PHE 0.010 0.001 PHE A 189 TRP 0.008 0.001 TRP R 331 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (10443) covalent geometry : angle 0.56893 / 0.29 (14157) SS BOND : bond 0.00351 / 0.33 ( 13) SS BOND : angle 1.06674 / 0.74 ( 26) hydrogen bonds : bond 0.03691 / 2.52 ( 458) hydrogen bonds : angle 3.99442 / 2.82 ( 1326) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 149 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 230 MET cc_start: 0.7626 (tpp) cc_final: 0.6940 (tpp) REVERT: R 317 ILE cc_start: 0.7664 (OUTLIER) cc_final: 0.7421 (tp) REVERT: R 399 TYR cc_start: 0.7900 (m-80) cc_final: 0.7622 (m-80) REVERT: R 457 PHE cc_start: 0.7479 (t80) cc_final: 0.7142 (m-10) REVERT: A 9 ASP cc_start: 0.8289 (t0) cc_final: 0.7801 (m-30) REVERT: A 18 MET cc_start: 0.7616 (ttp) cc_final: 0.7349 (ttm) REVERT: A 52 GLN cc_start: 0.8061 (tp40) cc_final: 0.7192 (mt0) REVERT: A 53 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7447 (mtt) REVERT: A 187 THR cc_start: 0.8756 (OUTLIER) cc_final: 0.8441 (p) REVERT: A 197 LYS cc_start: 0.8232 (mttt) cc_final: 0.7955 (mttp) REVERT: A 345 LYS cc_start: 0.7587 (tmmt) cc_final: 0.7182 (mtpp) REVERT: B 19 ARG cc_start: 0.7397 (tmm160) cc_final: 0.6848 (ttp-110) REVERT: B 42 ARG cc_start: 0.8277 (ttt-90) cc_final: 0.7476 (ttm-80) REVERT: B 44 GLN cc_start: 0.7754 (tt0) cc_final: 0.6890 (pp30) REVERT: B 46 ARG cc_start: 0.7898 (ttt-90) cc_final: 0.7583 (mtp85) REVERT: B 99 TRP cc_start: 0.8388 (m100) cc_final: 0.8113 (m100) REVERT: B 127 LYS cc_start: 0.8487 (mmtm) cc_final: 0.8057 (mmtp) REVERT: B 175 GLN cc_start: 0.8058 (pt0) cc_final: 0.7339 (mm110) REVERT: B 215 GLU cc_start: 0.8647 (mp0) cc_final: 0.8250 (mp0) REVERT: B 217 MET cc_start: 0.8196 (ptp) cc_final: 0.7926 (ptt) REVERT: B 218 CYS cc_start: 0.8488 (p) cc_final: 0.8136 (p) REVERT: B 228 ASP cc_start: 0.7894 (m-30) cc_final: 0.7458 (p0) REVERT: B 254 ASP cc_start: 0.8323 (t70) cc_final: 0.7974 (t0) REVERT: B 292 PHE cc_start: 0.8811 (m-10) cc_final: 0.8472 (m-10) REVERT: G 47 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7727 (mp0) REVERT: G 48 ASP cc_start: 0.8646 (t0) cc_final: 0.8229 (t0) REVERT: G 58 GLU cc_start: 0.8494 (mp0) cc_final: 0.8163 (mp0) REVERT: S 7 SER cc_start: 0.8900 (t) cc_final: 0.8605 (p) REVERT: S 13 GLN cc_start: 0.8310 (mm-40) cc_final: 0.8033 (mm-40) REVERT: S 46 GLU cc_start: 0.8416 (mt-10) cc_final: 0.7775 (tt0) REVERT: S 93 MET cc_start: 0.8078 (mtp) cc_final: 0.7736 (ttt) REVERT: S 113 GLN cc_start: 0.8707 (mm-40) cc_final: 0.8468 (mm-40) REVERT: S 141 GLU cc_start: 0.8806 (pt0) cc_final: 0.8557 (pt0) REVERT: S 148 ARG cc_start: 0.8036 (ttp80) cc_final: 0.6938 (ttm-80) REVERT: S 180 MET cc_start: 0.8519 (ptm) cc_final: 0.7988 (ptm) REVERT: S 208 GLU cc_start: 0.8607 (pt0) cc_final: 0.8097 (pm20) REVERT: S 234 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8118 (tm-30) outliers start: 38 outliers final: 30 residues processed: 174 average time/residue: 0.1222 time to fit residues: 29.2938 Evaluate side-chains 173 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 279 ILE Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 381 VAL Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 411 VAL Chi-restraints excluded: chain R residue 465 ILE Chi-restraints excluded: chain R residue 489 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 42 GLU Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 218 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 19 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 118 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.144814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.097637 restraints weight = 13655.304| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.63 r_work: 0.3083 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10456 Z= 0.167 Angle : 0.590 12.666 14183 Z= 0.298 Chirality : 0.042 0.169 1576 Planarity : 0.005 0.078 1804 Dihedral : 5.041 72.003 1421 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.67 % Favored : 95.10 % Rotamer: Outliers : 3.89 % Allowed : 15.02 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -0.99 (0.24), residues: 1286 helix: 1.45 (0.26), residues: 434 sheet: -1.74 (0.28), residues: 302 loop : -1.72 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 87 TYR 0.033 0.001 TYR S 223 PHE 0.012 0.001 PHE A 189 TRP 0.009 0.001 TRP S 47 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (10443) covalent geometry : angle 0.58849 / 0.30 (14157) SS BOND : bond 0.00359 / 0.34 ( 13) SS BOND : angle 1.09003 / 0.76 ( 26) hydrogen bonds : bond 0.03885 / 2.66 ( 458) hydrogen bonds : angle 4.05538 / 2.86 ( 1326) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 146 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 230 MET cc_start: 0.7638 (tpp) cc_final: 0.6947 (tpp) REVERT: R 317 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7405 (tp) REVERT: R 399 TYR cc_start: 0.7928 (m-80) cc_final: 0.7649 (m-80) REVERT: R 457 PHE cc_start: 0.7483 (t80) cc_final: 0.7171 (m-10) REVERT: A 9 ASP cc_start: 0.8346 (t0) cc_final: 0.7826 (m-30) REVERT: A 18 MET cc_start: 0.7631 (ttp) cc_final: 0.7360 (ttm) REVERT: A 52 GLN cc_start: 0.8064 (tp40) cc_final: 0.7238 (mt0) REVERT: A 53 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.7376 (mtt) REVERT: A 187 THR cc_start: 0.8775 (OUTLIER) cc_final: 0.8436 (p) REVERT: A 197 LYS cc_start: 0.8301 (mttt) cc_final: 0.8024 (mttp) REVERT: A 345 LYS cc_start: 0.7590 (tmmt) cc_final: 0.7187 (mtpp) REVERT: B 6 GLN cc_start: 0.6769 (pp30) cc_final: 0.6382 (pm20) REVERT: B 19 ARG cc_start: 0.7400 (tmm160) cc_final: 0.6840 (ttp-110) REVERT: B 42 ARG cc_start: 0.8282 (ttt-90) cc_final: 0.7543 (ttm-80) REVERT: B 44 GLN cc_start: 0.7722 (tt0) cc_final: 0.6880 (pp30) REVERT: B 46 ARG cc_start: 0.7922 (ttt-90) cc_final: 0.7598 (mtp85) REVERT: B 59 TYR cc_start: 0.9203 (m-80) cc_final: 0.8027 (m-80) REVERT: B 127 LYS cc_start: 0.8572 (mmtm) cc_final: 0.8168 (mmtp) REVERT: B 175 GLN cc_start: 0.8071 (pt0) cc_final: 0.7340 (mm110) REVERT: B 215 GLU cc_start: 0.8639 (mp0) cc_final: 0.8255 (mp0) REVERT: B 217 MET cc_start: 0.8231 (ptp) cc_final: 0.7944 (ptt) REVERT: B 218 CYS cc_start: 0.8524 (p) cc_final: 0.8222 (p) REVERT: B 228 ASP cc_start: 0.7946 (m-30) cc_final: 0.7480 (p0) REVERT: B 254 ASP cc_start: 0.8414 (t70) cc_final: 0.8026 (t0) REVERT: B 292 PHE cc_start: 0.8881 (m-10) cc_final: 0.8512 (m-10) REVERT: G 47 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7683 (mp0) REVERT: G 48 ASP cc_start: 0.8706 (t0) cc_final: 0.8298 (t0) REVERT: G 58 GLU cc_start: 0.8516 (mp0) cc_final: 0.8171 (mp0) REVERT: S 7 SER cc_start: 0.8891 (t) cc_final: 0.8608 (p) REVERT: S 13 GLN cc_start: 0.8317 (mm-40) cc_final: 0.8035 (mm-40) REVERT: S 46 GLU cc_start: 0.8421 (mt-10) cc_final: 0.7782 (tt0) REVERT: S 93 MET cc_start: 0.8104 (mtp) cc_final: 0.7779 (ttt) REVERT: S 113 GLN cc_start: 0.8746 (mm-40) cc_final: 0.8509 (mm-40) REVERT: S 141 GLU cc_start: 0.8776 (pt0) cc_final: 0.8458 (pt0) REVERT: S 148 ARG cc_start: 0.8019 (ttp80) cc_final: 0.6933 (ttm-80) REVERT: S 174 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7864 (pt0) REVERT: S 180 MET cc_start: 0.8565 (ptm) cc_final: 0.8026 (ptm) REVERT: S 208 GLU cc_start: 0.8677 (pt0) cc_final: 0.8474 (pt0) REVERT: S 234 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8151 (tm-30) outliers start: 43 outliers final: 36 residues processed: 175 average time/residue: 0.1131 time to fit residues: 27.5833 Evaluate side-chains 182 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 103 HIS Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 279 ILE Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 378 VAL Chi-restraints excluded: chain R residue 381 VAL Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 411 VAL Chi-restraints excluded: chain R residue 465 ILE Chi-restraints excluded: chain R residue 489 LEU Chi-restraints excluded: chain R residue 518 GLU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 42 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 104 optimal weight: 0.0670 chunk 103 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 113 optimal weight: 0.1980 chunk 74 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.6524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 476 ASN ** R 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.147474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.100625 restraints weight = 13620.463| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.64 r_work: 0.3128 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10456 Z= 0.115 Angle : 0.572 11.971 14183 Z= 0.287 Chirality : 0.041 0.173 1576 Planarity : 0.004 0.076 1804 Dihedral : 4.918 70.623 1421 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.51 % Favored : 95.26 % Rotamer: Outliers : 3.53 % Allowed : 15.38 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -0.88 (0.24), residues: 1286 helix: 1.56 (0.26), residues: 434 sheet: -1.63 (0.28), residues: 308 loop : -1.69 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG S 190 TYR 0.029 0.001 TYR S 223 PHE 0.010 0.001 PHE S 29 TRP 0.008 0.001 TRP R 331 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (10443) covalent geometry : angle 0.57104 / 0.29 (14157) SS BOND : bond 0.00274 / 0.25 ( 13) SS BOND : angle 0.94508 / 0.66 ( 26) hydrogen bonds : bond 0.03623 / 2.48 ( 458) hydrogen bonds : angle 3.94465 / 2.77 ( 1326) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 230 MET cc_start: 0.7620 (tpp) cc_final: 0.6904 (tpp) REVERT: R 317 ILE cc_start: 0.7623 (OUTLIER) cc_final: 0.7411 (tp) REVERT: R 457 PHE cc_start: 0.7536 (t80) cc_final: 0.7141 (m-10) REVERT: A 9 ASP cc_start: 0.8269 (t0) cc_final: 0.7801 (m-30) REVERT: A 18 MET cc_start: 0.7629 (ttp) cc_final: 0.7357 (ttm) REVERT: A 52 GLN cc_start: 0.8029 (tp40) cc_final: 0.7200 (mt0) REVERT: A 53 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7480 (mtt) REVERT: A 187 THR cc_start: 0.8748 (OUTLIER) cc_final: 0.8456 (p) REVERT: A 197 LYS cc_start: 0.8241 (mttt) cc_final: 0.7972 (mttp) REVERT: A 345 LYS cc_start: 0.7551 (tmmt) cc_final: 0.7156 (mtpp) REVERT: B 19 ARG cc_start: 0.7383 (tmm160) cc_final: 0.6837 (ttp-110) REVERT: B 42 ARG cc_start: 0.8282 (ttt-90) cc_final: 0.7507 (ttm-80) REVERT: B 44 GLN cc_start: 0.7788 (tt0) cc_final: 0.6940 (pp30) REVERT: B 46 ARG cc_start: 0.7917 (ttt-90) cc_final: 0.7602 (mtp85) REVERT: B 59 TYR cc_start: 0.9100 (m-80) cc_final: 0.7956 (m-80) REVERT: B 99 TRP cc_start: 0.8385 (m100) cc_final: 0.8107 (m100) REVERT: B 127 LYS cc_start: 0.8467 (mmtm) cc_final: 0.8035 (mmtp) REVERT: B 175 GLN cc_start: 0.8080 (pt0) cc_final: 0.7366 (mm110) REVERT: B 215 GLU cc_start: 0.8644 (mp0) cc_final: 0.8261 (mp0) REVERT: B 217 MET cc_start: 0.8193 (ptp) cc_final: 0.7918 (ptt) REVERT: B 218 CYS cc_start: 0.8478 (p) cc_final: 0.8084 (p) REVERT: B 228 ASP cc_start: 0.7920 (m-30) cc_final: 0.7455 (p0) REVERT: B 254 ASP cc_start: 0.8230 (t70) cc_final: 0.7848 (t0) REVERT: G 13 ARG cc_start: 0.7219 (ptp-170) cc_final: 0.6971 (ptp-170) REVERT: G 47 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7656 (mp0) REVERT: G 48 ASP cc_start: 0.8634 (t0) cc_final: 0.8210 (t0) REVERT: G 58 GLU cc_start: 0.8509 (mp0) cc_final: 0.8190 (mp0) REVERT: S 7 SER cc_start: 0.8901 (t) cc_final: 0.8610 (p) REVERT: S 13 GLN cc_start: 0.8331 (mm-40) cc_final: 0.8047 (mm-40) REVERT: S 46 GLU cc_start: 0.8429 (mt-10) cc_final: 0.7783 (tt0) REVERT: S 93 MET cc_start: 0.8065 (mtp) cc_final: 0.7710 (ttt) REVERT: S 141 GLU cc_start: 0.8779 (pt0) cc_final: 0.8520 (pt0) REVERT: S 148 ARG cc_start: 0.8002 (ttp80) cc_final: 0.6917 (ttm-80) REVERT: S 174 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7837 (pt0) REVERT: S 180 MET cc_start: 0.8518 (ptm) cc_final: 0.7993 (ptm) REVERT: S 208 GLU cc_start: 0.8595 (pt0) cc_final: 0.8282 (pt0) REVERT: S 234 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8130 (tm-30) outliers start: 39 outliers final: 32 residues processed: 180 average time/residue: 0.1110 time to fit residues: 28.0943 Evaluate side-chains 182 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 279 ILE Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 378 VAL Chi-restraints excluded: chain R residue 381 VAL Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 411 VAL Chi-restraints excluded: chain R residue 465 ILE Chi-restraints excluded: chain R residue 476 ASN Chi-restraints excluded: chain R residue 489 LEU Chi-restraints excluded: chain R residue 518 GLU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain S residue 42 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 34 optimal weight: 0.6980 chunk 24 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 54 optimal weight: 0.0470 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 overall best weight: 1.4682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.144831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.097404 restraints weight = 13526.735| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.72 r_work: 0.3077 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 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 : 0.004 0.041 10456 Z= 0.168 Angle : 0.602 11.632 14183 Z= 0.304 Chirality : 0.042 0.172 1576 Planarity : 0.005 0.077 1804 Dihedral : 4.990 70.977 1421 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.51 % Favored : 95.26 % Rotamer: Outliers : 3.17 % Allowed : 16.74 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -0.92 (0.24), residues: 1286 helix: 1.47 (0.26), residues: 434 sheet: -1.68 (0.28), residues: 302 loop : -1.65 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 190 TYR 0.037 0.001 TYR S 223 PHE 0.026 0.001 PHE R 455 TRP 0.009 0.001 TRP B 99 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (10443) covalent geometry : angle 0.60089 / 0.30 (14157) SS BOND : bond 0.00379 / 0.36 ( 13) SS BOND : angle 1.04074 / 0.73 ( 26) hydrogen bonds : bond 0.03831 / 2.63 ( 458) hydrogen bonds : angle 4.01208 / 2.82 ( 1326) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 230 MET cc_start: 0.7607 (tpp) cc_final: 0.6942 (tpp) REVERT: R 317 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.7410 (tp) REVERT: R 457 PHE cc_start: 0.7546 (t80) cc_final: 0.7162 (m-10) REVERT: A 9 ASP cc_start: 0.8327 (t0) cc_final: 0.7812 (m-30) REVERT: A 18 MET cc_start: 0.7622 (ttp) cc_final: 0.7342 (ttm) REVERT: A 52 GLN cc_start: 0.8058 (tp40) cc_final: 0.7231 (mt0) REVERT: A 53 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7433 (mtt) REVERT: A 187 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8399 (p) REVERT: A 197 LYS cc_start: 0.8304 (mttt) cc_final: 0.8022 (mttp) REVERT: A 345 LYS cc_start: 0.7587 (tmmt) cc_final: 0.7161 (mtpp) REVERT: B 6 GLN cc_start: 0.6765 (pp30) cc_final: 0.6335 (pm20) REVERT: B 19 ARG cc_start: 0.7411 (tmm160) cc_final: 0.6851 (ttp-110) REVERT: B 42 ARG cc_start: 0.8325 (ttt-90) cc_final: 0.7593 (ttm-80) REVERT: B 44 GLN cc_start: 0.7726 (tt0) cc_final: 0.6947 (pp30) REVERT: B 46 ARG cc_start: 0.7920 (ttt-90) cc_final: 0.7591 (mtp85) REVERT: B 59 TYR cc_start: 0.9190 (m-80) cc_final: 0.8017 (m-80) REVERT: B 127 LYS cc_start: 0.8502 (mmtm) cc_final: 0.8094 (mmtp) REVERT: B 175 GLN cc_start: 0.8099 (pt0) cc_final: 0.7383 (mm110) REVERT: B 215 GLU cc_start: 0.8639 (mp0) cc_final: 0.8258 (mp0) REVERT: B 217 MET cc_start: 0.8224 (ptp) cc_final: 0.7930 (ptt) REVERT: B 218 CYS cc_start: 0.8494 (p) cc_final: 0.8164 (p) REVERT: B 228 ASP cc_start: 0.7962 (m-30) cc_final: 0.7469 (p0) REVERT: B 254 ASP cc_start: 0.8391 (t70) cc_final: 0.7998 (t0) REVERT: B 292 PHE cc_start: 0.8855 (m-10) cc_final: 0.8495 (m-10) REVERT: G 47 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7649 (mp0) REVERT: G 58 GLU cc_start: 0.8502 (mp0) cc_final: 0.8179 (mp0) REVERT: S 7 SER cc_start: 0.8876 (t) cc_final: 0.8587 (p) REVERT: S 13 GLN cc_start: 0.8348 (mm-40) cc_final: 0.8064 (mm-40) REVERT: S 46 GLU cc_start: 0.8433 (mt-10) cc_final: 0.7779 (tt0) REVERT: S 93 MET cc_start: 0.8098 (mtp) cc_final: 0.7732 (ttt) REVERT: S 141 GLU cc_start: 0.8796 (pt0) cc_final: 0.8513 (pt0) REVERT: S 148 ARG cc_start: 0.7997 (ttp80) cc_final: 0.6905 (ttm-80) REVERT: S 180 MET cc_start: 0.8565 (ptm) cc_final: 0.8038 (ptm) REVERT: S 208 GLU cc_start: 0.8658 (pt0) cc_final: 0.8373 (pt0) REVERT: S 234 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8159 (tm-30) outliers start: 35 outliers final: 30 residues processed: 167 average time/residue: 0.1139 time to fit residues: 26.7290 Evaluate side-chains 174 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 279 ILE Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 378 VAL Chi-restraints excluded: chain R residue 381 VAL Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 411 VAL Chi-restraints excluded: chain R residue 465 ILE Chi-restraints excluded: chain R residue 489 LEU Chi-restraints excluded: chain R residue 518 GLU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain S residue 42 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 96 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 74 optimal weight: 0.2980 chunk 116 optimal weight: 0.9980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.142690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.094995 restraints weight = 13760.912| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.74 r_work: 0.3039 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10456 Z= 0.213 Angle : 0.638 10.725 14183 Z= 0.323 Chirality : 0.043 0.168 1576 Planarity : 0.005 0.080 1804 Dihedral : 5.215 72.338 1421 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.98 % Favored : 94.79 % Rotamer: Outliers : 3.35 % Allowed : 16.56 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -1.04 (0.24), residues: 1286 helix: 1.32 (0.26), residues: 434 sheet: -1.73 (0.28), residues: 304 loop : -1.68 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 190 TYR 0.036 0.001 TYR S 223 PHE 0.024 0.001 PHE R 455 TRP 0.013 0.001 TRP S 47 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.21 (10443) covalent geometry : angle 0.63650 / 0.32 (14157) SS BOND : bond 0.00430 / 0.41 ( 13) SS BOND : angle 1.12120 / 0.79 ( 26) hydrogen bonds : bond 0.04105 / 2.81 ( 458) hydrogen bonds : angle 4.18178 / 2.95 ( 1326) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3356.25 seconds wall clock time: 58 minutes 9.24 seconds (3489.24 seconds total)