Starting phenix.real_space_refine on Mon Jul 28 11:53:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xbk_22118/07_2025/6xbk_22118.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xbk_22118/07_2025/6xbk_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6xbk_22118/07_2025/6xbk_22118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xbk_22118/07_2025/6xbk_22118.map" model { file = "/net/cci-nas-00/data/ceres_data/6xbk_22118/07_2025/6xbk_22118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xbk_22118/07_2025/6xbk_22118.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.52, per 1000 atoms: 0.64 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: 2.61 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.20 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: 3.30 Time building geometry restraints manager: 3.12 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: 5934 25.09 - 50.18: 278 50.18 - 75.27: 19 75.27 - 100.35: 5 100.35 - 125.44: 2 Dihedral angle restraints: 6238 sinusoidal: 2482 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 6235 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: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 26.690 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 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 : 13.465 125.443 3785 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.69 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.019 0.003 TRP B 99 HIS 0.008 0.001 HIS R 340 PHE 0.022 0.002 PHE R 318 TYR 0.026 0.002 TYR S 103 ARG 0.011 0.001 ARG S 179 Details of bonding type rmsd hydrogen bonds : bond 0.19614 ( 458) hydrogen bonds : angle 7.57156 ( 1326) SS BOND : bond 0.00564 ( 13) SS BOND : angle 1.21820 ( 26) covalent geometry : bond 0.01382 (10443) covalent geometry : angle 1.70202 (14157) *********************** 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 : 1.245 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: 0.2749 time to fit residues: 75.9737 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 : 1.184 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 180 ASN R 340 HIS A 213 HIS 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.146634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.100529 restraints weight = 13576.797| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.58 r_work: 0.3130 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1791 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= 0.139 Angle : 0.614 10.151 14183 Z= 0.315 Chirality : 0.043 0.214 1576 Planarity : 0.006 0.136 1804 Dihedral : 5.743 81.748 1478 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.11 % Favored : 96.58 % Rotamer: Outliers : 2.26 % Allowed : 9.68 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.23), residues: 1286 helix: 0.96 (0.25), residues: 437 sheet: -2.24 (0.29), residues: 273 loop : -2.29 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 119 HIS 0.004 0.001 HIS S 35 PHE 0.017 0.001 PHE R 474 TYR 0.023 0.001 TYR S 223 ARG 0.005 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.04401 ( 458) hydrogen bonds : angle 4.69909 ( 1326) SS BOND : bond 0.00362 ( 13) SS BOND : angle 1.40012 ( 26) covalent geometry : bond 0.00313 (10443) covalent geometry : angle 0.61180 (14157) *********************** 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 188 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: R 119 TRP cc_start: 0.7822 (t60) cc_final: 0.7432 (t60) REVERT: R 144 ARG cc_start: 0.5523 (mmm-85) cc_final: 0.5250 (mmm160) REVERT: R 230 MET cc_start: 0.7335 (tpp) cc_final: 0.6935 (tpp) REVERT: R 457 PHE cc_start: 0.7562 (t80) cc_final: 0.7104 (m-10) REVERT: A 18 MET cc_start: 0.7531 (ttp) cc_final: 0.7264 (ttm) REVERT: A 345 LYS cc_start: 0.7660 (tmmt) cc_final: 0.7248 (mtpp) REVERT: B 19 ARG cc_start: 0.7485 (tmm160) cc_final: 0.6921 (ttp-110) REVERT: B 42 ARG cc_start: 0.8202 (ttt-90) cc_final: 0.7422 (ttm-80) REVERT: B 44 GLN cc_start: 0.7789 (tt0) cc_final: 0.6793 (pp30) REVERT: B 46 ARG cc_start: 0.7838 (ttt-90) cc_final: 0.7313 (mtp85) REVERT: B 127 LYS cc_start: 0.8479 (mmtm) cc_final: 0.8034 (mmtp) REVERT: B 175 GLN cc_start: 0.8020 (pt0) cc_final: 0.7341 (mm110) REVERT: B 215 GLU cc_start: 0.8693 (mp0) cc_final: 0.8316 (mp0) REVERT: B 217 MET cc_start: 0.8116 (ptp) cc_final: 0.7825 (ptt) REVERT: B 254 ASP cc_start: 0.8158 (t70) cc_final: 0.7803 (t0) REVERT: B 292 PHE cc_start: 0.8706 (m-10) cc_final: 0.8324 (m-10) REVERT: G 46 LYS cc_start: 0.8966 (mtmm) cc_final: 0.8612 (mtmm) REVERT: G 47 GLU cc_start: 0.8517 (mt-10) cc_final: 0.7847 (mp0) REVERT: G 48 ASP cc_start: 0.8661 (t0) cc_final: 0.8348 (t0) REVERT: G 58 GLU cc_start: 0.8294 (mp0) cc_final: 0.7937 (mp0) REVERT: S 13 GLN cc_start: 0.8311 (mm-40) cc_final: 0.8058 (mm-40) REVERT: S 46 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7831 (tt0) REVERT: S 148 ARG cc_start: 0.8138 (ttp80) cc_final: 0.7002 (ttm-80) REVERT: S 174 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.8005 (pt0) REVERT: S 180 MET cc_start: 0.8588 (ptm) cc_final: 0.8079 (ptm) REVERT: S 208 GLU cc_start: 0.8605 (pt0) cc_final: 0.8290 (pt0) REVERT: S 219 GLN cc_start: 0.9430 (pp30) cc_final: 0.8817 (pp30) REVERT: S 234 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7734 (tm-30) outliers start: 25 outliers final: 12 residues processed: 179 average time/residue: 0.2573 time to fit residues: 62.5548 Evaluate side-chains 157 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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 6 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 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 = 0.3903 r_free = 0.3903 target = 0.147163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.100788 restraints weight = 13687.877| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.62 r_work: 0.3132 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10456 Z= 0.127 Angle : 0.577 8.009 14183 Z= 0.294 Chirality : 0.042 0.196 1576 Planarity : 0.004 0.086 1804 Dihedral : 5.575 77.140 1477 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.97 % Favored : 95.72 % Rotamer: Outliers : 3.08 % Allowed : 10.05 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.23), residues: 1286 helix: 1.43 (0.26), residues: 426 sheet: -1.94 (0.30), residues: 275 loop : -2.06 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 331 HIS 0.003 0.001 HIS S 35 PHE 0.014 0.001 PHE R 474 TYR 0.027 0.001 TYR S 223 ARG 0.005 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.04014 ( 458) hydrogen bonds : angle 4.29681 ( 1326) SS BOND : bond 0.00297 ( 13) SS BOND : angle 1.07054 ( 26) covalent geometry : bond 0.00290 (10443) covalent geometry : angle 0.57583 (14157) *********************** 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 196 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 1.146 Fit side-chains revert: symmetry clash REVERT: R 119 TRP cc_start: 0.7754 (t60) cc_final: 0.7387 (t60) REVERT: R 230 MET cc_start: 0.7373 (tpp) cc_final: 0.6993 (tpp) REVERT: R 424 MET cc_start: 0.6726 (mmt) cc_final: 0.6335 (mtt) REVERT: R 457 PHE cc_start: 0.7528 (t80) cc_final: 0.7167 (m-10) REVERT: R 491 GLN cc_start: 0.8099 (tt0) cc_final: 0.7757 (tt0) REVERT: A 9 ASP cc_start: 0.8250 (t0) cc_final: 0.7903 (m-30) REVERT: A 18 MET cc_start: 0.7573 (ttp) cc_final: 0.7289 (ttm) REVERT: A 197 LYS cc_start: 0.8208 (mttt) cc_final: 0.7885 (mttp) REVERT: A 345 LYS cc_start: 0.7609 (tmmt) cc_final: 0.7239 (mtpp) REVERT: B 19 ARG cc_start: 0.7468 (tmm160) cc_final: 0.6877 (ttp-110) REVERT: B 42 ARG cc_start: 0.8246 (ttt-90) cc_final: 0.7446 (ttm-80) REVERT: B 44 GLN cc_start: 0.7786 (tt0) cc_final: 0.6813 (pp30) REVERT: B 46 ARG cc_start: 0.7833 (ttt-90) cc_final: 0.7494 (mtp85) REVERT: B 99 TRP cc_start: 0.8432 (m100) cc_final: 0.8159 (m100) REVERT: B 127 LYS cc_start: 0.8478 (mmtm) cc_final: 0.8024 (mmtp) REVERT: B 175 GLN cc_start: 0.8017 (pt0) cc_final: 0.7295 (mm110) REVERT: B 215 GLU cc_start: 0.8715 (mp0) cc_final: 0.8326 (mp0) REVERT: B 217 MET cc_start: 0.8115 (ptp) cc_final: 0.7820 (ptt) REVERT: B 228 ASP cc_start: 0.7951 (m-30) cc_final: 0.7731 (m-30) REVERT: B 254 ASP cc_start: 0.8123 (t70) cc_final: 0.7738 (t0) REVERT: B 267 ASP cc_start: 0.8790 (OUTLIER) cc_final: 0.8263 (t0) REVERT: B 292 PHE cc_start: 0.8717 (m-10) cc_final: 0.8283 (m-10) REVERT: G 13 ARG cc_start: 0.7419 (mtm-85) cc_final: 0.6814 (mtm-85) REVERT: G 46 LYS cc_start: 0.8949 (mtmm) cc_final: 0.8525 (mtmm) REVERT: G 47 GLU cc_start: 0.8519 (mt-10) cc_final: 0.7878 (mp0) REVERT: G 48 ASP cc_start: 0.8698 (t0) cc_final: 0.8446 (t0) REVERT: G 58 GLU cc_start: 0.8373 (mp0) cc_final: 0.7975 (mp0) REVERT: S 13 GLN cc_start: 0.8294 (mm-40) cc_final: 0.8034 (mm-40) REVERT: S 46 GLU cc_start: 0.8378 (mt-10) cc_final: 0.7823 (tt0) REVERT: S 93 MET cc_start: 0.8091 (mtp) cc_final: 0.7688 (ttt) REVERT: S 113 GLN cc_start: 0.8693 (mm-40) cc_final: 0.8314 (mm-40) REVERT: S 148 ARG cc_start: 0.8134 (ttp80) cc_final: 0.6987 (ttm-80) REVERT: S 174 GLN cc_start: 0.8358 (pt0) cc_final: 0.8043 (pt0) REVERT: S 180 MET cc_start: 0.8552 (ptm) cc_final: 0.8052 (ptm) REVERT: S 208 GLU cc_start: 0.8591 (pt0) cc_final: 0.7963 (pm20) REVERT: S 219 GLN cc_start: 0.9362 (pp30) cc_final: 0.8712 (pp30) REVERT: S 234 GLU cc_start: 0.8368 (tm-30) cc_final: 0.7748 (tm-30) outliers start: 34 outliers final: 22 residues processed: 187 average time/residue: 0.2538 time to fit residues: 64.6720 Evaluate side-chains 173 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 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 R residue 518 GLU 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 21 MET Chi-restraints excluded: chain G residue 41 CYS 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 203 THR 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 116 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 91 optimal weight: 0.6980 chunk 121 optimal weight: 0.8980 chunk 104 optimal weight: 0.0470 chunk 52 optimal weight: 0.0770 chunk 61 optimal weight: 9.9990 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 476 ASN R 491 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.147575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.101293 restraints weight = 13528.636| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.60 r_work: 0.3137 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10456 Z= 0.119 Angle : 0.543 7.358 14183 Z= 0.279 Chirality : 0.041 0.178 1576 Planarity : 0.004 0.080 1804 Dihedral : 5.408 72.925 1477 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.81 % Favored : 95.96 % Rotamer: Outliers : 3.17 % Allowed : 11.22 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.24), residues: 1286 helix: 1.60 (0.26), residues: 427 sheet: -1.73 (0.31), residues: 257 loop : -1.91 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 331 HIS 0.003 0.001 HIS S 35 PHE 0.012 0.001 PHE R 474 TYR 0.030 0.001 TYR S 223 ARG 0.005 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 458) hydrogen bonds : angle 4.06396 ( 1326) SS BOND : bond 0.00268 ( 13) SS BOND : angle 0.89519 ( 26) covalent geometry : bond 0.00268 (10443) covalent geometry : angle 0.54208 (14157) *********************** 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 192 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 119 TRP cc_start: 0.7743 (t60) cc_final: 0.7334 (t60) REVERT: R 399 TYR cc_start: 0.7909 (m-80) cc_final: 0.7665 (m-80) REVERT: R 424 MET cc_start: 0.6707 (mmt) cc_final: 0.6344 (mtt) REVERT: R 449 MET cc_start: 0.7679 (ttp) cc_final: 0.7421 (ttm) REVERT: R 457 PHE cc_start: 0.7510 (t80) cc_final: 0.7143 (m-10) REVERT: A 9 ASP cc_start: 0.8242 (t0) cc_final: 0.7782 (m-30) REVERT: A 18 MET cc_start: 0.7598 (ttp) cc_final: 0.7316 (ttm) REVERT: A 53 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7478 (mtm) REVERT: A 197 LYS cc_start: 0.8187 (mttt) cc_final: 0.7896 (mttp) REVERT: A 345 LYS cc_start: 0.7587 (tmmt) cc_final: 0.7192 (mtpp) REVERT: B 19 ARG cc_start: 0.7421 (tmm160) cc_final: 0.6832 (ttp-110) REVERT: B 42 ARG cc_start: 0.8176 (ttt-90) cc_final: 0.7469 (ttm-80) REVERT: B 44 GLN cc_start: 0.7714 (tt0) cc_final: 0.6820 (pp30) REVERT: B 46 ARG cc_start: 0.7849 (ttt-90) cc_final: 0.7502 (mtp85) REVERT: B 99 TRP cc_start: 0.8382 (m100) cc_final: 0.8170 (m100) REVERT: B 127 LYS cc_start: 0.8468 (mmtm) cc_final: 0.8012 (mmtp) REVERT: B 175 GLN cc_start: 0.8003 (pt0) cc_final: 0.7260 (mm110) REVERT: B 215 GLU cc_start: 0.8712 (mp0) cc_final: 0.8315 (mp0) REVERT: B 217 MET cc_start: 0.8108 (ptp) cc_final: 0.7850 (ptt) REVERT: B 228 ASP cc_start: 0.7878 (m-30) cc_final: 0.7356 (p0) REVERT: B 254 ASP cc_start: 0.8097 (t70) cc_final: 0.7726 (t0) REVERT: B 267 ASP cc_start: 0.8743 (OUTLIER) cc_final: 0.8245 (t0) REVERT: B 292 PHE cc_start: 0.8733 (m-10) cc_final: 0.8301 (m-10) REVERT: G 47 GLU cc_start: 0.8457 (mt-10) cc_final: 0.7799 (mp0) REVERT: G 58 GLU cc_start: 0.8380 (mp0) cc_final: 0.7953 (mp0) REVERT: S 7 SER cc_start: 0.8768 (t) cc_final: 0.8470 (p) REVERT: S 13 GLN cc_start: 0.8297 (mm-40) cc_final: 0.8029 (mm-40) REVERT: S 46 GLU cc_start: 0.8434 (mt-10) cc_final: 0.7862 (tt0) REVERT: S 93 MET cc_start: 0.8099 (mtp) cc_final: 0.7653 (ttt) REVERT: S 148 ARG cc_start: 0.8051 (ttp80) cc_final: 0.6912 (ttm-80) REVERT: S 174 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.8006 (pt0) REVERT: S 180 MET cc_start: 0.8520 (ptm) cc_final: 0.8053 (ptm) REVERT: S 208 GLU cc_start: 0.8622 (pt0) cc_final: 0.8210 (pt0) REVERT: S 234 GLU cc_start: 0.8438 (tm-30) cc_final: 0.7781 (tm-30) outliers start: 35 outliers final: 21 residues processed: 181 average time/residue: 0.2887 time to fit residues: 71.4840 Evaluate side-chains 168 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 1.182 ------------------------------------------------------------------------------- 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 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 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 39 LEU Chi-restraints excluded: chain A residue 53 MET 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 154 LEU 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 90 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN ** B 75 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 = 0.3855 r_free = 0.3855 target = 0.143201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.096464 restraints weight = 13556.164| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.58 r_work: 0.3067 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10456 Z= 0.205 Angle : 0.606 8.039 14183 Z= 0.312 Chirality : 0.043 0.168 1576 Planarity : 0.005 0.081 1804 Dihedral : 5.674 73.843 1477 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.51 % Favored : 95.18 % Rotamer: Outliers : 4.16 % Allowed : 12.13 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.23), residues: 1286 helix: 1.48 (0.26), residues: 427 sheet: -1.73 (0.29), residues: 282 loop : -1.92 (0.24), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.005 0.001 HIS A 188 PHE 0.014 0.001 PHE A 189 TYR 0.033 0.001 TYR S 223 ARG 0.004 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.04230 ( 458) hydrogen bonds : angle 4.18128 ( 1326) SS BOND : bond 0.00503 ( 13) SS BOND : angle 1.22997 ( 26) covalent geometry : bond 0.00488 (10443) covalent geometry : angle 0.60400 (14157) *********************** 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 192 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 146 time to evaluate : 1.307 Fit side-chains revert: symmetry clash REVERT: R 230 MET cc_start: 0.7640 (tpp) cc_final: 0.7042 (tpp) REVERT: R 317 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7511 (tp) REVERT: R 424 MET cc_start: 0.6844 (mmt) cc_final: 0.6470 (mtt) REVERT: R 449 MET cc_start: 0.7647 (ttp) cc_final: 0.7405 (ttm) REVERT: R 457 PHE cc_start: 0.7657 (t80) cc_final: 0.7209 (m-10) REVERT: A 9 ASP cc_start: 0.8342 (t0) cc_final: 0.7828 (m-30) REVERT: A 18 MET cc_start: 0.7649 (ttp) cc_final: 0.7379 (ttm) REVERT: A 53 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7325 (mtm) REVERT: A 197 LYS cc_start: 0.8315 (mttt) cc_final: 0.8011 (mttp) REVERT: A 345 LYS cc_start: 0.7643 (tmmt) cc_final: 0.7238 (mtpp) REVERT: B 19 ARG cc_start: 0.7427 (tmm160) cc_final: 0.6858 (ttp-110) REVERT: B 42 ARG cc_start: 0.8324 (ttt-90) cc_final: 0.7624 (ttm-80) REVERT: B 44 GLN cc_start: 0.7718 (tt0) cc_final: 0.6808 (pp30) REVERT: B 46 ARG cc_start: 0.7889 (ttt-90) cc_final: 0.7550 (mtp85) REVERT: B 127 LYS cc_start: 0.8616 (mmtm) cc_final: 0.8153 (mmtp) REVERT: B 175 GLN cc_start: 0.8063 (pt0) cc_final: 0.7354 (mm110) REVERT: B 215 GLU cc_start: 0.8661 (mp0) cc_final: 0.8274 (mp0) REVERT: B 217 MET cc_start: 0.8187 (ptp) cc_final: 0.7913 (ptt) REVERT: B 228 ASP cc_start: 0.8021 (m-30) cc_final: 0.7477 (p0) REVERT: B 254 ASP cc_start: 0.8418 (t70) cc_final: 0.8033 (t0) REVERT: B 267 ASP cc_start: 0.8724 (OUTLIER) cc_final: 0.8325 (t0) REVERT: B 292 PHE cc_start: 0.8849 (m-10) cc_final: 0.8527 (m-10) REVERT: G 22 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7363 (tt0) REVERT: G 47 GLU cc_start: 0.8444 (mt-10) cc_final: 0.7788 (mp0) REVERT: G 48 ASP cc_start: 0.8701 (t0) cc_final: 0.8069 (t0) REVERT: G 58 GLU cc_start: 0.8460 (mp0) cc_final: 0.8163 (mp0) REVERT: S 7 SER cc_start: 0.8880 (t) cc_final: 0.8609 (p) REVERT: S 13 GLN cc_start: 0.8347 (mm-40) cc_final: 0.8067 (mm-40) REVERT: S 46 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7848 (tt0) REVERT: S 93 MET cc_start: 0.8146 (mtp) cc_final: 0.7732 (ttt) REVERT: S 148 ARG cc_start: 0.8075 (ttp80) cc_final: 0.6991 (ttm-80) REVERT: S 180 MET cc_start: 0.8603 (ptm) cc_final: 0.8101 (ptm) REVERT: S 190 ARG cc_start: 0.8267 (mtm-85) cc_final: 0.8001 (mtm-85) REVERT: S 208 GLU cc_start: 0.8671 (pt0) cc_final: 0.8463 (pt0) REVERT: S 219 GLN cc_start: 0.9395 (pp30) cc_final: 0.8635 (pp30) REVERT: S 234 GLU cc_start: 0.8516 (tm-30) cc_final: 0.7829 (tm-30) outliers start: 46 outliers final: 32 residues processed: 177 average time/residue: 0.3074 time to fit residues: 75.7486 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 : 1.166 ------------------------------------------------------------------------------- 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 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 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 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 21 MET 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 5 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 102 optimal weight: 0.2980 chunk 90 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 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 = 0.3872 r_free = 0.3872 target = 0.144654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.098017 restraints weight = 13592.704| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.60 r_work: 0.3090 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2588 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= 0.150 Angle : 0.583 13.856 14183 Z= 0.294 Chirality : 0.042 0.178 1576 Planarity : 0.005 0.077 1804 Dihedral : 5.576 72.703 1477 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.74 % Favored : 95.02 % Rotamer: Outliers : 3.71 % Allowed : 13.39 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.24), residues: 1286 helix: 1.57 (0.26), residues: 428 sheet: -1.75 (0.28), residues: 302 loop : -1.77 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 331 HIS 0.004 0.001 HIS S 35 PHE 0.011 0.001 PHE A 189 TYR 0.029 0.001 TYR S 223 ARG 0.004 0.000 ARG S 87 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 458) hydrogen bonds : angle 4.07266 ( 1326) SS BOND : bond 0.00369 ( 13) SS BOND : angle 1.03375 ( 26) covalent geometry : bond 0.00353 (10443) covalent geometry : angle 0.58158 (14157) *********************** 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 192 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 1.302 Fit side-chains revert: symmetry clash REVERT: R 230 MET cc_start: 0.7613 (tpp) cc_final: 0.7016 (tpp) REVERT: R 317 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7455 (tp) REVERT: R 380 GLN cc_start: 0.6084 (OUTLIER) cc_final: 0.5822 (pm20) REVERT: R 424 MET cc_start: 0.6762 (mmt) cc_final: 0.6392 (mtt) REVERT: R 449 MET cc_start: 0.7635 (ttp) cc_final: 0.7385 (ttm) REVERT: R 457 PHE cc_start: 0.7527 (t80) cc_final: 0.7149 (m-10) REVERT: A 9 ASP cc_start: 0.8331 (t0) cc_final: 0.7822 (m-30) REVERT: A 18 MET cc_start: 0.7583 (ttp) cc_final: 0.7319 (ttm) REVERT: A 53 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7455 (mtm) REVERT: A 197 LYS cc_start: 0.8271 (mttt) cc_final: 0.7988 (mttp) REVERT: A 345 LYS cc_start: 0.7597 (tmmt) cc_final: 0.7181 (mtpp) REVERT: B 19 ARG cc_start: 0.7397 (tmm160) cc_final: 0.6844 (ttp-110) REVERT: B 42 ARG cc_start: 0.8331 (ttt-90) cc_final: 0.7649 (ttm-80) REVERT: B 44 GLN cc_start: 0.7777 (tt0) cc_final: 0.6964 (pp30) REVERT: B 46 ARG cc_start: 0.7865 (ttt-90) cc_final: 0.7541 (mtp85) REVERT: B 99 TRP cc_start: 0.8429 (m100) cc_final: 0.8218 (m100) REVERT: B 127 LYS cc_start: 0.8560 (mmtm) cc_final: 0.8081 (mmtp) REVERT: B 175 GLN cc_start: 0.8032 (pt0) cc_final: 0.7299 (mm110) REVERT: B 215 GLU cc_start: 0.8644 (mp0) cc_final: 0.8256 (mp0) REVERT: B 217 MET cc_start: 0.8203 (ptp) cc_final: 0.7919 (ptt) REVERT: B 218 CYS cc_start: 0.8532 (p) cc_final: 0.8226 (p) REVERT: B 228 ASP cc_start: 0.7939 (m-30) cc_final: 0.7478 (p0) REVERT: B 254 ASP cc_start: 0.8407 (t70) cc_final: 0.8026 (t0) REVERT: B 292 PHE cc_start: 0.8840 (m-10) cc_final: 0.8468 (m-10) REVERT: G 47 GLU cc_start: 0.8398 (mt-10) cc_final: 0.7729 (mp0) REVERT: G 48 ASP cc_start: 0.8670 (t0) cc_final: 0.8248 (t0) REVERT: G 58 GLU cc_start: 0.8445 (mp0) cc_final: 0.8138 (mp0) REVERT: S 7 SER cc_start: 0.8834 (t) cc_final: 0.8556 (p) REVERT: S 13 GLN cc_start: 0.8343 (mm-40) cc_final: 0.8060 (mm-40) REVERT: S 46 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7817 (tt0) REVERT: S 93 MET cc_start: 0.8099 (mtp) cc_final: 0.7717 (ttt) REVERT: S 113 GLN cc_start: 0.8704 (mm110) cc_final: 0.8316 (mm-40) REVERT: S 148 ARG cc_start: 0.8049 (ttp80) cc_final: 0.6956 (ttm-80) REVERT: S 180 MET cc_start: 0.8540 (ptm) cc_final: 0.8012 (ptm) REVERT: S 190 ARG cc_start: 0.8240 (mtm-85) cc_final: 0.8026 (mtm-85) REVERT: S 208 GLU cc_start: 0.8643 (pt0) cc_final: 0.8181 (pt0) REVERT: S 219 GLN cc_start: 0.9365 (pp30) cc_final: 0.8631 (pp30) REVERT: S 234 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8172 (tm-30) outliers start: 41 outliers final: 29 residues processed: 178 average time/residue: 0.3142 time to fit residues: 76.6988 Evaluate side-chains 174 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 380 GLN 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 B residue 47 THR 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 76 LYS 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 96 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 124 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.141775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.094711 restraints weight = 13899.447| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.62 r_work: 0.3042 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10456 Z= 0.230 Angle : 0.635 13.315 14183 Z= 0.322 Chirality : 0.044 0.173 1576 Planarity : 0.005 0.080 1804 Dihedral : 5.880 74.486 1477 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.13 % Favored : 94.56 % Rotamer: Outliers : 3.80 % Allowed : 14.30 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.24), residues: 1286 helix: 1.42 (0.26), residues: 428 sheet: -1.85 (0.28), residues: 305 loop : -1.75 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 99 HIS 0.005 0.001 HIS A 188 PHE 0.015 0.001 PHE B 241 TYR 0.032 0.001 TYR S 223 ARG 0.004 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.04282 ( 458) hydrogen bonds : angle 4.23260 ( 1326) SS BOND : bond 0.00459 ( 13) SS BOND : angle 1.06934 ( 26) covalent geometry : bond 0.00550 (10443) covalent geometry : angle 0.63372 (14157) *********************** 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 183 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 141 time to evaluate : 1.189 Fit side-chains revert: symmetry clash REVERT: R 230 MET cc_start: 0.7621 (tpp) cc_final: 0.6978 (tpp) REVERT: R 317 ILE cc_start: 0.7804 (OUTLIER) cc_final: 0.7514 (tp) REVERT: R 424 MET cc_start: 0.6826 (mmt) cc_final: 0.6456 (mtt) REVERT: R 449 MET cc_start: 0.7657 (ttp) cc_final: 0.7402 (ttm) REVERT: R 457 PHE cc_start: 0.7591 (t80) cc_final: 0.7174 (m-10) REVERT: A 9 ASP cc_start: 0.8429 (t0) cc_final: 0.7868 (m-30) REVERT: A 18 MET cc_start: 0.7651 (ttp) cc_final: 0.7389 (ttm) REVERT: A 53 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7379 (mtm) REVERT: A 197 LYS cc_start: 0.8342 (mttt) cc_final: 0.8050 (mttp) REVERT: A 345 LYS cc_start: 0.7650 (tmmt) cc_final: 0.7214 (mtpp) REVERT: B 19 ARG cc_start: 0.7436 (tmm160) cc_final: 0.6892 (ttp-110) REVERT: B 42 ARG cc_start: 0.8323 (ttt-90) cc_final: 0.7719 (ttm-80) REVERT: B 46 ARG cc_start: 0.7899 (ttt-90) cc_final: 0.7557 (mtp85) REVERT: B 127 LYS cc_start: 0.8641 (mmtm) cc_final: 0.8219 (mmtp) REVERT: B 175 GLN cc_start: 0.8145 (pt0) cc_final: 0.7395 (mm110) REVERT: B 217 MET cc_start: 0.8247 (ptp) cc_final: 0.7939 (ptt) REVERT: B 218 CYS cc_start: 0.8547 (p) cc_final: 0.8237 (p) REVERT: B 228 ASP cc_start: 0.8049 (m-30) cc_final: 0.7579 (p0) REVERT: B 254 ASP cc_start: 0.8452 (t70) cc_final: 0.7980 (t0) REVERT: B 292 PHE cc_start: 0.8896 (m-10) cc_final: 0.8607 (m-10) REVERT: G 47 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7709 (mp0) REVERT: G 58 GLU cc_start: 0.8495 (mp0) cc_final: 0.8143 (mp0) REVERT: S 7 SER cc_start: 0.8870 (t) cc_final: 0.8617 (p) REVERT: S 13 GLN cc_start: 0.8367 (mm-40) cc_final: 0.8084 (mm-40) REVERT: S 46 GLU cc_start: 0.8462 (mt-10) cc_final: 0.7847 (tt0) REVERT: S 93 MET cc_start: 0.8157 (mtp) cc_final: 0.7769 (ttt) REVERT: S 113 GLN cc_start: 0.8779 (mm110) cc_final: 0.8345 (mm-40) REVERT: S 148 ARG cc_start: 0.8049 (ttp80) cc_final: 0.6987 (ttm-80) REVERT: S 180 MET cc_start: 0.8638 (ptm) cc_final: 0.8109 (ptm) REVERT: S 190 ARG cc_start: 0.8269 (mtm-85) cc_final: 0.7886 (mtm-85) REVERT: S 208 GLU cc_start: 0.8693 (pt0) cc_final: 0.7974 (pm20) REVERT: S 234 GLU cc_start: 0.8488 (tm-30) cc_final: 0.7867 (tm-30) outliers start: 42 outliers final: 34 residues processed: 171 average time/residue: 0.2690 time to fit residues: 63.3188 Evaluate side-chains 173 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 89 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.144409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.097519 restraints weight = 13671.550| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.62 r_work: 0.3082 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10456 Z= 0.146 Angle : 0.586 13.157 14183 Z= 0.293 Chirality : 0.042 0.181 1576 Planarity : 0.004 0.076 1804 Dihedral : 5.685 73.054 1477 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.90 % Favored : 94.87 % Rotamer: Outliers : 3.35 % Allowed : 15.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.24), residues: 1286 helix: 1.43 (0.25), residues: 434 sheet: -1.73 (0.29), residues: 295 loop : -1.71 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 99 HIS 0.004 0.001 HIS S 35 PHE 0.011 0.001 PHE A 189 TYR 0.029 0.001 TYR S 223 ARG 0.004 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03887 ( 458) hydrogen bonds : angle 4.07092 ( 1326) SS BOND : bond 0.00335 ( 13) SS BOND : angle 0.91421 ( 26) covalent geometry : bond 0.00339 (10443) covalent geometry : angle 0.58478 (14157) *********************** 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 182 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 145 time to evaluate : 4.380 Fit side-chains revert: symmetry clash REVERT: R 131 MET cc_start: 0.7160 (tpp) cc_final: 0.6887 (tpp) REVERT: R 230 MET cc_start: 0.7653 (tpp) cc_final: 0.6964 (tpp) REVERT: R 317 ILE cc_start: 0.7662 (OUTLIER) cc_final: 0.7443 (tp) REVERT: R 424 MET cc_start: 0.6697 (mmt) cc_final: 0.6313 (mtt) REVERT: R 449 MET cc_start: 0.7626 (ttp) cc_final: 0.7376 (ttm) REVERT: R 457 PHE cc_start: 0.7520 (t80) cc_final: 0.7192 (m-10) REVERT: A 9 ASP cc_start: 0.8359 (t0) cc_final: 0.7832 (m-30) REVERT: A 18 MET cc_start: 0.7604 (ttp) cc_final: 0.7350 (ttm) REVERT: A 53 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.7491 (mtm) REVERT: A 187 THR cc_start: 0.8781 (OUTLIER) cc_final: 0.8459 (p) REVERT: A 197 LYS cc_start: 0.8301 (mttt) cc_final: 0.8020 (mttp) REVERT: A 345 LYS cc_start: 0.7602 (tmmt) cc_final: 0.7180 (mtpp) REVERT: B 19 ARG cc_start: 0.7440 (tmm160) cc_final: 0.6910 (ttp-110) REVERT: B 42 ARG cc_start: 0.8304 (ttt-90) cc_final: 0.7714 (ttm-80) REVERT: B 46 ARG cc_start: 0.7873 (ttt-90) cc_final: 0.7527 (mtp85) REVERT: B 99 TRP cc_start: 0.8441 (m100) cc_final: 0.8217 (m100) REVERT: B 127 LYS cc_start: 0.8609 (mmtm) cc_final: 0.8145 (mmtp) REVERT: B 175 GLN cc_start: 0.8061 (pt0) cc_final: 0.7361 (mm110) REVERT: B 215 GLU cc_start: 0.8634 (mp0) cc_final: 0.8251 (mp0) REVERT: B 217 MET cc_start: 0.8215 (ptp) cc_final: 0.7902 (ptt) REVERT: B 218 CYS cc_start: 0.8504 (p) cc_final: 0.8171 (p) REVERT: B 228 ASP cc_start: 0.7930 (m-30) cc_final: 0.7473 (p0) REVERT: B 254 ASP cc_start: 0.8445 (t70) cc_final: 0.8056 (t0) REVERT: B 292 PHE cc_start: 0.8879 (m-10) cc_final: 0.8555 (m-10) REVERT: G 47 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7672 (mp0) REVERT: G 48 ASP cc_start: 0.8609 (t0) cc_final: 0.8091 (t0) REVERT: G 58 GLU cc_start: 0.8526 (mp0) cc_final: 0.8192 (mp0) REVERT: S 7 SER cc_start: 0.8862 (t) cc_final: 0.8599 (p) REVERT: S 13 GLN cc_start: 0.8336 (mm-40) cc_final: 0.8058 (mm-40) REVERT: S 46 GLU cc_start: 0.8456 (mt-10) cc_final: 0.7841 (tt0) REVERT: S 93 MET cc_start: 0.8093 (mtp) cc_final: 0.7715 (ttt) REVERT: S 113 GLN cc_start: 0.8720 (mm110) cc_final: 0.8380 (mm-40) REVERT: S 148 ARG cc_start: 0.8008 (ttp80) cc_final: 0.6923 (ttm-80) REVERT: S 180 MET cc_start: 0.8564 (ptm) cc_final: 0.8009 (ptm) REVERT: S 208 GLU cc_start: 0.8631 (pt0) cc_final: 0.8173 (pt0) REVERT: S 234 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8137 (tm-30) outliers start: 37 outliers final: 32 residues processed: 171 average time/residue: 0.3256 time to fit residues: 77.6160 Evaluate side-chains 174 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 1.350 ------------------------------------------------------------------------------- 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 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 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 186 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 86 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 121 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 25 optimal weight: 0.0070 chunk 127 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 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 = 0.144126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.097137 restraints weight = 13657.700| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.62 r_work: 0.3080 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2797 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= 0.158 Angle : 0.593 12.614 14183 Z= 0.298 Chirality : 0.042 0.175 1576 Planarity : 0.005 0.077 1804 Dihedral : 5.611 72.666 1477 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.74 % Favored : 95.02 % Rotamer: Outliers : 3.35 % Allowed : 15.84 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.23), residues: 1286 helix: 1.42 (0.25), residues: 434 sheet: -1.76 (0.28), residues: 306 loop : -1.70 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 99 HIS 0.004 0.001 HIS S 35 PHE 0.012 0.001 PHE A 189 TYR 0.029 0.001 TYR S 223 ARG 0.004 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03887 ( 458) hydrogen bonds : angle 4.06462 ( 1326) SS BOND : bond 0.00361 ( 13) SS BOND : angle 0.90027 ( 26) covalent geometry : bond 0.00374 (10443) covalent geometry : angle 0.59227 (14157) *********************** 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 180 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 1.513 Fit side-chains revert: symmetry clash REVERT: R 131 MET cc_start: 0.7291 (tpp) cc_final: 0.7055 (tpp) REVERT: R 230 MET cc_start: 0.7646 (tpp) cc_final: 0.6928 (tpp) REVERT: R 317 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7408 (tp) REVERT: R 424 MET cc_start: 0.6728 (mmt) cc_final: 0.6342 (mtt) REVERT: R 449 MET cc_start: 0.7666 (ttp) cc_final: 0.7416 (ttm) REVERT: R 457 PHE cc_start: 0.7510 (t80) cc_final: 0.7135 (m-10) REVERT: A 9 ASP cc_start: 0.8370 (t0) cc_final: 0.7840 (m-30) REVERT: A 18 MET cc_start: 0.7619 (ttp) cc_final: 0.7357 (ttm) REVERT: A 53 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7487 (mtm) REVERT: A 187 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8439 (p) REVERT: A 197 LYS cc_start: 0.8311 (mttt) cc_final: 0.8029 (mttp) REVERT: A 345 LYS cc_start: 0.7605 (tmmt) cc_final: 0.7203 (mtpp) REVERT: B 19 ARG cc_start: 0.7437 (tmm160) cc_final: 0.6909 (ttp-110) REVERT: B 42 ARG cc_start: 0.8308 (ttt-90) cc_final: 0.7759 (ttm-80) REVERT: B 46 ARG cc_start: 0.7869 (ttt-90) cc_final: 0.7548 (mtp85) REVERT: B 127 LYS cc_start: 0.8555 (mmtm) cc_final: 0.8081 (mmtp) REVERT: B 175 GLN cc_start: 0.8059 (pt0) cc_final: 0.7355 (mm110) REVERT: B 215 GLU cc_start: 0.8636 (mp0) cc_final: 0.8258 (mp0) REVERT: B 217 MET cc_start: 0.8232 (ptp) cc_final: 0.7928 (ptt) REVERT: B 218 CYS cc_start: 0.8503 (p) cc_final: 0.8157 (p) REVERT: B 228 ASP cc_start: 0.7943 (m-30) cc_final: 0.7487 (p0) REVERT: B 254 ASP cc_start: 0.8433 (t70) cc_final: 0.8034 (t0) REVERT: B 292 PHE cc_start: 0.8894 (m-10) cc_final: 0.8574 (m-10) REVERT: G 47 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7648 (mp0) REVERT: G 48 ASP cc_start: 0.8672 (t0) cc_final: 0.8156 (t0) REVERT: G 58 GLU cc_start: 0.8537 (mp0) cc_final: 0.8194 (mp0) REVERT: S 7 SER cc_start: 0.8857 (t) cc_final: 0.8593 (p) REVERT: S 13 GLN cc_start: 0.8340 (mm-40) cc_final: 0.8048 (mm-40) REVERT: S 46 GLU cc_start: 0.8447 (mt-10) cc_final: 0.7837 (tt0) REVERT: S 93 MET cc_start: 0.8060 (mtp) cc_final: 0.7674 (ttt) REVERT: S 141 GLU cc_start: 0.8787 (pt0) cc_final: 0.8495 (pt0) REVERT: S 148 ARG cc_start: 0.7991 (ttp80) cc_final: 0.6911 (ttm-80) REVERT: S 180 MET cc_start: 0.8560 (ptm) cc_final: 0.8011 (ptm) REVERT: S 234 GLU cc_start: 0.8401 (tm-30) cc_final: 0.8119 (tm-30) outliers start: 37 outliers final: 30 residues processed: 170 average time/residue: 0.3064 time to fit residues: 72.3586 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 : 1.044 ------------------------------------------------------------------------------- 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 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 187 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 278 ILE 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 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 27 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 43 optimal weight: 20.0000 chunk 4 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.143498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.096530 restraints weight = 13640.534| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.61 r_work: 0.3069 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10456 Z= 0.175 Angle : 0.603 11.858 14183 Z= 0.303 Chirality : 0.042 0.175 1576 Planarity : 0.005 0.077 1804 Dihedral : 5.646 72.903 1477 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.13 % Favored : 94.63 % Rotamer: Outliers : 3.17 % Allowed : 15.93 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.23), residues: 1286 helix: 1.38 (0.25), residues: 434 sheet: -1.78 (0.28), residues: 306 loop : -1.68 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 99 HIS 0.004 0.001 HIS B 54 PHE 0.012 0.001 PHE A 189 TYR 0.029 0.001 TYR S 223 ARG 0.004 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03956 ( 458) hydrogen bonds : angle 4.09697 ( 1326) SS BOND : bond 0.00379 ( 13) SS BOND : angle 0.91599 ( 26) covalent geometry : bond 0.00413 (10443) covalent geometry : angle 0.60248 (14157) ********************** 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 176 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 1.178 Fit side-chains revert: symmetry clash REVERT: R 230 MET cc_start: 0.7615 (tpp) cc_final: 0.6937 (tpp) REVERT: R 317 ILE cc_start: 0.7752 (OUTLIER) cc_final: 0.7441 (tp) REVERT: R 424 MET cc_start: 0.6705 (mmt) cc_final: 0.6326 (mtt) REVERT: R 449 MET cc_start: 0.7645 (ttp) cc_final: 0.7397 (ttm) REVERT: R 457 PHE cc_start: 0.7508 (t80) cc_final: 0.7133 (m-10) REVERT: A 9 ASP cc_start: 0.8371 (t0) cc_final: 0.7833 (m-30) REVERT: A 18 MET cc_start: 0.7618 (ttp) cc_final: 0.7355 (ttm) REVERT: A 53 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7510 (mtm) REVERT: A 187 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8427 (p) REVERT: A 197 LYS cc_start: 0.8310 (mttt) cc_final: 0.8028 (mttp) REVERT: A 345 LYS cc_start: 0.7596 (tmmt) cc_final: 0.7187 (mtpp) REVERT: B 19 ARG cc_start: 0.7410 (tmm160) cc_final: 0.6886 (ttp-110) REVERT: B 42 ARG cc_start: 0.8307 (ttt-90) cc_final: 0.7768 (ttm-80) REVERT: B 46 ARG cc_start: 0.7853 (ttt-90) cc_final: 0.7539 (mtp85) REVERT: B 127 LYS cc_start: 0.8554 (mmtm) cc_final: 0.8085 (mmtp) REVERT: B 175 GLN cc_start: 0.8049 (pt0) cc_final: 0.7354 (mm110) REVERT: B 215 GLU cc_start: 0.8640 (mp0) cc_final: 0.8262 (mp0) REVERT: B 217 MET cc_start: 0.8228 (ptp) cc_final: 0.7922 (ptt) REVERT: B 218 CYS cc_start: 0.8507 (p) cc_final: 0.8152 (p) REVERT: B 228 ASP cc_start: 0.7940 (m-30) cc_final: 0.7474 (p0) REVERT: B 254 ASP cc_start: 0.8441 (t70) cc_final: 0.8028 (t0) REVERT: B 292 PHE cc_start: 0.8899 (m-10) cc_final: 0.8571 (m-10) REVERT: G 48 ASP cc_start: 0.8693 (t0) cc_final: 0.8190 (t0) REVERT: G 58 GLU cc_start: 0.8546 (mp0) cc_final: 0.8192 (mp0) REVERT: S 7 SER cc_start: 0.8860 (t) cc_final: 0.8603 (p) REVERT: S 13 GLN cc_start: 0.8331 (mm-40) cc_final: 0.8044 (mm-40) REVERT: S 46 GLU cc_start: 0.8440 (mt-10) cc_final: 0.7823 (tt0) REVERT: S 93 MET cc_start: 0.8089 (mtp) cc_final: 0.7708 (ttt) REVERT: S 141 GLU cc_start: 0.8771 (pt0) cc_final: 0.8408 (pt0) REVERT: S 148 ARG cc_start: 0.7998 (ttp80) cc_final: 0.6937 (ttm-80) REVERT: S 180 MET cc_start: 0.8585 (ptm) cc_final: 0.8039 (ptm) REVERT: S 208 GLU cc_start: 0.8529 (pt0) cc_final: 0.8088 (pm20) REVERT: S 211 ASP cc_start: 0.8407 (t0) cc_final: 0.7992 (t0) REVERT: S 234 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8120 (tm-30) outliers start: 35 outliers final: 28 residues processed: 167 average time/residue: 0.2500 time to fit residues: 57.8202 Evaluate side-chains 171 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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 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 187 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 278 ILE 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 267 ASP Chi-restraints excluded: chain B residue 270 ILE 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 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 23 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 115 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.144221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.097388 restraints weight = 13637.668| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.61 r_work: 0.3080 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2896 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 : 0.602 11.230 14183 Z= 0.301 Chirality : 0.042 0.176 1576 Planarity : 0.004 0.077 1804 Dihedral : 5.558 72.661 1477 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.82 % Favored : 94.95 % Rotamer: Outliers : 3.08 % Allowed : 16.29 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.24), residues: 1286 helix: 1.43 (0.26), residues: 434 sheet: -1.77 (0.28), residues: 306 loop : -1.67 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 99 HIS 0.004 0.001 HIS S 35 PHE 0.012 0.001 PHE A 189 TYR 0.028 0.001 TYR S 223 ARG 0.004 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 458) hydrogen bonds : angle 4.05558 ( 1326) SS BOND : bond 0.00349 ( 13) SS BOND : angle 0.86734 ( 26) covalent geometry : bond 0.00370 (10443) covalent geometry : angle 0.60138 (14157) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8202.69 seconds wall clock time: 147 minutes 49.20 seconds (8869.20 seconds total)