Starting phenix.real_space_refine on Fri Oct 23 02:00:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xsg_67181/10_2026/9xsg_67181.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xsg_67181/10_2026/9xsg_67181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xsg_67181/10_2026/9xsg_67181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xsg_67181/10_2026/9xsg_67181.map" model { file = "/net/cci-nas-00/data/ceres_data/9xsg_67181/10_2026/9xsg_67181.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xsg_67181/10_2026/9xsg_67181.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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 54 5.16 5 C 4765 2.51 5 N 1311 2.21 5 O 1434 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7564 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1794 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 12, 'TRANS': 219} Chain: "B" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1794 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "E" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2694 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 11, 'TRANS': 325} Chain breaks: 5 Chain: "D" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1282 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Time building chain proxies: 1.61, per 1000 atoms: 0.21 Number of scatterers: 7564 At special positions: 0 Unit cell: (84.46, 87.74, 125.46, 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 54 16.00 O 1434 8.00 N 1311 7.00 C 4765 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 70 " distance=2.03 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 218 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 197 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 234 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 70 " distance=2.03 Simple disulfide: pdb=" SG CYS B 148 " - pdb=" SG CYS B 218 " distance=2.04 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 197 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 234 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 375.3 milliseconds 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1802 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 7 sheets defined 33.3% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 247 through 260 removed outlier: 3.569A pdb=" N TRP A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 180 Processing helix chain 'B' and resid 247 through 260 removed outlier: 3.720A pdb=" N TRP B 253 " --> pdb=" O LYS B 249 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE B 254 " --> pdb=" O HIS B 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 17 removed outlier: 3.537A pdb=" N VAL E 13 " --> pdb=" O THR E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.538A pdb=" N ALA E 31 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP E 32 " --> pdb=" O VAL E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing helix chain 'E' and resid 58 through 62 Processing helix chain 'E' and resid 126 through 133 removed outlier: 3.640A pdb=" N LEU E 133 " --> pdb=" O TYR E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 148 removed outlier: 3.570A pdb=" N ARG E 147 " --> pdb=" O PRO E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 183 Processing helix chain 'E' and resid 253 through 268 removed outlier: 3.797A pdb=" N MET E 261 " --> pdb=" O LYS E 257 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL E 264 " --> pdb=" O ASP E 260 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU E 268 " --> pdb=" O VAL E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 283 removed outlier: 3.547A pdb=" N SER E 279 " --> pdb=" O ASP E 275 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS E 282 " --> pdb=" O ASN E 278 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS E 283 " --> pdb=" O SER E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 304 removed outlier: 3.991A pdb=" N GLN E 291 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 319 removed outlier: 3.717A pdb=" N SER E 318 " --> pdb=" O PRO E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 342 removed outlier: 3.721A pdb=" N LEU E 342 " --> pdb=" O LEU E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 358 removed outlier: 4.287A pdb=" N PHE E 350 " --> pdb=" O GLU E 346 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU E 356 " --> pdb=" O ALA E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 372 removed outlier: 3.652A pdb=" N LYS E 364 " --> pdb=" O LEU E 360 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP E 365 " --> pdb=" O PRO E 361 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS E 368 " --> pdb=" O LYS E 364 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL E 370 " --> pdb=" O GLN E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 375 No H-bonds generated for 'chain 'E' and resid 373 through 375' Processing helix chain 'E' and resid 388 through 409 removed outlier: 3.718A pdb=" N TYR E 398 " --> pdb=" O LEU E 394 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE E 403 " --> pdb=" O VAL E 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 264 Processing helix chain 'D' and resid 269 through 283 removed outlier: 3.500A pdb=" N LEU D 277 " --> pdb=" O ARG D 273 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS D 282 " --> pdb=" O ASN D 278 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS D 283 " --> pdb=" O SER D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 304 Processing helix chain 'D' and resid 313 through 318 removed outlier: 3.661A pdb=" N LEU D 316 " --> pdb=" O LYS D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 344 Processing helix chain 'D' and resid 349 through 357 removed outlier: 3.669A pdb=" N ALA D 354 " --> pdb=" O PHE D 350 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU D 356 " --> pdb=" O ALA D 352 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS D 357 " --> pdb=" O GLU D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 374 removed outlier: 3.563A pdb=" N LEU D 363 " --> pdb=" O THR D 359 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS D 364 " --> pdb=" O LEU D 360 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASP D 365 " --> pdb=" O PRO D 361 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN D 366 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN D 374 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 378 Processing helix chain 'D' and resid 388 through 409 removed outlier: 3.609A pdb=" N GLU D 409 " --> pdb=" O LEU D 405 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 95 removed outlier: 3.655A pdb=" N GLN A 77 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ALA A 55 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ALA A 67 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP A 63 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N LEU A 115 " --> pdb=" O PRO A 102 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU A 117 " --> pdb=" O GLU A 100 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLU A 100 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLN A 119 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 174 removed outlier: 3.690A pdb=" N THR A 172 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY A 199 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N CYS A 197 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL A 242 " --> pdb=" O SER A 227 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N PHE A 222 " --> pdb=" O CYS A 218 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N CYS A 218 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 33 through 34 removed outlier: 4.300A pdb=" N CYS B 197 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL B 242 " --> pdb=" O SER B 227 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU B 216 " --> pdb=" O ARG B 223 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ALA B 151 " --> pdb=" O PRO B 215 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 217 " --> pdb=" O GLN B 149 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN B 149 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 93 through 95 removed outlier: 3.729A pdb=" N GLN B 77 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 46 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA B 57 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B 59 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP B 63 " --> pdb=" O ILE B 59 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU B 117 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLU B 100 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N GLN B 119 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 23 through 24 removed outlier: 3.913A pdb=" N ILE E 23 " --> pdb=" O TYR E 207 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR E 207 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL E 204 " --> pdb=" O THR E 164 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N THR E 164 " --> pdb=" O VAL E 204 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER E 206 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LYS E 210 " --> pdb=" O VAL E 158 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N VAL E 158 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU E 212 " --> pdb=" O TYR E 156 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N TYR E 156 " --> pdb=" O LEU E 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 48 through 57 removed outlier: 7.279A pdb=" N LEU E 39 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N HIS E 38 " --> pdb=" O VAL E 158 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL E 158 " --> pdb=" O HIS E 38 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN E 154 " --> pdb=" O GLU E 42 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N TYR E 156 " --> pdb=" O LEU E 212 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU E 212 " --> pdb=" O TYR E 156 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N VAL E 158 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LYS E 210 " --> pdb=" O VAL E 158 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER E 206 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N THR E 164 " --> pdb=" O VAL E 204 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL E 204 " --> pdb=" O THR E 164 " (cutoff:3.500A) 272 hydrogen bonds defined for protein. 759 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2525 1.35 - 1.47: 1557 1.47 - 1.59: 3518 1.59 - 1.71: 0 1.71 - 1.82: 83 Bond restraints: 7683 Sorted by residual: bond pdb=" N ARG A 50 " pdb=" CA ARG A 50 " ideal model delta sigma weight residual 1.458 1.481 -0.024 1.33e-02 5.65e+03 3.12e+00 bond pdb=" CB PRO B 215 " pdb=" CG PRO B 215 " ideal model delta sigma weight residual 1.492 1.554 -0.062 5.00e-02 4.00e+02 1.55e+00 bond pdb=" CB PRO B 136 " pdb=" CG PRO B 136 " ideal model delta sigma weight residual 1.492 1.553 -0.061 5.00e-02 4.00e+02 1.50e+00 bond pdb=" CB GLU E 377 " pdb=" CG GLU E 377 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.08e+00 bond pdb=" CB VAL B 242 " pdb=" CG2 VAL B 242 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.41e-01 ... (remaining 7678 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 10118 1.70 - 3.39: 196 3.39 - 5.09: 33 5.09 - 6.78: 7 6.78 - 8.48: 5 Bond angle restraints: 10359 Sorted by residual: angle pdb=" N ARG A 50 " pdb=" CA ARG A 50 " pdb=" C ARG A 50 " ideal model delta sigma weight residual 112.54 108.57 3.97 1.22e+00 6.72e-01 1.06e+01 angle pdb=" CA PRO B 215 " pdb=" N PRO B 215 " pdb=" CD PRO B 215 " ideal model delta sigma weight residual 112.00 107.52 4.48 1.40e+00 5.10e-01 1.02e+01 angle pdb=" N ILE B 85 " pdb=" CA ILE B 85 " pdb=" C ILE B 85 " ideal model delta sigma weight residual 112.96 109.85 3.11 1.00e+00 1.00e+00 9.66e+00 angle pdb=" CA GLY A 229 " pdb=" C GLY A 229 " pdb=" N LEU A 230 " ideal model delta sigma weight residual 114.84 118.02 -3.18 1.06e+00 8.90e-01 8.97e+00 angle pdb=" CA PRO B 136 " pdb=" N PRO B 136 " pdb=" CD PRO B 136 " ideal model delta sigma weight residual 112.00 107.86 4.14 1.40e+00 5.10e-01 8.73e+00 ... (remaining 10354 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 3924 17.37 - 34.75: 616 34.75 - 52.12: 180 52.12 - 69.49: 33 69.49 - 86.86: 14 Dihedral angle restraints: 4767 sinusoidal: 1989 harmonic: 2778 Sorted by residual: dihedral pdb=" CB CYS B 179 " pdb=" SG CYS B 179 " pdb=" SG CYS B 197 " pdb=" CB CYS B 197 " ideal model delta sinusoidal sigma weight residual 93.00 43.67 49.33 1 1.00e+01 1.00e-02 3.34e+01 dihedral pdb=" CB CYS B 148 " pdb=" SG CYS B 148 " pdb=" SG CYS B 218 " pdb=" CB CYS B 218 " ideal model delta sinusoidal sigma weight residual 93.00 54.19 38.81 1 1.00e+01 1.00e-02 2.12e+01 dihedral pdb=" CA CYS A 208 " pdb=" CB CYS A 208 " pdb=" SG CYS A 208 " pdb=" SG CYS A 234 " ideal model delta sinusoidal sigma weight residual 79.00 18.25 60.75 1 2.00e+01 2.50e-03 1.23e+01 ... (remaining 4764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 731 0.030 - 0.059: 302 0.059 - 0.089: 75 0.089 - 0.119: 70 0.119 - 0.149: 7 Chirality restraints: 1185 Sorted by residual: chirality pdb=" CB VAL E 400 " pdb=" CA VAL E 400 " pdb=" CG1 VAL E 400 " pdb=" CG2 VAL E 400 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CB VAL A 242 " pdb=" CA VAL A 242 " pdb=" CG1 VAL A 242 " pdb=" CG2 VAL A 242 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA VAL B 225 " pdb=" N VAL B 225 " pdb=" C VAL B 225 " pdb=" CB VAL B 225 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.16e-01 ... (remaining 1182 not shown) Planarity restraints: 1330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 135 " 0.066 5.00e-02 4.00e+02 9.75e-02 1.52e+01 pdb=" N PRO B 136 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO B 136 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 136 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 214 " 0.042 5.00e-02 4.00e+02 6.21e-02 6.17e+00 pdb=" N PRO B 215 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 215 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 215 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 36 " 0.040 5.00e-02 4.00e+02 5.98e-02 5.71e+00 pdb=" N PRO B 37 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 37 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 37 " 0.033 5.00e-02 4.00e+02 ... (remaining 1327 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 221 2.68 - 3.24: 7459 3.24 - 3.79: 12213 3.79 - 4.35: 16525 4.35 - 4.90: 26654 Nonbonded interactions: 63072 Sorted by model distance: nonbonded pdb=" O ALA B 151 " pdb=" OG SER B 214 " model vdw 2.128 3.040 nonbonded pdb=" O LEU B 48 " pdb=" OG SER B 76 " model vdw 2.139 3.040 nonbonded pdb=" O SER A 47 " pdb=" OG SER A 47 " model vdw 2.199 3.040 nonbonded pdb=" O GLN E 366 " pdb=" OG SER E 369 " model vdw 2.209 3.040 nonbonded pdb=" NE ARG A 50 " pdb=" OD2 ASP E 250 " model vdw 2.217 3.120 ... (remaining 63067 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.530 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 7691 Z= 0.136 Angle : 0.610 8.480 10375 Z= 0.320 Chirality : 0.041 0.149 1185 Planarity : 0.005 0.098 1330 Dihedral : 18.338 86.864 2941 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.35 % Allowed : 35.77 % Favored : 63.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.28), residues: 947 helix: 0.05 (0.33), residues: 252 sheet: -1.30 (0.47), residues: 136 loop : -0.43 (0.28), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 225 TYR 0.009 0.001 TYR E 387 PHE 0.033 0.001 PHE A 228 TRP 0.024 0.002 TRP A 162 HIS 0.003 0.001 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 7683) covalent geometry : angle 0.60884 / 0.32 (10359) SS BOND : bond 0.00384 / 0.18 ( 8) SS BOND : angle 1.00504 / 0.62 ( 16) hydrogen bonds : bond 0.27375 / 18.91 ( 269) hydrogen bonds : angle 9.50728 / 6.50 ( 759) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 149 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 16 MET cc_start: 0.0961 (tpt) cc_final: 0.0693 (tpt) REVERT: E 51 HIS cc_start: 0.7342 (m170) cc_final: 0.6817 (m170) outliers start: 3 outliers final: 0 residues processed: 150 average time/residue: 0.0917 time to fit residues: 18.5296 Evaluate side-chains 105 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.3980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 366 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.085792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.064815 restraints weight = 30502.639| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 4.75 r_work: 0.3222 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7691 Z= 0.224 Angle : 0.723 9.243 10375 Z= 0.367 Chirality : 0.044 0.154 1185 Planarity : 0.005 0.043 1330 Dihedral : 4.350 17.849 1029 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 6.02 % Allowed : 28.81 % Favored : 65.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.28), residues: 947 helix: -0.09 (0.29), residues: 287 sheet: -1.54 (0.42), residues: 147 loop : -0.48 (0.30), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 182 TYR 0.011 0.002 TYR B 103 PHE 0.022 0.002 PHE A 228 TRP 0.011 0.001 TRP A 162 HIS 0.005 0.001 HIS E 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.22 ( 7683) covalent geometry : angle 0.72175 / 0.37 (10359) SS BOND : bond 0.00424 / 0.19 ( 8) SS BOND : angle 1.16221 / 0.72 ( 16) hydrogen bonds : bond 0.05306 / 3.58 ( 269) hydrogen bonds : angle 6.75218 / 4.69 ( 759) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 125 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.9548 (mmm) cc_final: 0.9112 (mmt) REVERT: A 219 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8662 (mp0) REVERT: B 147 MET cc_start: 0.8509 (tpp) cc_final: 0.8226 (mmm) REVERT: E 16 MET cc_start: 0.2193 (tpt) cc_final: 0.1760 (tpt) REVERT: E 163 GLU cc_start: 0.4967 (OUTLIER) cc_final: 0.4638 (mp0) REVERT: E 220 MET cc_start: 0.3805 (tpp) cc_final: 0.3362 (mmm) REVERT: E 326 LEU cc_start: 0.8974 (tp) cc_final: 0.8762 (tt) REVERT: E 371 MET cc_start: 0.7071 (ttp) cc_final: 0.6758 (ttp) outliers start: 51 outliers final: 21 residues processed: 164 average time/residue: 0.0859 time to fit residues: 19.4051 Evaluate side-chains 131 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 398 TYR Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 403 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: [27, 63, 59, 22, 80, 82, 85, 74, 75, 36, 66] chunk 27 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 GLN E 374 ASN D 295 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.085488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.064656 restraints weight = 30314.044| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 4.62 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7691 Z= 0.183 Angle : 0.680 8.963 10375 Z= 0.341 Chirality : 0.043 0.176 1185 Planarity : 0.004 0.042 1330 Dihedral : 4.333 19.250 1029 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.25 % Allowed : 30.34 % Favored : 65.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.28), residues: 947 helix: 0.20 (0.30), residues: 287 sheet: -1.25 (0.47), residues: 124 loop : -0.50 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 182 TYR 0.017 0.002 TYR E 156 PHE 0.017 0.001 PHE A 228 TRP 0.009 0.001 TRP E 375 HIS 0.004 0.001 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 ( 7683) covalent geometry : angle 0.67886 / 0.34 (10359) SS BOND : bond 0.00369 / 0.16 ( 8) SS BOND : angle 1.03300 / 0.64 ( 16) hydrogen bonds : bond 0.04304 / 2.87 ( 269) hydrogen bonds : angle 6.20273 / 4.29 ( 759) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7629 (mmm) cc_final: 0.7370 (mmp) REVERT: B 34 GLU cc_start: 0.8193 (pp20) cc_final: 0.7982 (tm-30) REVERT: E 1 MET cc_start: 0.6365 (mmm) cc_final: 0.5429 (tpt) REVERT: E 16 MET cc_start: 0.1578 (tpt) cc_final: 0.1338 (tpt) REVERT: E 163 GLU cc_start: 0.4643 (OUTLIER) cc_final: 0.4359 (mp0) REVERT: E 220 MET cc_start: 0.3522 (tpp) cc_final: 0.3020 (mmm) REVERT: E 326 LEU cc_start: 0.8901 (tp) cc_final: 0.8676 (tt) outliers start: 36 outliers final: 18 residues processed: 145 average time/residue: 0.0882 time to fit residues: 17.4070 Evaluate side-chains 127 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 403 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: [70, 59, 66, 31, 55, 85, 33, 93, 89, 48, 83] chunk 70 optimal weight: 0.5980 chunk 59 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 85 optimal weight: 0.0040 chunk 33 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 223 HIS D 278 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.086215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.065326 restraints weight = 30232.213| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 4.70 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7691 Z= 0.134 Angle : 0.663 10.212 10375 Z= 0.327 Chirality : 0.043 0.162 1185 Planarity : 0.004 0.045 1330 Dihedral : 4.359 17.945 1029 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.84 % Allowed : 29.40 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.28), residues: 947 helix: 0.23 (0.30), residues: 293 sheet: -1.29 (0.46), residues: 126 loop : -0.46 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 182 TYR 0.011 0.001 TYR E 387 PHE 0.017 0.001 PHE A 228 TRP 0.027 0.001 TRP E 375 HIS 0.005 0.001 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 ( 7683) covalent geometry : angle 0.66199 / 0.33 (10359) SS BOND : bond 0.00512 / 0.25 ( 8) SS BOND : angle 1.26828 / 0.81 ( 16) hydrogen bonds : bond 0.03755 / 2.50 ( 269) hydrogen bonds : angle 5.91145 / 4.09 ( 759) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 119 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7626 (mmm) cc_final: 0.7373 (mmp) REVERT: E 1 MET cc_start: 0.6394 (mmm) cc_final: 0.5432 (tpt) REVERT: E 22 MET cc_start: 0.3540 (pmm) cc_final: 0.3254 (pmm) REVERT: E 220 MET cc_start: 0.3884 (tpp) cc_final: 0.3374 (mmm) REVERT: E 294 GLU cc_start: 0.8658 (pp20) cc_final: 0.8335 (pp20) REVERT: E 326 LEU cc_start: 0.8851 (tp) cc_final: 0.8629 (tt) outliers start: 41 outliers final: 24 residues processed: 156 average time/residue: 0.0769 time to fit residues: 16.6846 Evaluate side-chains 137 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 223 HIS Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 403 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: [9, 34, 41, 57, 45, 86, 32, 89, 12, 7, 15] chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 89 optimal weight: 0.2980 chunk 12 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 15 optimal weight: 0.5980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 ASN ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.085154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.064272 restraints weight = 30848.809| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 4.66 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7691 Z= 0.185 Angle : 0.666 8.456 10375 Z= 0.331 Chirality : 0.043 0.186 1185 Planarity : 0.004 0.048 1330 Dihedral : 4.335 17.481 1029 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 4.25 % Allowed : 28.81 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.28), residues: 947 helix: 0.19 (0.30), residues: 299 sheet: -1.40 (0.45), residues: 126 loop : -0.49 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 182 TYR 0.014 0.002 TYR B 103 PHE 0.014 0.002 PHE A 228 TRP 0.022 0.001 TRP E 375 HIS 0.010 0.001 HIS E 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 ( 7683) covalent geometry : angle 0.66466 / 0.33 (10359) SS BOND : bond 0.00423 / 0.20 ( 8) SS BOND : angle 1.13620 / 0.72 ( 16) hydrogen bonds : bond 0.03749 / 2.50 ( 269) hydrogen bonds : angle 5.77251 / 4.01 ( 759) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8661 (tpm170) cc_final: 0.8401 (tpm170) REVERT: A 95 MET cc_start: 0.7769 (mmm) cc_final: 0.7532 (mmp) REVERT: A 112 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7605 (mm-30) REVERT: E 1 MET cc_start: 0.6588 (mmm) cc_final: 0.5666 (tpt) REVERT: E 22 MET cc_start: 0.3570 (pmm) cc_final: 0.3270 (pmm) REVERT: E 163 GLU cc_start: 0.4556 (OUTLIER) cc_final: 0.4268 (mp0) REVERT: E 220 MET cc_start: 0.3991 (tpp) cc_final: 0.3112 (mmm) REVERT: E 326 LEU cc_start: 0.8873 (tp) cc_final: 0.8648 (tt) outliers start: 36 outliers final: 24 residues processed: 146 average time/residue: 0.0857 time to fit residues: 17.3417 Evaluate side-chains 131 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 51 HIS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 223 HIS Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 363 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: [18, 66, 63, 67, 53, 76, 3, 72, 29, 57, 91] chunk 18 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 63 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 0.0010 chunk 76 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 chunk 72 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.086094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.065471 restraints weight = 30488.958| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 4.63 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7691 Z= 0.131 Angle : 0.677 11.007 10375 Z= 0.329 Chirality : 0.042 0.175 1185 Planarity : 0.004 0.047 1330 Dihedral : 4.284 19.657 1029 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.66 % Allowed : 30.22 % Favored : 66.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.28), residues: 947 helix: 0.16 (0.30), residues: 300 sheet: -1.23 (0.46), residues: 124 loop : -0.47 (0.29), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 182 TYR 0.012 0.001 TYR D 387 PHE 0.014 0.001 PHE A 228 TRP 0.017 0.001 TRP E 375 HIS 0.007 0.001 HIS E 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 7683) covalent geometry : angle 0.67664 / 0.33 (10359) SS BOND : bond 0.00284 / 0.14 ( 8) SS BOND : angle 0.98741 / 0.63 ( 16) hydrogen bonds : bond 0.03555 / 2.38 ( 269) hydrogen bonds : angle 5.67918 / 3.93 ( 759) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7729 (mmm) cc_final: 0.7493 (mmp) REVERT: A 112 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7833 (mm-30) REVERT: E 1 MET cc_start: 0.6509 (mmm) cc_final: 0.5624 (tpt) REVERT: E 22 MET cc_start: 0.3434 (pmm) cc_final: 0.3201 (pmm) REVERT: E 163 GLU cc_start: 0.4392 (OUTLIER) cc_final: 0.4148 (mp0) REVERT: E 220 MET cc_start: 0.4034 (tpp) cc_final: 0.3183 (mmm) REVERT: E 326 LEU cc_start: 0.8844 (tp) cc_final: 0.8621 (tt) REVERT: E 365 ASP cc_start: 0.9376 (m-30) cc_final: 0.9109 (p0) REVERT: D 261 MET cc_start: 0.9101 (ttp) cc_final: 0.8873 (tmm) REVERT: D 293 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8990 (tt) outliers start: 31 outliers final: 22 residues processed: 146 average time/residue: 0.0840 time to fit residues: 16.8658 Evaluate side-chains 134 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 51 HIS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 363 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: [59, 51, 69, 68, 50, 71, 70, 56, 88, 30, 66] chunk 59 optimal weight: 20.0000 chunk 51 optimal weight: 7.9990 chunk 69 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 70 optimal weight: 0.3980 chunk 56 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 250 HIS ** 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 = 0.3975 r_free = 0.3975 target = 0.086592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.065489 restraints weight = 31466.424| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 4.80 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7691 Z= 0.141 Angle : 0.680 8.980 10375 Z= 0.333 Chirality : 0.043 0.189 1185 Planarity : 0.004 0.049 1330 Dihedral : 4.330 23.097 1029 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.37 % Allowed : 28.57 % Favored : 67.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.28), residues: 947 helix: 0.13 (0.30), residues: 299 sheet: -1.17 (0.45), residues: 124 loop : -0.50 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG E 290 TYR 0.013 0.002 TYR B 103 PHE 0.014 0.001 PHE D 337 TRP 0.014 0.001 TRP E 375 HIS 0.005 0.001 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 7683) covalent geometry : angle 0.67971 / 0.33 (10359) SS BOND : bond 0.00306 / 0.15 ( 8) SS BOND : angle 0.91299 / 0.57 ( 16) hydrogen bonds : bond 0.03416 / 2.22 ( 269) hydrogen bonds : angle 5.58687 / 3.89 ( 759) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8659 (tpm170) cc_final: 0.8423 (tpm170) REVERT: A 112 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7986 (mm-30) REVERT: E 1 MET cc_start: 0.6652 (mmm) cc_final: 0.5797 (tpt) REVERT: E 22 MET cc_start: 0.3537 (pmm) cc_final: 0.3264 (pmm) REVERT: E 220 MET cc_start: 0.4343 (tpp) cc_final: 0.3318 (mmm) REVERT: E 294 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8646 (tm-30) REVERT: E 326 LEU cc_start: 0.8828 (tp) cc_final: 0.8621 (tt) REVERT: E 365 ASP cc_start: 0.9381 (m-30) cc_final: 0.9101 (p0) REVERT: D 293 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8992 (tt) outliers start: 37 outliers final: 26 residues processed: 149 average time/residue: 0.0802 time to fit residues: 16.5813 Evaluate side-chains 136 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain E residue 37 PHE Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 51 HIS Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 350 PHE Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 363 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: [7, 36, 24, 53, 71, 85, 72, 13, 45, 76, 61] chunk 7 optimal weight: 0.0470 chunk 36 optimal weight: 7.9990 chunk 24 optimal weight: 0.5980 chunk 53 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 85 optimal weight: 0.0670 chunk 72 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 250 HIS ** 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 = 0.4001 r_free = 0.4001 target = 0.087721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.066646 restraints weight = 31478.583| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 4.85 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7691 Z= 0.125 Angle : 0.708 13.620 10375 Z= 0.340 Chirality : 0.044 0.203 1185 Planarity : 0.004 0.052 1330 Dihedral : 4.340 22.268 1029 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.42 % Allowed : 29.75 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.28), residues: 947 helix: 0.21 (0.30), residues: 298 sheet: -0.98 (0.48), residues: 112 loop : -0.44 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 290 TYR 0.009 0.001 TYR D 398 PHE 0.022 0.001 PHE D 337 TRP 0.015 0.001 TRP E 375 HIS 0.005 0.001 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.12 ( 7683) covalent geometry : angle 0.70764 / 0.34 (10359) SS BOND : bond 0.00312 / 0.16 ( 8) SS BOND : angle 0.86231 / 0.53 ( 16) hydrogen bonds : bond 0.03279 / 2.15 ( 269) hydrogen bonds : angle 5.43594 / 3.80 ( 759) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8572 (tpm170) cc_final: 0.8333 (tpm170) REVERT: A 95 MET cc_start: 0.7585 (mmm) cc_final: 0.7324 (mmp) REVERT: A 112 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8044 (mm-30) REVERT: B 112 GLU cc_start: 0.8293 (tp30) cc_final: 0.7919 (tp30) REVERT: E 1 MET cc_start: 0.6626 (mmm) cc_final: 0.5773 (tpt) REVERT: E 22 MET cc_start: 0.3459 (pmm) cc_final: 0.3181 (pmm) REVERT: E 220 MET cc_start: 0.4538 (tpp) cc_final: 0.3653 (mmm) REVERT: E 294 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8506 (tm-30) REVERT: E 349 GLN cc_start: 0.9186 (pp30) cc_final: 0.8711 (pp30) REVERT: E 365 ASP cc_start: 0.9369 (m-30) cc_final: 0.9093 (p0) REVERT: E 387 TYR cc_start: 0.6228 (OUTLIER) cc_final: 0.5832 (t80) REVERT: D 254 MET cc_start: 0.8111 (ptp) cc_final: 0.7865 (ptt) REVERT: D 293 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.9011 (tt) REVERT: D 296 ARG cc_start: 0.8954 (ttm-80) cc_final: 0.8744 (ttm-80) outliers start: 29 outliers final: 23 residues processed: 146 average time/residue: 0.0811 time to fit residues: 16.3259 Evaluate side-chains 141 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain E residue 37 PHE Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 350 PHE Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 363 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: [94, 82, 48, 64, 22, 59, 5, 7, 60, 41, 28] chunk 94 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 22 optimal weight: 0.4980 chunk 59 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.086760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.065095 restraints weight = 30891.577| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 5.02 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7691 Z= 0.143 Angle : 0.726 11.612 10375 Z= 0.354 Chirality : 0.043 0.184 1185 Planarity : 0.004 0.052 1330 Dihedral : 4.305 21.577 1029 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.42 % Allowed : 30.34 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.28), residues: 947 helix: 0.18 (0.30), residues: 304 sheet: -1.44 (0.47), residues: 118 loop : -0.40 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 202 TYR 0.010 0.001 TYR B 103 PHE 0.019 0.001 PHE D 337 TRP 0.015 0.001 TRP E 375 HIS 0.005 0.001 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 ( 7683) covalent geometry : angle 0.72604 / 0.35 (10359) SS BOND : bond 0.00292 / 0.15 ( 8) SS BOND : angle 0.84167 / 0.51 ( 16) hydrogen bonds : bond 0.03235 / 2.12 ( 269) hydrogen bonds : angle 5.40490 / 3.79 ( 759) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8748 (tpm170) cc_final: 0.8493 (tpm170) REVERT: A 95 MET cc_start: 0.7676 (mmm) cc_final: 0.7337 (mmp) REVERT: A 112 GLU cc_start: 0.8572 (mm-30) cc_final: 0.7890 (mm-30) REVERT: B 112 GLU cc_start: 0.8614 (tp30) cc_final: 0.8107 (tp30) REVERT: E 1 MET cc_start: 0.6858 (mmm) cc_final: 0.5913 (tpt) REVERT: E 22 MET cc_start: 0.3689 (pmm) cc_final: 0.3264 (pmm) REVERT: E 37 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.8047 (t80) REVERT: E 208 ARG cc_start: 0.4520 (OUTLIER) cc_final: 0.4167 (mtm-85) REVERT: E 220 MET cc_start: 0.4486 (tpp) cc_final: 0.3480 (mmm) REVERT: E 254 MET cc_start: 0.8498 (ppp) cc_final: 0.8262 (ppp) REVERT: E 294 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8753 (tm-30) REVERT: E 349 GLN cc_start: 0.9303 (pp30) cc_final: 0.8835 (pp30) REVERT: E 365 ASP cc_start: 0.9403 (m-30) cc_final: 0.9106 (p0) REVERT: E 387 TYR cc_start: 0.6484 (OUTLIER) cc_final: 0.6086 (t80) REVERT: D 254 MET cc_start: 0.8284 (ptp) cc_final: 0.8064 (ptt) REVERT: D 293 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8965 (tt) REVERT: D 296 ARG cc_start: 0.9119 (ttm-80) cc_final: 0.8899 (ttm-80) outliers start: 29 outliers final: 23 residues processed: 141 average time/residue: 0.0878 time to fit residues: 16.9326 Evaluate side-chains 143 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain E residue 37 PHE Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 350 PHE Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 363 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: [77, 13, 1, 68, 65, 9, 51, 46, 70, 16, 86] chunk 77 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 65 optimal weight: 0.3980 chunk 9 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 46 optimal weight: 8.9990 chunk 70 optimal weight: 0.3980 chunk 16 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.087040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.066104 restraints weight = 31502.075| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 4.82 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7691 Z= 0.139 Angle : 0.737 13.654 10375 Z= 0.355 Chirality : 0.043 0.207 1185 Planarity : 0.004 0.053 1330 Dihedral : 4.304 21.225 1029 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.42 % Allowed : 30.34 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.28), residues: 947 helix: 0.20 (0.30), residues: 305 sheet: -1.32 (0.51), residues: 106 loop : -0.46 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 290 TYR 0.010 0.001 TYR B 103 PHE 0.016 0.001 PHE D 337 TRP 0.015 0.001 TRP E 375 HIS 0.005 0.001 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 7683) covalent geometry : angle 0.73672 / 0.35 (10359) SS BOND : bond 0.00303 / 0.15 ( 8) SS BOND : angle 0.88464 / 0.53 ( 16) hydrogen bonds : bond 0.03194 / 2.11 ( 269) hydrogen bonds : angle 5.38440 / 3.78 ( 759) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7663 (mmm) cc_final: 0.7369 (mmp) REVERT: A 112 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8256 (mm-30) REVERT: A 147 MET cc_start: 0.8187 (tpt) cc_final: 0.7863 (tpp) REVERT: B 112 GLU cc_start: 0.8312 (tp30) cc_final: 0.7912 (tp30) REVERT: E 1 MET cc_start: 0.6656 (mmm) cc_final: 0.5782 (tpt) REVERT: E 22 MET cc_start: 0.3488 (pmm) cc_final: 0.3106 (pmm) REVERT: E 37 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.7940 (t80) REVERT: E 208 ARG cc_start: 0.4537 (OUTLIER) cc_final: 0.4179 (mtm-85) REVERT: E 220 MET cc_start: 0.4452 (tpp) cc_final: 0.3584 (mmm) REVERT: E 254 MET cc_start: 0.8319 (ppp) cc_final: 0.8102 (ppp) REVERT: E 294 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8519 (tm-30) REVERT: E 349 GLN cc_start: 0.9200 (pp30) cc_final: 0.8720 (pp30) REVERT: E 365 ASP cc_start: 0.9369 (m-30) cc_final: 0.9052 (p0) REVERT: E 387 TYR cc_start: 0.6256 (OUTLIER) cc_final: 0.5868 (t80) REVERT: D 293 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9014 (tt) REVERT: D 296 ARG cc_start: 0.8966 (ttm-80) cc_final: 0.8741 (ttm-80) outliers start: 29 outliers final: 21 residues processed: 146 average time/residue: 0.0852 time to fit residues: 16.9547 Evaluate side-chains 143 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain E residue 37 PHE Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 350 PHE Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 363 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: [74, 2, 90, 61, 91, 77, 89, 40, 69, 82, 60] chunk 74 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 40 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 GLN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.087071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.066050 restraints weight = 31083.203| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 4.80 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7691 Z= 0.141 Angle : 0.727 11.164 10375 Z= 0.351 Chirality : 0.043 0.207 1185 Planarity : 0.004 0.051 1330 Dihedral : 4.288 19.674 1029 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.19 % Allowed : 30.93 % Favored : 65.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.28), residues: 947 helix: 0.23 (0.30), residues: 304 sheet: -1.27 (0.51), residues: 106 loop : -0.45 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 290 TYR 0.014 0.001 TYR D 387 PHE 0.017 0.001 PHE D 337 TRP 0.015 0.001 TRP E 375 HIS 0.005 0.001 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 7683) covalent geometry : angle 0.72648 / 0.35 (10359) SS BOND : bond 0.00282 / 0.14 ( 8) SS BOND : angle 0.87758 / 0.53 ( 16) hydrogen bonds : bond 0.03144 / 2.07 ( 269) hydrogen bonds : angle 5.36029 / 3.77 ( 759) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1589.77 seconds wall clock time: 28 minutes 12.69 seconds (1692.69 seconds total)