Starting phenix.real_space_refine on Thu Sep 18 07:32:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vsu_43506/09_2025/8vsu_43506.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vsu_43506/09_2025/8vsu_43506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vsu_43506/09_2025/8vsu_43506.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vsu_43506/09_2025/8vsu_43506.map" model { file = "/net/cci-nas-00/data/ceres_data/8vsu_43506/09_2025/8vsu_43506.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vsu_43506/09_2025/8vsu_43506.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.102 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 41 5.16 5 C 4859 2.51 5 N 1301 2.21 5 O 1391 1.98 5 H 7646 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15240 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5458 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 9, 'TRANS': 318} Chain: "C" Number of atoms: 4900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 4900 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 21, 'TRANS': 285} Chain: "B" Number of atoms: 4855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 4855 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 17, 'TRANS': 288} Chain breaks: 1 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.03, per 1000 atoms: 0.20 Number of scatterers: 15240 At special positions: 0 Unit cell: (87.675, 88.51, 106.045, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 41 16.00 P 2 15.00 O 1391 8.00 N 1301 7.00 C 4859 6.00 H 7646 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 477.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1782 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 8 sheets defined 58.7% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 11 through 27 Processing helix chain 'A' and resid 32 through 56 removed outlier: 3.654A pdb=" N ALA A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 Processing helix chain 'A' and resid 78 through 86 Processing helix chain 'A' and resid 87 through 90 Processing helix chain 'A' and resid 91 through 107 removed outlier: 3.744A pdb=" N LYS A 96 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN A 104 " --> pdb=" O GLN A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 121 Processing helix chain 'A' and resid 124 through 133 removed outlier: 3.798A pdb=" N PHE A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 136 No H-bonds generated for 'chain 'A' and resid 134 through 136' Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 153 through 162 Processing helix chain 'A' and resid 163 through 167 removed outlier: 3.672A pdb=" N TYR A 167 " --> pdb=" O GLU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 177 through 194 removed outlier: 3.646A pdb=" N ASP A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 Processing helix chain 'A' and resid 206 through 219 removed outlier: 3.612A pdb=" N SER A 212 " --> pdb=" O ASP A 208 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LYS A 216 " --> pdb=" O SER A 212 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 218 " --> pdb=" O TYR A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 239 removed outlier: 3.629A pdb=" N ASP A 239 " --> pdb=" O GLU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 Processing helix chain 'A' and resid 252 through 263 removed outlier: 3.505A pdb=" N LEU A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 284 removed outlier: 3.546A pdb=" N VAL A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL A 280 " --> pdb=" O HIS A 276 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE A 281 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 282 " --> pdb=" O PHE A 278 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN A 284 " --> pdb=" O VAL A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 298 Processing helix chain 'A' and resid 298 through 307 Processing helix chain 'A' and resid 316 through 332 removed outlier: 3.886A pdb=" N ASN A 320 " --> pdb=" O ASP A 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 86 removed outlier: 3.532A pdb=" N ARG C 86 " --> pdb=" O LYS C 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 82 through 86' Processing helix chain 'C' and resid 90 through 103 Processing helix chain 'C' and resid 136 through 141 Processing helix chain 'C' and resid 149 through 170 removed outlier: 3.575A pdb=" N GLY C 155 " --> pdb=" O CYS C 151 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN C 159 " --> pdb=" O GLY C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 194 through 198 removed outlier: 4.308A pdb=" N VAL C 197 " --> pdb=" O ASP C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 233 through 251 removed outlier: 3.585A pdb=" N ASP C 237 " --> pdb=" O GLY C 233 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TRP C 239 " --> pdb=" O LYS C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 269 Processing helix chain 'C' and resid 279 through 289 Processing helix chain 'C' and resid 299 through 306 Processing helix chain 'C' and resid 306 through 311 Processing helix chain 'C' and resid 337 through 345 Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 105 through 107 No H-bonds generated for 'chain 'B' and resid 105 through 107' Processing helix chain 'B' and resid 108 through 125 removed outlier: 3.859A pdb=" N GLU B 118 " --> pdb=" O PHE B 114 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 160 Processing helix chain 'B' and resid 168 through 189 removed outlier: 3.602A pdb=" N TYR B 185 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 217 Processing helix chain 'B' and resid 237 through 244 removed outlier: 3.748A pdb=" N LEU B 241 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Proline residue: B 242 - end of helix Processing helix chain 'B' and resid 245 through 250 Processing helix chain 'B' and resid 258 through 275 removed outlier: 4.281A pdb=" N ILE B 262 " --> pdb=" O ALA B 258 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR B 263 " --> pdb=" O LYS B 259 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER B 264 " --> pdb=" O SER B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 293 Processing helix chain 'B' and resid 349 through 359 Processing helix chain 'B' and resid 363 through 367 Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'B' and resid 375 through 382 removed outlier: 6.085A pdb=" N PHE B 378 " --> pdb=" O ASN B 375 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN B 381 " --> pdb=" O PHE B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 394 Proline residue: B 391 - end of helix Processing sheet with id=AA1, first strand: chain 'C' and resid 45 through 46 removed outlier: 4.987A pdb=" N GLU C 65 " --> pdb=" O GLY C 52 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LEU C 54 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL C 63 " --> pdb=" O LEU C 54 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS C 62 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LYS C 124 " --> pdb=" O TYR C 118 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N TYR C 118 " --> pdb=" O LYS C 124 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TYR C 126 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL C 116 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL C 128 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 134 through 135 removed outlier: 3.781A pdb=" N CYS C 134 " --> pdb=" O LEU C 184 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 172 through 173 Processing sheet with id=AA4, first strand: chain 'C' and resid 209 through 210 Processing sheet with id=AA5, first strand: chain 'B' and resid 69 through 78 removed outlier: 6.809A pdb=" N LEU B 87 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL B 74 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N VAL B 85 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N GLY B 76 " --> pdb=" O MET B 83 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N MET B 83 " --> pdb=" O GLY B 76 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 135 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N SER B 148 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N TYR B 133 " --> pdb=" O SER B 148 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 Processing sheet with id=AA7, first strand: chain 'B' and resid 201 through 203 Processing sheet with id=AA8, first strand: chain 'B' and resid 221 through 222 363 hydrogen bonds defined for protein. 1032 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: 4.03 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.74 - 0.96: 22 0.96 - 1.17: 7608 1.17 - 1.39: 2601 1.39 - 1.60: 5111 1.60 - 1.82: 67 Bond restraints: 15409 Sorted by residual: bond pdb=" N LYS B 91 " pdb=" H LYS B 91 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CD2 TYR A 325 " pdb=" HD2 TYR A 325 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" NH1 ARG A 113 " pdb="HH11 ARG A 113 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CE1 TYR B 152 " pdb=" HE1 TYR B 152 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CE1 HIS C 313 " pdb=" HE1 HIS C 313 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 15404 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 24822 2.95 - 5.91: 2384 5.91 - 8.86: 703 8.86 - 11.81: 10 11.81 - 14.77: 13 Bond angle restraints: 27932 Sorted by residual: angle pdb=" CA ASP B 301 " pdb=" CB ASP B 301 " pdb=" CG ASP B 301 " ideal model delta sigma weight residual 112.60 117.73 -5.13 1.00e+00 1.00e+00 2.63e+01 angle pdb=" CA PHE C 298 " pdb=" CB PHE C 298 " pdb=" CG PHE C 298 " ideal model delta sigma weight residual 113.80 118.88 -5.08 1.00e+00 1.00e+00 2.58e+01 angle pdb=" O1B ADP B2001 " pdb=" PB ADP B2001 " pdb=" O2B ADP B2001 " ideal model delta sigma weight residual 119.90 105.13 14.77 3.00e+00 1.11e-01 2.42e+01 angle pdb=" CA PHE B 279 " pdb=" CB PHE B 279 " pdb=" CG PHE B 279 " ideal model delta sigma weight residual 113.80 118.48 -4.68 1.00e+00 1.00e+00 2.19e+01 angle pdb=" CA PHE C 148 " pdb=" CB PHE C 148 " pdb=" CG PHE C 148 " ideal model delta sigma weight residual 113.80 118.43 -4.63 1.00e+00 1.00e+00 2.14e+01 ... (remaining 27927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.69: 6808 21.69 - 43.37: 232 43.37 - 65.06: 164 65.06 - 86.74: 22 86.74 - 108.43: 2 Dihedral angle restraints: 7228 sinusoidal: 3975 harmonic: 3253 Sorted by residual: dihedral pdb=" CA GLY C 288 " pdb=" C GLY C 288 " pdb=" N MET C 289 " pdb=" CA MET C 289 " ideal model delta harmonic sigma weight residual 180.00 150.99 29.01 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" C5' ADP B2001 " pdb=" O5' ADP B2001 " pdb=" PA ADP B2001 " pdb=" O2A ADP B2001 " ideal model delta sinusoidal sigma weight residual -60.00 48.43 -108.43 1 2.00e+01 2.50e-03 3.16e+01 dihedral pdb=" CA GLN B 358 " pdb=" C GLN B 358 " pdb=" N CYS B 359 " pdb=" CA CYS B 359 " ideal model delta harmonic sigma weight residual 180.00 153.33 26.67 0 5.00e+00 4.00e-02 2.85e+01 ... (remaining 7225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 661 0.067 - 0.133: 363 0.133 - 0.200: 115 0.200 - 0.267: 19 0.267 - 0.334: 6 Chirality restraints: 1164 Sorted by residual: chirality pdb=" C2' ADP B2001 " pdb=" C1' ADP B2001 " pdb=" C3' ADP B2001 " pdb=" O2' ADP B2001 " both_signs ideal model delta sigma weight residual False -2.51 -2.84 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA SER C 193 " pdb=" N SER C 193 " pdb=" C SER C 193 " pdb=" CB SER C 193 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA SER B 195 " pdb=" N SER B 195 " pdb=" C SER B 195 " pdb=" CB SER B 195 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 1161 not shown) Planarity restraints: 2229 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 207 " 0.139 2.00e-02 2.50e+03 5.75e-02 9.92e+01 pdb=" CG TYR A 207 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR A 207 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR A 207 " -0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR A 207 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR A 207 " -0.037 2.00e-02 2.50e+03 pdb=" CZ TYR A 207 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 207 " 0.103 2.00e-02 2.50e+03 pdb=" HD1 TYR A 207 " -0.049 2.00e-02 2.50e+03 pdb=" HD2 TYR A 207 " -0.024 2.00e-02 2.50e+03 pdb=" HE1 TYR A 207 " -0.000 2.00e-02 2.50e+03 pdb=" HE2 TYR A 207 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 243 " 0.106 2.00e-02 2.50e+03 4.81e-02 9.25e+01 pdb=" CG TRP B 243 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP B 243 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP B 243 " -0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP B 243 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TRP B 243 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 243 " -0.057 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 243 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 243 " -0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP B 243 " 0.028 2.00e-02 2.50e+03 pdb=" HD1 TRP B 243 " -0.005 2.00e-02 2.50e+03 pdb=" HE1 TRP B 243 " -0.075 2.00e-02 2.50e+03 pdb=" HE3 TRP B 243 " -0.090 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 243 " 0.021 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 243 " -0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP B 243 " 0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 227 " 0.198 9.50e-02 1.11e+02 8.72e-02 7.75e+01 pdb=" NE ARG A 227 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG A 227 " 0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG A 227 " 0.026 2.00e-02 2.50e+03 pdb=" NH2 ARG A 227 " 0.015 2.00e-02 2.50e+03 pdb="HH11 ARG A 227 " -0.117 2.00e-02 2.50e+03 pdb="HH12 ARG A 227 " 0.095 2.00e-02 2.50e+03 pdb="HH21 ARG A 227 " -0.018 2.00e-02 2.50e+03 pdb="HH22 ARG A 227 " -0.062 2.00e-02 2.50e+03 ... (remaining 2226 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 778 2.18 - 2.79: 26413 2.79 - 3.39: 41785 3.39 - 4.00: 55814 4.00 - 4.60: 81224 Nonbonded interactions: 206014 Sorted by model distance: nonbonded pdb=" OD2 ASP C 208 " pdb=" HG SER C 232 " model vdw 1.577 2.450 nonbonded pdb=" OD1 ASP B 301 " pdb=" HG SER B 303 " model vdw 1.597 2.450 nonbonded pdb=" OD1 ASP C 207 " pdb=" HG1 THR C 209 " model vdw 1.609 2.450 nonbonded pdb=" OE1 GLU C 65 " pdb=" HG1 THR C 336 " model vdw 1.614 2.450 nonbonded pdb=" HH TYR A 223 " pdb=" OE1 GLU B 105 " model vdw 1.618 2.450 ... (remaining 206009 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 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: 0.090 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.360 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 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 : 0.013 0.141 7763 Z= 0.767 Angle : 1.761 14.765 10493 Z= 1.194 Chirality : 0.086 0.334 1164 Planarity : 0.013 0.117 1339 Dihedral : 12.495 108.425 2943 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 0.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.12 % Allowed : 0.60 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.25), residues: 933 helix: -1.20 (0.20), residues: 478 sheet: -0.48 (0.52), residues: 87 loop : 0.04 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 100 TYR 0.119 0.016 TYR A 207 PHE 0.052 0.010 PHE A 188 TRP 0.067 0.013 TRP B 243 HIS 0.010 0.002 HIS B 200 Details of bonding type rmsd covalent geometry : bond 0.01258 ( 7763) covalent geometry : angle 1.76097 (10493) hydrogen bonds : bond 0.22313 ( 363) hydrogen bonds : angle 6.73502 ( 1032) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 0.484 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 257 LYS cc_start: 0.8469 (mttt) cc_final: 0.8250 (mtmt) REVERT: C 104 ARG cc_start: 0.7980 (ptt90) cc_final: 0.7401 (mmt90) REVERT: B 287 MET cc_start: 0.8750 (tmm) cc_final: 0.8542 (tmm) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 1.6247 time to fit residues: 275.0031 Evaluate side-chains 117 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A 329 GLN C 220 GLN B 227 GLN B 286 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.132301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.101127 restraints weight = 26691.944| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.10 r_work: 0.3085 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 7763 Z= 0.154 Angle : 0.614 6.966 10493 Z= 0.330 Chirality : 0.042 0.149 1164 Planarity : 0.005 0.046 1339 Dihedral : 7.087 118.507 1030 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.79 % Allowed : 6.44 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.27), residues: 933 helix: 0.55 (0.24), residues: 479 sheet: -0.17 (0.55), residues: 75 loop : 0.16 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 148 TYR 0.011 0.001 TYR C 246 PHE 0.025 0.002 PHE A 188 TRP 0.004 0.001 TRP C 308 HIS 0.006 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 7763) covalent geometry : angle 0.61399 (10493) hydrogen bonds : bond 0.06503 ( 363) hydrogen bonds : angle 4.76211 ( 1032) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 GLN cc_start: 0.7950 (mt0) cc_final: 0.7727 (mt0) REVERT: A 72 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7837 (tp-100) REVERT: A 215 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7297 (pp20) REVERT: A 257 LYS cc_start: 0.8323 (mttt) cc_final: 0.7835 (mtmt) REVERT: C 42 ARG cc_start: 0.7502 (ttp-110) cc_final: 0.7180 (tpt170) REVERT: C 262 LYS cc_start: 0.8221 (mmmm) cc_final: 0.7856 (mttt) REVERT: C 271 SER cc_start: 0.8916 (t) cc_final: 0.8608 (m) REVERT: B 247 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7626 (pm20) REVERT: B 287 MET cc_start: 0.8795 (tmm) cc_final: 0.8520 (tmm) REVERT: B 362 ARG cc_start: 0.7865 (ttt180) cc_final: 0.7598 (ttm-80) outliers start: 15 outliers final: 5 residues processed: 125 average time/residue: 1.6271 time to fit residues: 212.9738 Evaluate side-chains 106 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 247 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 91 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN C 220 GLN B 225 GLN B 227 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.132189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.101611 restraints weight = 26663.979| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.04 r_work: 0.3078 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7763 Z= 0.161 Angle : 0.566 5.956 10493 Z= 0.297 Chirality : 0.041 0.152 1164 Planarity : 0.004 0.049 1339 Dihedral : 6.437 114.531 1030 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 0.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.79 % Allowed : 7.88 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.27), residues: 933 helix: 1.11 (0.24), residues: 482 sheet: -0.32 (0.58), residues: 75 loop : -0.03 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 333 TYR 0.014 0.001 TYR C 246 PHE 0.021 0.002 PHE A 188 TRP 0.007 0.001 TRP C 239 HIS 0.013 0.001 HIS B 162 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 7763) covalent geometry : angle 0.56613 (10493) hydrogen bonds : bond 0.05454 ( 363) hydrogen bonds : angle 4.23803 ( 1032) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.7597 (tp30) cc_final: 0.7377 (tp30) REVERT: A 72 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.8040 (tp-100) REVERT: A 215 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7251 (pp20) REVERT: A 257 LYS cc_start: 0.8348 (mttt) cc_final: 0.7869 (mtmt) REVERT: C 42 ARG cc_start: 0.7573 (ttp-110) cc_final: 0.7218 (tpt90) REVERT: C 262 LYS cc_start: 0.8276 (mmmm) cc_final: 0.7930 (mttt) REVERT: C 271 SER cc_start: 0.8959 (t) cc_final: 0.8709 (m) REVERT: B 247 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7729 (pm20) REVERT: B 287 MET cc_start: 0.8765 (tmm) cc_final: 0.8562 (tmm) REVERT: B 362 ARG cc_start: 0.7910 (ttt180) cc_final: 0.7670 (ttm-80) REVERT: B 390 LEU cc_start: 0.6674 (OUTLIER) cc_final: 0.6469 (tt) outliers start: 15 outliers final: 4 residues processed: 111 average time/residue: 1.5268 time to fit residues: 177.8598 Evaluate side-chains 101 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 22 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN C 345 HIS B 141 ASN B 227 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.132764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.102131 restraints weight = 26585.601| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.04 r_work: 0.3098 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7763 Z= 0.118 Angle : 0.507 5.833 10493 Z= 0.261 Chirality : 0.039 0.150 1164 Planarity : 0.004 0.045 1339 Dihedral : 6.034 109.489 1030 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 0.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.19 % Allowed : 9.07 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.28), residues: 933 helix: 1.54 (0.25), residues: 484 sheet: -0.39 (0.58), residues: 75 loop : -0.06 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 333 TYR 0.009 0.001 TYR C 246 PHE 0.017 0.001 PHE A 188 TRP 0.004 0.001 TRP C 239 HIS 0.005 0.001 HIS B 162 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 7763) covalent geometry : angle 0.50655 (10493) hydrogen bonds : bond 0.04456 ( 363) hydrogen bonds : angle 3.97592 ( 1032) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 257 LYS cc_start: 0.8292 (mttt) cc_final: 0.7811 (mtmt) REVERT: C 42 ARG cc_start: 0.7532 (ttp-110) cc_final: 0.7225 (tpt90) REVERT: C 45 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8738 (mp) REVERT: C 262 LYS cc_start: 0.8259 (mmmm) cc_final: 0.7933 (mttt) REVERT: C 271 SER cc_start: 0.8963 (t) cc_final: 0.8712 (m) REVERT: B 362 ARG cc_start: 0.7927 (ttt180) cc_final: 0.7693 (ttm-80) REVERT: B 380 LYS cc_start: 0.8053 (mttm) cc_final: 0.7628 (mtmp) REVERT: B 390 LEU cc_start: 0.6735 (OUTLIER) cc_final: 0.6461 (tt) outliers start: 10 outliers final: 3 residues processed: 103 average time/residue: 1.6639 time to fit residues: 179.4937 Evaluate side-chains 99 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 0.1980 chunk 11 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 289 GLN B 141 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.132994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.102384 restraints weight = 26516.064| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.04 r_work: 0.2897 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7763 Z= 0.112 Angle : 0.498 6.002 10493 Z= 0.254 Chirality : 0.039 0.144 1164 Planarity : 0.004 0.044 1339 Dihedral : 5.748 101.366 1030 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.95 % Allowed : 9.79 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.28), residues: 933 helix: 1.91 (0.25), residues: 478 sheet: -0.37 (0.59), residues: 75 loop : -0.04 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 134 TYR 0.009 0.001 TYR C 246 PHE 0.017 0.001 PHE A 188 TRP 0.004 0.001 TRP C 239 HIS 0.004 0.001 HIS B 162 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 7763) covalent geometry : angle 0.49771 (10493) hydrogen bonds : bond 0.04164 ( 363) hydrogen bonds : angle 3.86476 ( 1032) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7193 (tm-30) REVERT: A 257 LYS cc_start: 0.8045 (mttt) cc_final: 0.7529 (mtmt) REVERT: A 289 GLN cc_start: 0.7815 (tp40) cc_final: 0.7365 (tp-100) REVERT: A 293 ASP cc_start: 0.7768 (m-30) cc_final: 0.7500 (m-30) REVERT: C 42 ARG cc_start: 0.7564 (ttp-110) cc_final: 0.7082 (tpt90) REVERT: C 262 LYS cc_start: 0.8058 (mmmm) cc_final: 0.7718 (mttt) REVERT: C 271 SER cc_start: 0.8950 (t) cc_final: 0.8630 (m) REVERT: B 362 ARG cc_start: 0.8007 (ttt180) cc_final: 0.7698 (ttm-80) REVERT: B 380 LYS cc_start: 0.7818 (mttm) cc_final: 0.7347 (mtmp) REVERT: B 390 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.6232 (tt) outliers start: 8 outliers final: 3 residues processed: 101 average time/residue: 1.5544 time to fit residues: 164.8754 Evaluate side-chains 101 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 47 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.131064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.100572 restraints weight = 26559.025| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.02 r_work: 0.2884 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7763 Z= 0.139 Angle : 0.510 6.311 10493 Z= 0.262 Chirality : 0.040 0.147 1164 Planarity : 0.004 0.045 1339 Dihedral : 5.702 93.119 1030 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.19 % Allowed : 10.26 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.28), residues: 933 helix: 1.89 (0.25), residues: 478 sheet: -0.34 (0.60), residues: 75 loop : -0.06 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 134 TYR 0.010 0.001 TYR C 246 PHE 0.020 0.001 PHE A 188 TRP 0.004 0.001 TRP C 239 HIS 0.005 0.001 HIS B 193 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 7763) covalent geometry : angle 0.51003 (10493) hydrogen bonds : bond 0.04517 ( 363) hydrogen bonds : angle 3.86927 ( 1032) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7154 (tm-30) REVERT: A 215 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7311 (pp20) REVERT: A 257 LYS cc_start: 0.8058 (mttt) cc_final: 0.7539 (mtmt) REVERT: C 42 ARG cc_start: 0.7531 (ttp-170) cc_final: 0.7063 (tpt90) REVERT: C 262 LYS cc_start: 0.8116 (mmmm) cc_final: 0.7763 (mttt) REVERT: C 271 SER cc_start: 0.8956 (t) cc_final: 0.8633 (m) REVERT: B 81 ASP cc_start: 0.8623 (t0) cc_final: 0.7931 (t0) REVERT: B 362 ARG cc_start: 0.8022 (ttt180) cc_final: 0.7706 (ttm-80) REVERT: B 380 LYS cc_start: 0.7789 (mttm) cc_final: 0.7289 (mtmp) REVERT: B 390 LEU cc_start: 0.6465 (OUTLIER) cc_final: 0.6255 (tt) outliers start: 10 outliers final: 5 residues processed: 105 average time/residue: 1.5393 time to fit residues: 169.9660 Evaluate side-chains 103 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 36 optimal weight: 0.1980 chunk 65 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.133815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.103302 restraints weight = 26205.103| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.04 r_work: 0.2916 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 7763 Z= 0.095 Angle : 0.480 6.188 10493 Z= 0.241 Chirality : 0.038 0.147 1164 Planarity : 0.004 0.042 1339 Dihedral : 5.429 92.396 1030 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 0.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.72 % Allowed : 11.46 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.28), residues: 933 helix: 2.18 (0.25), residues: 478 sheet: -0.30 (0.60), residues: 75 loop : 0.02 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 134 TYR 0.007 0.001 TYR C 246 PHE 0.013 0.001 PHE A 188 TRP 0.003 0.000 TRP B 144 HIS 0.003 0.001 HIS B 162 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 7763) covalent geometry : angle 0.48029 (10493) hydrogen bonds : bond 0.03662 ( 363) hydrogen bonds : angle 3.69716 ( 1032) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 257 LYS cc_start: 0.8053 (mttt) cc_final: 0.7559 (mtmt) REVERT: C 42 ARG cc_start: 0.7488 (ttp-170) cc_final: 0.7043 (tpt90) REVERT: C 162 ASP cc_start: 0.8283 (m-30) cc_final: 0.7952 (m-30) REVERT: C 262 LYS cc_start: 0.8101 (mmmm) cc_final: 0.7739 (mttt) REVERT: C 271 SER cc_start: 0.8955 (t) cc_final: 0.8623 (m) REVERT: B 362 ARG cc_start: 0.8024 (ttt180) cc_final: 0.7699 (ttm-80) REVERT: B 380 LYS cc_start: 0.7720 (mttm) cc_final: 0.7233 (mtmp) REVERT: B 390 LEU cc_start: 0.6504 (OUTLIER) cc_final: 0.6263 (tt) outliers start: 6 outliers final: 2 residues processed: 102 average time/residue: 1.4407 time to fit residues: 155.0471 Evaluate side-chains 99 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 96 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 3 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.132545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.101933 restraints weight = 26796.053| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.04 r_work: 0.3035 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7763 Z= 0.103 Angle : 0.480 6.394 10493 Z= 0.242 Chirality : 0.039 0.144 1164 Planarity : 0.004 0.042 1339 Dihedral : 5.342 81.281 1030 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 0.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.84 % Allowed : 11.46 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.28), residues: 933 helix: 2.25 (0.25), residues: 478 sheet: -0.51 (0.55), residues: 85 loop : 0.09 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 171 TYR 0.008 0.001 TYR C 246 PHE 0.016 0.001 PHE A 188 TRP 0.004 0.001 TRP C 239 HIS 0.003 0.001 HIS B 193 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 7763) covalent geometry : angle 0.48002 (10493) hydrogen bonds : bond 0.03803 ( 363) hydrogen bonds : angle 3.67779 ( 1032) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 LYS cc_start: 0.8251 (mttt) cc_final: 0.7791 (mtmt) REVERT: A 288 THR cc_start: 0.8350 (OUTLIER) cc_final: 0.8109 (p) REVERT: C 42 ARG cc_start: 0.7501 (ttp-170) cc_final: 0.7153 (tpt90) REVERT: C 162 ASP cc_start: 0.8332 (m-30) cc_final: 0.8006 (m-30) REVERT: C 262 LYS cc_start: 0.8284 (mmmm) cc_final: 0.7911 (mttt) REVERT: C 271 SER cc_start: 0.8978 (t) cc_final: 0.8698 (m) REVERT: B 362 ARG cc_start: 0.8000 (ttt180) cc_final: 0.7744 (ttm-80) REVERT: B 380 LYS cc_start: 0.7836 (mttm) cc_final: 0.7348 (mtmp) REVERT: B 390 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6399 (tt) outliers start: 7 outliers final: 2 residues processed: 103 average time/residue: 1.4805 time to fit residues: 160.6385 Evaluate side-chains 101 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 21 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 78 optimal weight: 0.1980 chunk 59 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.133486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.102963 restraints weight = 26466.044| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.03 r_work: 0.2927 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7763 Z= 0.094 Angle : 0.475 6.446 10493 Z= 0.238 Chirality : 0.038 0.146 1164 Planarity : 0.004 0.041 1339 Dihedral : 5.158 75.081 1030 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 0.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.48 % Allowed : 11.69 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.28), residues: 933 helix: 2.36 (0.25), residues: 479 sheet: -0.45 (0.55), residues: 85 loop : 0.13 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 134 TYR 0.007 0.001 TYR C 246 PHE 0.013 0.001 PHE A 188 TRP 0.003 0.001 TRP B 144 HIS 0.002 0.000 HIS B 193 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 7763) covalent geometry : angle 0.47545 (10493) hydrogen bonds : bond 0.03535 ( 363) hydrogen bonds : angle 3.61308 ( 1032) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 101 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 257 LYS cc_start: 0.8063 (mttt) cc_final: 0.7573 (mtmt) REVERT: A 288 THR cc_start: 0.8230 (OUTLIER) cc_final: 0.7964 (p) REVERT: A 293 ASP cc_start: 0.7625 (m-30) cc_final: 0.7374 (m-30) REVERT: C 42 ARG cc_start: 0.7522 (ttp-170) cc_final: 0.7068 (tpt90) REVERT: C 262 LYS cc_start: 0.8128 (mmmm) cc_final: 0.7754 (mttt) REVERT: C 271 SER cc_start: 0.8974 (t) cc_final: 0.8636 (m) REVERT: B 140 ASP cc_start: 0.7600 (t70) cc_final: 0.7359 (t70) REVERT: B 362 ARG cc_start: 0.8042 (ttt180) cc_final: 0.7729 (ttm-80) REVERT: B 380 LYS cc_start: 0.7698 (mttm) cc_final: 0.7202 (mtmp) REVERT: B 390 LEU cc_start: 0.6507 (OUTLIER) cc_final: 0.6239 (tt) outliers start: 4 outliers final: 2 residues processed: 103 average time/residue: 1.4576 time to fit residues: 158.1372 Evaluate side-chains 103 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 chunk 9 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.130957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.099392 restraints weight = 26649.880| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.16 r_work: 0.2876 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7763 Z= 0.147 Angle : 0.519 6.878 10493 Z= 0.263 Chirality : 0.040 0.143 1164 Planarity : 0.004 0.044 1339 Dihedral : 5.149 65.723 1030 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.48 % Allowed : 12.05 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.28), residues: 933 helix: 2.22 (0.25), residues: 477 sheet: -0.48 (0.56), residues: 85 loop : 0.04 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 333 TYR 0.011 0.001 TYR C 246 PHE 0.022 0.001 PHE A 188 TRP 0.004 0.001 TRP C 239 HIS 0.005 0.001 HIS B 193 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 7763) covalent geometry : angle 0.51913 (10493) hydrogen bonds : bond 0.04399 ( 363) hydrogen bonds : angle 3.73094 ( 1032) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 257 LYS cc_start: 0.8011 (mttt) cc_final: 0.7505 (mtmt) REVERT: A 288 THR cc_start: 0.8241 (p) cc_final: 0.7983 (p) REVERT: C 42 ARG cc_start: 0.7519 (ttp-170) cc_final: 0.7040 (tpt90) REVERT: C 262 LYS cc_start: 0.8141 (mmmm) cc_final: 0.7756 (mttt) REVERT: C 271 SER cc_start: 0.8969 (t) cc_final: 0.8616 (m) REVERT: B 362 ARG cc_start: 0.8100 (ttt180) cc_final: 0.7774 (ttm-80) REVERT: B 380 LYS cc_start: 0.7686 (mttm) cc_final: 0.7177 (mtmp) REVERT: B 390 LEU cc_start: 0.6476 (OUTLIER) cc_final: 0.6234 (tt) outliers start: 4 outliers final: 1 residues processed: 101 average time/residue: 1.4533 time to fit residues: 154.7051 Evaluate side-chains 99 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 79 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 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 = 0.3463 r_free = 0.3463 target = 0.131731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.101300 restraints weight = 26340.895| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.02 r_work: 0.2884 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7763 Z= 0.139 Angle : 0.517 6.724 10493 Z= 0.263 Chirality : 0.040 0.145 1164 Planarity : 0.004 0.044 1339 Dihedral : 5.040 62.535 1030 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.36 % Allowed : 12.29 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.28), residues: 933 helix: 2.22 (0.25), residues: 477 sheet: -0.25 (0.61), residues: 75 loop : -0.06 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 333 TYR 0.011 0.001 TYR C 246 PHE 0.019 0.001 PHE A 188 TRP 0.004 0.001 TRP C 239 HIS 0.004 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 7763) covalent geometry : angle 0.51699 (10493) hydrogen bonds : bond 0.04329 ( 363) hydrogen bonds : angle 3.72031 ( 1032) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5767.98 seconds wall clock time: 98 minutes 19.18 seconds (5899.18 seconds total)