Starting phenix.real_space_refine on Mon Jan 20 09:37:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vsu_43506/01_2025/8vsu_43506.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vsu_43506/01_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_43506/01_2025/8vsu_43506.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vsu_43506/01_2025/8vsu_43506.map" model { file = "/net/cci-nas-00/data/ceres_data/8vsu_43506/01_2025/8vsu_43506.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vsu_43506/01_2025/8vsu_43506.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 7.03, per 1000 atoms: 0.46 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: 3.64 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.22 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: 5.41 Time building geometry restraints manager: 4.32 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: 0.930 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: 0.260 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 32.410 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.500 ------------------------------------------------------------------------------- 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= 0.813 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (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 TRP 0.067 0.013 TRP B 243 HIS 0.010 0.002 HIS B 200 PHE 0.052 0.010 PHE A 188 TYR 0.119 0.016 TYR A 207 ARG 0.010 0.001 ARG B 100 *********************** 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 : 1.123 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: 3.0466 time to fit residues: 517.7463 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 : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.3446 r_free = 0.3446 target = 0.130978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.099217 restraints weight = 26749.297| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.17 r_work: 0.2877 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7763 Z= 0.213 Angle : 0.605 6.623 10493 Z= 0.325 Chirality : 0.042 0.146 1164 Planarity : 0.005 0.045 1339 Dihedral : 7.027 120.454 1030 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 0.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.91 % Allowed : 6.09 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.27), residues: 933 helix: 0.64 (0.24), residues: 479 sheet: -0.17 (0.55), residues: 75 loop : 0.20 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 308 HIS 0.007 0.001 HIS A 276 PHE 0.024 0.002 PHE A 188 TYR 0.011 0.001 TYR C 246 ARG 0.004 0.000 ARG A 148 *********************** 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: 16 poor density : 113 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 GLN cc_start: 0.7863 (mt0) cc_final: 0.7590 (mt0) REVERT: A 72 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7595 (tp-100) REVERT: A 215 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7255 (pp20) REVERT: A 257 LYS cc_start: 0.8093 (mttt) cc_final: 0.7558 (mtmt) REVERT: C 42 ARG cc_start: 0.7528 (ttp-110) cc_final: 0.7026 (tpt170) REVERT: C 262 LYS cc_start: 0.7978 (mmmm) cc_final: 0.7621 (mttt) REVERT: C 271 SER cc_start: 0.8868 (t) cc_final: 0.8502 (m) REVERT: C 312 LYS cc_start: 0.8360 (ttmt) cc_final: 0.8142 (tttp) REVERT: B 247 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7480 (pm20) REVERT: B 287 MET cc_start: 0.8672 (tmm) cc_final: 0.8437 (tmm) REVERT: B 362 ARG cc_start: 0.7906 (ttt180) cc_final: 0.7586 (ttm-80) outliers start: 16 outliers final: 6 residues processed: 125 average time/residue: 3.0552 time to fit residues: 401.6425 Evaluate side-chains 111 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 1.364 ------------------------------------------------------------------------------- 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 C residue 334 SER 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 39 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN 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 = 0.3485 r_free = 0.3485 target = 0.134028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.103524 restraints weight = 26284.055| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.04 r_work: 0.3117 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7763 Z= 0.160 Angle : 0.524 5.806 10493 Z= 0.271 Chirality : 0.040 0.149 1164 Planarity : 0.004 0.045 1339 Dihedral : 6.263 119.620 1030 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 0.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.31 % Allowed : 8.11 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.27), residues: 933 helix: 1.43 (0.24), residues: 477 sheet: -0.23 (0.58), residues: 75 loop : 0.06 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 239 HIS 0.012 0.001 HIS B 162 PHE 0.016 0.001 PHE A 188 TYR 0.011 0.001 TYR C 246 ARG 0.003 0.000 ARG B 134 *********************** 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: 11 poor density : 103 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7997 (tp-100) REVERT: A 257 LYS cc_start: 0.8347 (mttt) cc_final: 0.7874 (mtmt) REVERT: C 42 ARG cc_start: 0.7584 (ttp-110) cc_final: 0.7282 (tpt90) REVERT: C 262 LYS cc_start: 0.8253 (mmmm) cc_final: 0.7919 (mttt) REVERT: C 271 SER cc_start: 0.8931 (t) cc_final: 0.8684 (m) REVERT: C 336 THR cc_start: 0.7392 (OUTLIER) cc_final: 0.6992 (t) REVERT: B 81 ASP cc_start: 0.8583 (t0) cc_final: 0.7965 (t0) REVERT: B 287 MET cc_start: 0.8737 (tmm) cc_final: 0.8520 (tmm) REVERT: B 362 ARG cc_start: 0.7871 (ttt180) cc_final: 0.7636 (ttm-80) REVERT: B 390 LEU cc_start: 0.6705 (OUTLIER) cc_final: 0.6490 (tt) outliers start: 11 outliers final: 2 residues processed: 111 average time/residue: 2.8629 time to fit residues: 335.4231 Evaluate side-chains 104 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain B residue 206 ASP 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 3 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN A 289 GLN C 345 HIS ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.132801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.102168 restraints weight = 26486.269| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.04 r_work: 0.3101 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7763 Z= 0.208 Angle : 0.513 5.838 10493 Z= 0.265 Chirality : 0.040 0.149 1164 Planarity : 0.004 0.046 1339 Dihedral : 6.023 108.993 1030 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 0.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.31 % Allowed : 8.71 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.27), residues: 933 helix: 1.60 (0.24), residues: 484 sheet: -0.33 (0.59), residues: 75 loop : 0.02 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 239 HIS 0.004 0.001 HIS B 193 PHE 0.020 0.001 PHE A 188 TYR 0.010 0.001 TYR C 246 ARG 0.002 0.000 ARG C 333 *********************** 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 108 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.8018 (tp-100) REVERT: A 141 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7701 (tp) REVERT: A 215 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7277 (pp20) REVERT: A 257 LYS cc_start: 0.8308 (mttt) cc_final: 0.7823 (mtmt) REVERT: C 42 ARG cc_start: 0.7597 (ttp-110) cc_final: 0.7248 (tpt90) REVERT: C 45 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8714 (mp) REVERT: C 262 LYS cc_start: 0.8268 (mmmm) cc_final: 0.7922 (mttt) REVERT: C 271 SER cc_start: 0.8953 (t) cc_final: 0.8696 (m) REVERT: B 81 ASP cc_start: 0.8594 (t0) cc_final: 0.7961 (t0) REVERT: B 362 ARG cc_start: 0.7939 (ttt180) cc_final: 0.7698 (ttm-80) REVERT: B 390 LEU cc_start: 0.6688 (OUTLIER) cc_final: 0.6447 (tt) outliers start: 11 outliers final: 3 residues processed: 104 average time/residue: 2.8788 time to fit residues: 316.1997 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 : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 141 LEU 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 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 65 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 88 optimal weight: 0.0470 chunk 67 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.134872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.104202 restraints weight = 26521.732| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.06 r_work: 0.3034 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7763 Z= 0.130 Angle : 0.479 5.798 10493 Z= 0.242 Chirality : 0.038 0.146 1164 Planarity : 0.004 0.042 1339 Dihedral : 5.684 105.652 1030 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.84 % Allowed : 9.31 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.28), residues: 933 helix: 1.96 (0.25), residues: 485 sheet: -0.44 (0.59), residues: 77 loop : 0.00 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 239 HIS 0.006 0.001 HIS B 162 PHE 0.013 0.001 PHE A 188 TYR 0.007 0.001 TYR C 166 ARG 0.004 0.000 ARG B 134 *********************** 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: 7 poor density : 97 time to evaluate : 1.316 Fit side-chains revert: symmetry clash REVERT: A 141 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7602 (tp) REVERT: A 257 LYS cc_start: 0.8233 (mttt) cc_final: 0.7746 (mtmt) REVERT: A 293 ASP cc_start: 0.7785 (m-30) cc_final: 0.7545 (m-30) REVERT: C 42 ARG cc_start: 0.7589 (ttp-110) cc_final: 0.7211 (tpt90) REVERT: C 262 LYS cc_start: 0.8196 (mmmm) cc_final: 0.7857 (mttt) REVERT: C 271 SER cc_start: 0.8939 (t) cc_final: 0.8663 (m) REVERT: B 362 ARG cc_start: 0.7936 (ttt180) cc_final: 0.7677 (ttm-80) REVERT: B 380 LYS cc_start: 0.7878 (mttm) cc_final: 0.7412 (mtmp) REVERT: B 390 LEU cc_start: 0.6623 (OUTLIER) cc_final: 0.6346 (tt) outliers start: 7 outliers final: 1 residues processed: 102 average time/residue: 2.8647 time to fit residues: 308.3707 Evaluate side-chains 100 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 97 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 332 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 24 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 58 optimal weight: 0.5980 chunk 2 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN B 141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.132410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.101508 restraints weight = 26468.224| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.06 r_work: 0.3004 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7763 Z= 0.226 Angle : 0.509 6.305 10493 Z= 0.262 Chirality : 0.040 0.145 1164 Planarity : 0.004 0.044 1339 Dihedral : 5.659 92.594 1030 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 0.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.28), residues: 933 helix: 1.90 (0.25), residues: 484 sheet: -0.30 (0.60), residues: 75 loop : 0.00 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 239 HIS 0.005 0.001 HIS B 193 PHE 0.022 0.001 PHE A 188 TYR 0.011 0.001 TYR C 246 ARG 0.003 0.000 ARG B 134 *********************** 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 105 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7715 (tp) REVERT: A 215 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7343 (pp20) REVERT: A 257 LYS cc_start: 0.8223 (mttt) cc_final: 0.7731 (mtmt) REVERT: C 42 ARG cc_start: 0.7580 (ttp-110) cc_final: 0.7198 (tpt90) REVERT: C 262 LYS cc_start: 0.8260 (mmmm) cc_final: 0.7900 (mttt) REVERT: C 271 SER cc_start: 0.8958 (t) cc_final: 0.8691 (m) REVERT: B 362 ARG cc_start: 0.7971 (ttt180) cc_final: 0.7715 (ttm-80) REVERT: B 380 LYS cc_start: 0.7870 (mttm) cc_final: 0.7391 (mtmp) REVERT: B 390 LEU cc_start: 0.6622 (OUTLIER) cc_final: 0.6366 (tt) outliers start: 10 outliers final: 5 residues processed: 102 average time/residue: 2.8547 time to fit residues: 308.5820 Evaluate side-chains 100 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 141 LEU 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 232 SER Chi-restraints excluded: chain C residue 342 GLU 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 90 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 0.0870 chunk 57 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 overall best weight: 1.0962 ------------------------------------------------------------------------------- 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 = 0.3467 r_free = 0.3467 target = 0.132281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.100703 restraints weight = 26711.218| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.16 r_work: 0.2887 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3702 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= 0.174 Angle : 0.498 6.281 10493 Z= 0.253 Chirality : 0.039 0.146 1164 Planarity : 0.004 0.047 1339 Dihedral : 5.539 92.027 1030 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 0.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.60 % Allowed : 11.22 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.28), residues: 933 helix: 2.13 (0.25), residues: 478 sheet: -0.32 (0.60), residues: 75 loop : 0.04 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 239 HIS 0.006 0.001 HIS B 162 PHE 0.017 0.001 PHE A 188 TYR 0.009 0.001 TYR C 246 ARG 0.007 0.000 ARG B 134 *********************** 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 102 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 257 LYS cc_start: 0.7984 (mttt) cc_final: 0.7467 (mtmt) REVERT: C 42 ARG cc_start: 0.7559 (ttp-110) cc_final: 0.7035 (tpt90) REVERT: C 262 LYS cc_start: 0.8075 (mmmm) cc_final: 0.7721 (mttt) REVERT: C 271 SER cc_start: 0.8948 (t) cc_final: 0.8598 (m) REVERT: B 362 ARG cc_start: 0.8022 (ttt180) cc_final: 0.7700 (ttm-80) REVERT: B 380 LYS cc_start: 0.7663 (mttm) cc_final: 0.7178 (mtmp) REVERT: B 390 LEU cc_start: 0.6419 (OUTLIER) cc_final: 0.6187 (tt) outliers start: 5 outliers final: 3 residues processed: 102 average time/residue: 2.8100 time to fit residues: 303.3874 Evaluate side-chains 100 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 342 GLU 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 82 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 0.0370 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- 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 = 0.3481 r_free = 0.3481 target = 0.133204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.102817 restraints weight = 26407.720| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.02 r_work: 0.2910 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7763 Z= 0.165 Angle : 0.487 6.410 10493 Z= 0.247 Chirality : 0.039 0.144 1164 Planarity : 0.004 0.043 1339 Dihedral : 5.391 83.723 1030 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.28), residues: 933 helix: 2.21 (0.25), residues: 478 sheet: -0.55 (0.55), residues: 85 loop : 0.08 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 239 HIS 0.007 0.001 HIS B 162 PHE 0.016 0.001 PHE A 188 TYR 0.009 0.001 TYR C 246 ARG 0.008 0.000 ARG B 134 *********************** 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 104 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 257 LYS cc_start: 0.8065 (mttt) cc_final: 0.7561 (mtmt) REVERT: C 42 ARG cc_start: 0.7538 (ttp-170) cc_final: 0.7077 (tpt90) REVERT: C 262 LYS cc_start: 0.8133 (mmmm) cc_final: 0.7773 (mttt) REVERT: C 271 SER cc_start: 0.8965 (t) cc_final: 0.8627 (m) REVERT: B 362 ARG cc_start: 0.8032 (ttt180) cc_final: 0.7728 (ttm-80) REVERT: B 380 LYS cc_start: 0.7703 (mttm) cc_final: 0.7210 (mtmp) REVERT: B 390 LEU cc_start: 0.6497 (OUTLIER) cc_final: 0.6261 (tt) outliers start: 4 outliers final: 3 residues processed: 103 average time/residue: 2.8351 time to fit residues: 308.3149 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 : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain C residue 232 SER 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 57 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 40 optimal weight: 0.0070 chunk 62 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 80 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 = 0.3503 r_free = 0.3503 target = 0.135108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.104483 restraints weight = 26471.507| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.06 r_work: 0.3130 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3947 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= 0.132 Angle : 0.473 6.331 10493 Z= 0.236 Chirality : 0.038 0.148 1164 Planarity : 0.004 0.045 1339 Dihedral : 5.140 75.867 1030 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.60 % Allowed : 11.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.28), residues: 933 helix: 2.38 (0.25), residues: 480 sheet: -0.22 (0.60), residues: 75 loop : 0.10 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 144 HIS 0.005 0.001 HIS B 162 PHE 0.012 0.001 PHE A 188 TYR 0.007 0.001 TYR C 261 ARG 0.007 0.000 ARG B 134 *********************** 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 107 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 257 LYS cc_start: 0.8260 (mttt) cc_final: 0.7799 (mtmt) REVERT: A 288 THR cc_start: 0.8316 (p) cc_final: 0.8073 (p) REVERT: C 42 ARG cc_start: 0.7534 (ttp-170) cc_final: 0.7197 (tpt90) REVERT: C 262 LYS cc_start: 0.8264 (mmmm) cc_final: 0.7916 (mttt) REVERT: C 271 SER cc_start: 0.8985 (t) cc_final: 0.8706 (m) REVERT: B 362 ARG cc_start: 0.7981 (ttt180) cc_final: 0.7738 (ttm-80) REVERT: B 380 LYS cc_start: 0.7839 (mttm) cc_final: 0.7366 (mtmp) REVERT: B 390 LEU cc_start: 0.6691 (OUTLIER) cc_final: 0.6406 (tt) outliers start: 5 outliers final: 3 residues processed: 106 average time/residue: 2.6316 time to fit residues: 295.8698 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 : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain C residue 232 SER 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 80 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 ASN B 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.133050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.102095 restraints weight = 26563.789| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.07 r_work: 0.2903 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7763 Z= 0.213 Angle : 0.501 6.814 10493 Z= 0.254 Chirality : 0.039 0.142 1164 Planarity : 0.004 0.047 1339 Dihedral : 5.091 67.466 1030 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.84 % Allowed : 11.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.28), residues: 933 helix: 2.28 (0.25), residues: 479 sheet: -0.49 (0.55), residues: 85 loop : 0.10 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 239 HIS 0.004 0.001 HIS B 193 PHE 0.019 0.001 PHE A 188 TYR 0.010 0.001 TYR C 246 ARG 0.008 0.000 ARG B 134 ********************** 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 103 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7642 (tp) REVERT: A 257 LYS cc_start: 0.8072 (mttt) cc_final: 0.7578 (mtmt) REVERT: A 288 THR cc_start: 0.8294 (p) cc_final: 0.8063 (p) REVERT: C 42 ARG cc_start: 0.7553 (ttp-170) cc_final: 0.7082 (tpt90) REVERT: C 262 LYS cc_start: 0.8143 (mmmm) cc_final: 0.7753 (mttt) REVERT: C 271 SER cc_start: 0.8980 (t) cc_final: 0.8641 (m) REVERT: B 362 ARG cc_start: 0.8077 (ttt180) cc_final: 0.7774 (ttm-80) REVERT: B 380 LYS cc_start: 0.7710 (mttm) cc_final: 0.7199 (mtmp) REVERT: B 390 LEU cc_start: 0.6518 (OUTLIER) cc_final: 0.6277 (tt) outliers start: 7 outliers final: 5 residues processed: 100 average time/residue: 2.7387 time to fit residues: 289.8413 Evaluate side-chains 102 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 206 ASP 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 2 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 64 optimal weight: 0.0270 chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 ASN ** B 162 HIS ** 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 = 0.3467 r_free = 0.3467 target = 0.132300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.100708 restraints weight = 26511.234| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.16 r_work: 0.2891 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 7763 Z= 0.231 Angle : 0.888 59.199 10493 Z= 0.549 Chirality : 0.039 0.201 1164 Planarity : 0.004 0.043 1339 Dihedral : 5.079 67.523 1030 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.95 % Allowed : 11.46 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.28), residues: 933 helix: 2.27 (0.25), residues: 479 sheet: -0.49 (0.55), residues: 85 loop : 0.08 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 239 HIS 0.004 0.001 HIS B 193 PHE 0.019 0.001 PHE A 188 TYR 0.010 0.001 TYR C 246 ARG 0.005 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10438.02 seconds wall clock time: 183 minutes 26.02 seconds (11006.02 seconds total)