Starting phenix.real_space_refine on Thu Mar 13 09:35:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ys6_34073/03_2025/7ys6_34073.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ys6_34073/03_2025/7ys6_34073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ys6_34073/03_2025/7ys6_34073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ys6_34073/03_2025/7ys6_34073.map" model { file = "/net/cci-nas-00/data/ceres_data/7ys6_34073/03_2025/7ys6_34073.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ys6_34073/03_2025/7ys6_34073.cif" } resolution = 3.0 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 5584 2.51 5 N 1527 2.21 5 O 1621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8794 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2037 Classifications: {'peptide': 269} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 252} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "D" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1787 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1920 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'SRO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.38, per 1000 atoms: 0.61 Number of scatterers: 8794 At special positions: 0 Unit cell: (123.509, 131.16, 96.184, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 1621 8.00 N 1527 7.00 C 5584 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.99 Conformation dependent library (CDL) restraints added in 1.1 seconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 13 sheets defined 36.0% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 31 through 54 removed outlier: 4.103A pdb=" N VAL A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 58 removed outlier: 3.745A pdb=" N ARG A 58 " --> pdb=" O PRO A 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 55 through 58' Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 62 through 79 Processing helix chain 'A' and resid 79 through 90 removed outlier: 3.706A pdb=" N ALA A 83 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 98 through 129 removed outlier: 3.600A pdb=" N LEU A 129 " --> pdb=" O TYR A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 138 Processing helix chain 'A' and resid 139 through 160 Processing helix chain 'A' and resid 185 through 197 Processing helix chain 'A' and resid 197 through 224 Processing helix chain 'A' and resid 265 through 294 removed outlier: 4.284A pdb=" N PHE A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Proline residue: A 283 - end of helix Processing helix chain 'A' and resid 298 through 316 removed outlier: 3.728A pdb=" N PHE A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER A 313 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR A 314 " --> pdb=" O TYR A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 323 Processing helix chain 'A' and resid 324 through 335 Processing helix chain 'C' and resid 21 through 42 removed outlier: 3.652A pdb=" N CYS C 42 " --> pdb=" O ALA C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 51 Processing helix chain 'D' and resid 7 through 24 removed outlier: 3.916A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.554A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.809A pdb=" N SER E 31 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.131A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 38 removed outlier: 3.960A pdb=" N GLN B 35 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 235 through 239 removed outlier: 3.500A pdb=" N PHE B 238 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASN B 239 " --> pdb=" O GLN B 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 235 through 239' Processing helix chain 'B' and resid 264 through 278 Processing helix chain 'B' and resid 295 through 300 removed outlier: 4.168A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 311 removed outlier: 3.643A pdb=" N ASP B 310 " --> pdb=" O SER B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 351 removed outlier: 4.123A pdb=" N ILE B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ILE B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER B 349 " --> pdb=" O PHE B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 391 removed outlier: 3.703A pdb=" N VAL B 375 " --> pdb=" O ASN B 371 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TYR B 391 " --> pdb=" O HIS B 387 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 66 through 68 Processing sheet with id=AA2, first strand: chain 'C' and resid 75 through 80 removed outlier: 3.863A pdb=" N ALA C 77 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER C 91 " --> pdb=" O LYS C 95 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LYS C 95 " --> pdb=" O SER C 91 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS C 108 " --> pdb=" O ILE C 98 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP C 100 " --> pdb=" O LYS C 106 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LYS C 106 " --> pdb=" O ASP C 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 117 through 122 removed outlier: 3.880A pdb=" N GLY C 132 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N CYS C 138 " --> pdb=" O GLU C 155 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N GLU C 155 " --> pdb=" O CYS C 138 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE C 140 " --> pdb=" O SER C 153 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG C 151 " --> pdb=" O ASN C 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 163 through 168 removed outlier: 3.523A pdb=" N CYS C 165 " --> pdb=" O SER C 177 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE C 174 " --> pdb=" O TRP C 186 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 206 through 209 removed outlier: 3.886A pdb=" N SER C 206 " --> pdb=" O GLY C 219 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE C 216 " --> pdb=" O TRP C 228 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA C 225 " --> pdb=" O THR C 238 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N THR C 238 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU C 227 " --> pdb=" O ARG C 236 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 246 through 251 removed outlier: 3.770A pdb=" N SER C 262 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N THR C 266 " --> pdb=" O SER C 262 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET C 279 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASP C 271 " --> pdb=" O GLU C 277 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLU C 277 " --> pdb=" O ASP C 271 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 293 through 295 removed outlier: 3.530A pdb=" N GLY C 323 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASP C 315 " --> pdb=" O ARG C 321 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ARG C 321 " --> pdb=" O ASP C 315 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.970A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.920A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.838A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR E 228 " --> pdb=" O PHE E 177 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 207 through 214 removed outlier: 4.153A pdb=" N VAL B 224 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 9.514A pdb=" N ALA B 243 " --> pdb=" O THR B 40 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ARG B 42 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ILE B 245 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU B 44 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL B 247 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU B 46 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ILE B 244 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N PHE B 290 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N PHE B 246 " --> pdb=" O PHE B 290 " (cutoff:3.500A) 410 hydrogen bonds defined for protein. 1176 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: 2.71 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1515 1.32 - 1.44: 2408 1.44 - 1.57: 4961 1.57 - 1.69: 6 1.69 - 1.81: 89 Bond restraints: 8979 Sorted by residual: bond pdb=" CA TYR D 40 " pdb=" C TYR D 40 " ideal model delta sigma weight residual 1.524 1.440 0.084 1.26e-02 6.30e+03 4.40e+01 bond pdb=" CA PHE B 363 " pdb=" C PHE B 363 " ideal model delta sigma weight residual 1.530 1.456 0.073 1.11e-02 8.12e+03 4.36e+01 bond pdb=" N TYR A 320 " pdb=" CA TYR A 320 " ideal model delta sigma weight residual 1.462 1.522 -0.061 9.50e-03 1.11e+04 4.06e+01 bond pdb=" CA ASP C 245 " pdb=" C ASP C 245 " ideal model delta sigma weight residual 1.527 1.451 0.075 1.34e-02 5.57e+03 3.16e+01 bond pdb=" CA PHE C 252 " pdb=" C PHE C 252 " ideal model delta sigma weight residual 1.528 1.464 0.065 1.18e-02 7.18e+03 3.00e+01 ... (remaining 8974 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 11555 2.29 - 4.57: 478 4.57 - 6.86: 98 6.86 - 9.14: 34 9.14 - 11.43: 7 Bond angle restraints: 12172 Sorted by residual: angle pdb=" N CYS B 365 " pdb=" CA CYS B 365 " pdb=" C CYS B 365 " ideal model delta sigma weight residual 109.41 98.81 10.60 1.52e+00 4.33e-01 4.87e+01 angle pdb=" N PHE B 222 " pdb=" CA PHE B 222 " pdb=" C PHE B 222 " ideal model delta sigma weight residual 107.80 118.91 -11.11 1.73e+00 3.34e-01 4.12e+01 angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 132.97 -11.43 1.91e+00 2.74e-01 3.58e+01 angle pdb=" N ASN A 312 " pdb=" CA ASN A 312 " pdb=" C ASN A 312 " ideal model delta sigma weight residual 111.69 104.87 6.82 1.23e+00 6.61e-01 3.07e+01 angle pdb=" C ASN A 316 " pdb=" N PRO A 317 " pdb=" CA PRO A 317 " ideal model delta sigma weight residual 119.82 114.42 5.40 9.80e-01 1.04e+00 3.03e+01 ... (remaining 12167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 4684 17.89 - 35.78: 534 35.78 - 53.67: 94 53.67 - 71.55: 22 71.55 - 89.44: 5 Dihedral angle restraints: 5339 sinusoidal: 2077 harmonic: 3262 Sorted by residual: dihedral pdb=" CA PHE A 197 " pdb=" C PHE A 197 " pdb=" N PHE A 198 " pdb=" CA PHE A 198 " ideal model delta harmonic sigma weight residual -180.00 -158.33 -21.67 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA TYR E 101 " pdb=" C TYR E 101 " pdb=" N TYR E 102 " pdb=" CA TYR E 102 " ideal model delta harmonic sigma weight residual 180.00 158.95 21.05 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA LEU A 77 " pdb=" C LEU A 77 " pdb=" N VAL A 78 " pdb=" CA VAL A 78 " ideal model delta harmonic sigma weight residual -180.00 -159.40 -20.60 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 5336 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1157 0.078 - 0.157: 179 0.157 - 0.235: 34 0.235 - 0.314: 6 0.314 - 0.392: 2 Chirality restraints: 1378 Sorted by residual: chirality pdb=" CB VAL A 279 " pdb=" CA VAL A 279 " pdb=" CG1 VAL A 279 " pdb=" CG2 VAL A 279 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CA PHE B 222 " pdb=" N PHE B 222 " pdb=" C PHE B 222 " pdb=" CB PHE B 222 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CA ASN E 194 " pdb=" N ASN E 194 " pdb=" C ASN E 194 " pdb=" CB ASN E 194 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.42e+00 ... (remaining 1375 not shown) Planarity restraints: 1549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 213 " -0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C THR C 213 " 0.067 2.00e-02 2.50e+03 pdb=" O THR C 213 " -0.025 2.00e-02 2.50e+03 pdb=" N ARG C 214 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET E 192 " -0.019 2.00e-02 2.50e+03 3.79e-02 1.44e+01 pdb=" C MET E 192 " 0.066 2.00e-02 2.50e+03 pdb=" O MET E 192 " -0.024 2.00e-02 2.50e+03 pdb=" N SER E 193 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 193 " -0.018 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C SER E 193 " 0.064 2.00e-02 2.50e+03 pdb=" O SER E 193 " -0.024 2.00e-02 2.50e+03 pdb=" N ASN E 194 " -0.022 2.00e-02 2.50e+03 ... (remaining 1546 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.28: 8 2.28 - 2.94: 3613 2.94 - 3.59: 11700 3.59 - 4.25: 20248 4.25 - 4.90: 34558 Nonbonded interactions: 70127 Sorted by model distance: nonbonded pdb=" O SER C 208 " pdb=" CE2 PHE C 251 " model vdw 1.631 3.340 nonbonded pdb=" OH TYR B 253 " pdb=" CZ PHE B 315 " model vdw 1.883 3.340 nonbonded pdb=" C SER C 208 " pdb=" CE2 PHE C 251 " model vdw 2.018 3.570 nonbonded pdb=" CZ TYR B 253 " pdb=" CG2 ILE B 308 " model vdw 2.038 3.680 nonbonded pdb=" OG SER E 204 " pdb=" OG1 THR E 215 " model vdw 2.088 3.040 ... (remaining 70122 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 23.460 Find NCS groups from input model: 0.150 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:20.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 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 : 0.007 0.131 8979 Z= 0.466 Angle : 1.108 11.431 12172 Z= 0.644 Chirality : 0.063 0.392 1378 Planarity : 0.009 0.099 1549 Dihedral : 15.446 89.442 3230 Min Nonbonded Distance : 1.631 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.53 % Allowed : 19.94 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -2.80 (0.22), residues: 1111 helix: -2.86 (0.17), residues: 356 sheet: -0.94 (0.30), residues: 275 loop : -1.41 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 166 HIS 0.006 0.001 HIS B 357 PHE 0.031 0.002 PHE A 277 TYR 0.018 0.002 TYR E 103 ARG 0.023 0.001 ARG C 236 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 222 time to evaluate : 1.324 Fit side-chains REVERT: A 78 VAL cc_start: 0.7499 (m) cc_final: 0.7236 (p) REVERT: A 270 LEU cc_start: 0.7363 (mp) cc_final: 0.7128 (mt) REVERT: C 62 MET cc_start: 0.7847 (mtt) cc_final: 0.7611 (mtm) REVERT: C 151 ARG cc_start: 0.7719 (ptp-110) cc_final: 0.7457 (ptp-110) REVERT: C 170 ASP cc_start: 0.7359 (m-30) cc_final: 0.7128 (m-30) REVERT: C 171 ASP cc_start: 0.6747 (m-30) cc_final: 0.6519 (m-30) REVERT: C 172 ASN cc_start: 0.7880 (t0) cc_final: 0.7423 (t0) REVERT: C 192 GLN cc_start: 0.7838 (mm-40) cc_final: 0.7606 (mm-40) REVERT: C 205 MET cc_start: 0.7312 (mmm) cc_final: 0.7078 (mmm) REVERT: C 234 MET cc_start: 0.7240 (ppp) cc_final: 0.7004 (pmt) REVERT: C 237 GLN cc_start: 0.7712 (mt0) cc_final: 0.7511 (mt0) REVERT: C 294 SER cc_start: 0.8302 (m) cc_final: 0.8070 (t) REVERT: E 5 VAL cc_start: 0.8375 (t) cc_final: 0.8135 (t) REVERT: E 36 TRP cc_start: 0.8261 (m100) cc_final: 0.8012 (m100) REVERT: E 59 TYR cc_start: 0.8461 (m-80) cc_final: 0.8210 (m-80) REVERT: E 71 SER cc_start: 0.7476 (p) cc_final: 0.7165 (t) REVERT: E 166 LEU cc_start: 0.8231 (tt) cc_final: 0.7786 (mt) REVERT: E 197 SER cc_start: 0.8113 (p) cc_final: 0.7869 (p) REVERT: B 28 LYS cc_start: 0.8235 (ptmt) cc_final: 0.8029 (ptmt) REVERT: B 34 LYS cc_start: 0.7779 (tppt) cc_final: 0.7579 (tppt) REVERT: B 224 VAL cc_start: 0.7675 (OUTLIER) cc_final: 0.7217 (m) REVERT: B 331 ASP cc_start: 0.4354 (t70) cc_final: 0.4122 (t70) outliers start: 5 outliers final: 0 residues processed: 226 average time/residue: 1.5358 time to fit residues: 370.7817 Evaluate side-chains 192 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 191 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 224 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 HIS ** B 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN B 292 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.142207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.128132 restraints weight = 12786.639| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 1.97 r_work: 0.3575 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8979 Z= 0.287 Angle : 0.632 8.878 12172 Z= 0.326 Chirality : 0.044 0.155 1378 Planarity : 0.005 0.054 1549 Dihedral : 4.873 29.538 1233 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.32 % Allowed : 21.62 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.95 (0.24), residues: 1111 helix: -0.03 (0.25), residues: 355 sheet: -0.74 (0.30), residues: 288 loop : -0.87 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 47 HIS 0.005 0.001 HIS C 108 PHE 0.016 0.002 PHE B 212 TYR 0.014 0.002 TYR E 190 ARG 0.010 0.001 ARG B 385 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 217 time to evaluate : 0.931 Fit side-chains REVERT: A 78 VAL cc_start: 0.7562 (m) cc_final: 0.7362 (p) REVERT: A 108 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7807 (ttp) REVERT: A 212 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.7122 (mt) REVERT: A 217 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.8061 (ttpp) REVERT: C 36 ARG cc_start: 0.7293 (ttp80) cc_final: 0.7021 (ttp-170) REVERT: C 62 MET cc_start: 0.7930 (mtt) cc_final: 0.7705 (mtm) REVERT: C 146 ARG cc_start: 0.7578 (ttm170) cc_final: 0.7356 (mtm180) REVERT: C 172 ASN cc_start: 0.8138 (t0) cc_final: 0.7894 (t0) REVERT: C 192 GLN cc_start: 0.8273 (mm-40) cc_final: 0.8038 (mm-40) REVERT: C 251 PHE cc_start: 0.8574 (OUTLIER) cc_final: 0.8169 (m-80) REVERT: C 260 THR cc_start: 0.8299 (m) cc_final: 0.8043 (p) REVERT: C 351 SER cc_start: 0.7401 (m) cc_final: 0.7122 (m) REVERT: E 71 SER cc_start: 0.7995 (OUTLIER) cc_final: 0.7649 (t) REVERT: E 166 LEU cc_start: 0.8497 (tt) cc_final: 0.8084 (mt) REVERT: E 197 SER cc_start: 0.8172 (p) cc_final: 0.7947 (p) REVERT: E 214 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7449 (tp) REVERT: B 28 LYS cc_start: 0.8354 (ptmt) cc_final: 0.8122 (ptmt) REVERT: B 216 LYS cc_start: 0.8236 (mmtt) cc_final: 0.7881 (mmtt) REVERT: B 340 PHE cc_start: 0.8017 (t80) cc_final: 0.7810 (t80) REVERT: B 356 ARG cc_start: 0.7487 (ttm110) cc_final: 0.7210 (ttp-110) REVERT: B 371 ASN cc_start: 0.8389 (m-40) cc_final: 0.8166 (m110) REVERT: B 373 ARG cc_start: 0.8182 (mtp85) cc_final: 0.7972 (mmm160) REVERT: B 374 ARG cc_start: 0.8263 (mtt-85) cc_final: 0.8057 (mtt180) outliers start: 41 outliers final: 16 residues processed: 237 average time/residue: 1.0943 time to fit residues: 277.8130 Evaluate side-chains 224 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 251 PHE Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 369 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 62 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 ASN ** B 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN B 387 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.140898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.127000 restraints weight = 12795.678| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.93 r_work: 0.3557 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8979 Z= 0.300 Angle : 0.603 9.238 12172 Z= 0.309 Chirality : 0.044 0.220 1378 Planarity : 0.005 0.055 1549 Dihedral : 4.731 25.827 1232 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.80 % Allowed : 22.05 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.35 (0.25), residues: 1111 helix: 0.98 (0.27), residues: 361 sheet: -0.66 (0.30), residues: 276 loop : -0.81 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 47 HIS 0.005 0.001 HIS E 35 PHE 0.014 0.002 PHE C 216 TYR 0.014 0.002 TYR E 175 ARG 0.012 0.001 ARG B 342 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 210 time to evaluate : 0.987 Fit side-chains REVERT: A 78 VAL cc_start: 0.7580 (OUTLIER) cc_final: 0.7342 (p) REVERT: A 108 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7752 (ttp) REVERT: A 279 VAL cc_start: 0.8024 (p) cc_final: 0.7734 (m) REVERT: A 313 SER cc_start: 0.7930 (m) cc_final: 0.7684 (t) REVERT: C 36 ARG cc_start: 0.7190 (ttp80) cc_final: 0.6831 (ttp-170) REVERT: C 62 MET cc_start: 0.7970 (mtt) cc_final: 0.7762 (mtm) REVERT: C 86 LEU cc_start: 0.8649 (mm) cc_final: 0.8442 (mp) REVERT: C 146 ARG cc_start: 0.7545 (ttm170) cc_final: 0.7325 (mtm180) REVERT: C 167 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8128 (mmt180) REVERT: C 172 ASN cc_start: 0.8157 (t0) cc_final: 0.7853 (t0) REVERT: C 251 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.8154 (m-80) REVERT: C 335 LEU cc_start: 0.8112 (tt) cc_final: 0.7764 (tp) REVERT: C 351 SER cc_start: 0.7487 (m) cc_final: 0.7169 (m) REVERT: E 71 SER cc_start: 0.8065 (OUTLIER) cc_final: 0.7659 (t) REVERT: E 166 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8170 (mt) REVERT: E 192 MET cc_start: 0.7185 (OUTLIER) cc_final: 0.6887 (ptm) REVERT: E 197 SER cc_start: 0.8175 (p) cc_final: 0.7950 (p) REVERT: E 214 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7327 (tp) REVERT: B 28 LYS cc_start: 0.8412 (ptmt) cc_final: 0.8174 (ptmt) REVERT: B 29 GLN cc_start: 0.7963 (tp40) cc_final: 0.7513 (tp-100) REVERT: B 216 LYS cc_start: 0.8228 (mmtt) cc_final: 0.7880 (mmtt) REVERT: B 274 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8269 (tppp) REVERT: B 286 SER cc_start: 0.8392 (OUTLIER) cc_final: 0.8170 (m) REVERT: B 331 ASP cc_start: 0.4506 (t70) cc_final: 0.4118 (t70) REVERT: B 340 PHE cc_start: 0.8005 (t80) cc_final: 0.7800 (t80) REVERT: B 342 ARG cc_start: 0.7301 (ttp80) cc_final: 0.6652 (ttp80) outliers start: 55 outliers final: 20 residues processed: 239 average time/residue: 1.0946 time to fit residues: 279.9569 Evaluate side-chains 234 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 204 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 167 ARG Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 251 PHE Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 369 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 26 optimal weight: 0.3980 chunk 89 optimal weight: 0.6980 chunk 76 optimal weight: 0.4980 chunk 40 optimal weight: 0.2980 chunk 93 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 ASN C 192 GLN C 283 HIS B 371 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.141122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.127307 restraints weight = 12649.653| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.91 r_work: 0.3563 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8979 Z= 0.228 Angle : 0.553 8.973 12172 Z= 0.282 Chirality : 0.042 0.145 1378 Planarity : 0.004 0.055 1549 Dihedral : 4.538 30.579 1232 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 5.38 % Allowed : 21.94 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.03 (0.25), residues: 1111 helix: 1.43 (0.28), residues: 367 sheet: -0.62 (0.30), residues: 277 loop : -0.72 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 314 HIS 0.004 0.001 HIS C 283 PHE 0.012 0.001 PHE C 216 TYR 0.014 0.001 TYR E 190 ARG 0.009 0.000 ARG B 280 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 209 time to evaluate : 0.908 Fit side-chains REVERT: A 78 VAL cc_start: 0.7538 (OUTLIER) cc_final: 0.7315 (p) REVERT: A 108 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7712 (ttp) REVERT: A 279 VAL cc_start: 0.7926 (p) cc_final: 0.7669 (m) REVERT: A 313 SER cc_start: 0.7680 (m) cc_final: 0.7423 (t) REVERT: A 315 MET cc_start: 0.6413 (mmt) cc_final: 0.6001 (mmt) REVERT: C 36 ARG cc_start: 0.7198 (ttp80) cc_final: 0.6746 (ttp-170) REVERT: C 86 LEU cc_start: 0.8635 (mm) cc_final: 0.8429 (mp) REVERT: C 167 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.8002 (mmt180) REVERT: C 172 ASN cc_start: 0.8137 (t0) cc_final: 0.7838 (t0) REVERT: C 251 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.8094 (m-80) REVERT: C 335 LEU cc_start: 0.8038 (tt) cc_final: 0.7773 (tt) REVERT: C 351 SER cc_start: 0.7513 (m) cc_final: 0.7160 (m) REVERT: E 71 SER cc_start: 0.8095 (OUTLIER) cc_final: 0.7671 (t) REVERT: E 166 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8190 (mt) REVERT: E 197 SER cc_start: 0.8163 (p) cc_final: 0.7932 (p) REVERT: B 28 LYS cc_start: 0.8314 (ptmt) cc_final: 0.8061 (ptmt) REVERT: B 29 GLN cc_start: 0.7914 (tp40) cc_final: 0.7474 (tp-100) REVERT: B 34 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7620 (tppt) REVERT: B 216 LYS cc_start: 0.8236 (mmtt) cc_final: 0.7939 (tmtt) REVERT: B 239 ASN cc_start: 0.7463 (m-40) cc_final: 0.7236 (m110) REVERT: B 274 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8249 (tppp) REVERT: B 331 ASP cc_start: 0.4508 (t70) cc_final: 0.4094 (t70) REVERT: B 391 TYR cc_start: 0.8367 (m-80) cc_final: 0.8109 (m-80) outliers start: 51 outliers final: 23 residues processed: 236 average time/residue: 1.0782 time to fit residues: 272.2702 Evaluate side-chains 235 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 204 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 167 ARG Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 251 PHE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 369 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 36 optimal weight: 0.0980 chunk 44 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 ASN C 192 GLN B 371 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.140760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.126956 restraints weight = 12638.439| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.91 r_work: 0.3563 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8979 Z= 0.228 Angle : 0.554 8.274 12172 Z= 0.283 Chirality : 0.042 0.147 1378 Planarity : 0.004 0.053 1549 Dihedral : 4.508 32.414 1232 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 5.06 % Allowed : 23.73 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.10 (0.25), residues: 1111 helix: 1.53 (0.28), residues: 372 sheet: -0.59 (0.30), residues: 277 loop : -0.63 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 314 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE C 216 TYR 0.013 0.001 TYR E 190 ARG 0.010 0.000 ARG B 280 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 207 time to evaluate : 0.921 Fit side-chains REVERT: A 78 VAL cc_start: 0.7527 (OUTLIER) cc_final: 0.7307 (p) REVERT: A 101 LEU cc_start: 0.5658 (OUTLIER) cc_final: 0.5107 (tp) REVERT: A 108 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7716 (ttp) REVERT: A 217 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7996 (ptpp) REVERT: A 269 THR cc_start: 0.7888 (OUTLIER) cc_final: 0.7346 (m) REVERT: A 279 VAL cc_start: 0.7950 (p) cc_final: 0.7696 (m) REVERT: A 313 SER cc_start: 0.7776 (m) cc_final: 0.7463 (t) REVERT: C 86 LEU cc_start: 0.8639 (mm) cc_final: 0.8415 (mp) REVERT: C 167 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7919 (mmt180) REVERT: C 172 ASN cc_start: 0.8090 (t0) cc_final: 0.7797 (t0) REVERT: C 190 THR cc_start: 0.8659 (t) cc_final: 0.8455 (p) REVERT: C 251 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.8120 (m-80) REVERT: C 303 LEU cc_start: 0.8294 (mp) cc_final: 0.8043 (mp) REVERT: C 324 VAL cc_start: 0.8543 (t) cc_final: 0.8321 (p) REVERT: C 335 LEU cc_start: 0.7980 (tt) cc_final: 0.7769 (tt) REVERT: E 71 SER cc_start: 0.8121 (OUTLIER) cc_final: 0.7690 (t) REVERT: E 166 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8208 (mt) REVERT: E 197 SER cc_start: 0.8110 (p) cc_final: 0.7878 (p) REVERT: B 28 LYS cc_start: 0.8318 (ptmt) cc_final: 0.8072 (ptmt) REVERT: B 216 LYS cc_start: 0.8250 (mmtt) cc_final: 0.7939 (tmtt) REVERT: B 235 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7938 (mm) REVERT: B 283 ARG cc_start: 0.7600 (mtm-85) cc_final: 0.7365 (mtm-85) REVERT: B 342 ARG cc_start: 0.7315 (ttp80) cc_final: 0.6793 (ttp80) outliers start: 48 outliers final: 24 residues processed: 232 average time/residue: 1.1579 time to fit residues: 286.5453 Evaluate side-chains 238 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 204 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 167 ARG Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 251 PHE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 369 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 7 optimal weight: 0.1980 chunk 85 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 37 optimal weight: 0.3980 chunk 86 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 ASN C 149 ASN B 292 ASN B 371 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.141359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.127571 restraints weight = 12680.424| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.92 r_work: 0.3574 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8979 Z= 0.202 Angle : 0.543 7.837 12172 Z= 0.277 Chirality : 0.042 0.155 1378 Planarity : 0.004 0.052 1549 Dihedral : 4.443 34.994 1232 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.85 % Allowed : 23.95 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.25 (0.25), residues: 1111 helix: 1.77 (0.28), residues: 366 sheet: -0.61 (0.30), residues: 279 loop : -0.54 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 151 HIS 0.003 0.001 HIS E 35 PHE 0.015 0.001 PHE E 68 TYR 0.013 0.001 TYR E 190 ARG 0.011 0.000 ARG B 280 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 203 time to evaluate : 1.005 Fit side-chains REVERT: A 78 VAL cc_start: 0.7531 (OUTLIER) cc_final: 0.7310 (p) REVERT: A 80 MET cc_start: 0.5701 (mtm) cc_final: 0.5282 (mtm) REVERT: A 101 LEU cc_start: 0.5645 (OUTLIER) cc_final: 0.5090 (tp) REVERT: A 108 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7719 (ttp) REVERT: A 269 THR cc_start: 0.7878 (OUTLIER) cc_final: 0.7330 (m) REVERT: A 279 VAL cc_start: 0.7921 (OUTLIER) cc_final: 0.7675 (m) REVERT: A 313 SER cc_start: 0.7914 (m) cc_final: 0.7549 (t) REVERT: C 86 LEU cc_start: 0.8638 (mm) cc_final: 0.8397 (mt) REVERT: C 167 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7849 (mmt180) REVERT: C 172 ASN cc_start: 0.8073 (t0) cc_final: 0.7768 (t0) REVERT: C 217 VAL cc_start: 0.7844 (p) cc_final: 0.7604 (m) REVERT: C 232 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7486 (mm-30) REVERT: C 251 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.8104 (m-80) REVERT: C 324 VAL cc_start: 0.8539 (t) cc_final: 0.8332 (p) REVERT: C 335 LEU cc_start: 0.7928 (tt) cc_final: 0.7607 (tp) REVERT: E 71 SER cc_start: 0.8157 (p) cc_final: 0.7710 (t) REVERT: E 166 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8199 (mt) REVERT: E 197 SER cc_start: 0.8114 (p) cc_final: 0.7871 (p) REVERT: B 216 LYS cc_start: 0.8219 (mmtt) cc_final: 0.7905 (tmtt) REVERT: B 235 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7939 (mm) REVERT: B 274 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8263 (tppp) REVERT: B 283 ARG cc_start: 0.7560 (mtm-85) cc_final: 0.7337 (mtm-85) REVERT: B 342 ARG cc_start: 0.7306 (ttp80) cc_final: 0.6793 (ttp80) outliers start: 46 outliers final: 27 residues processed: 229 average time/residue: 1.1978 time to fit residues: 293.5722 Evaluate side-chains 237 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 200 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 167 ARG Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 251 PHE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 369 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 107 optimal weight: 0.0570 overall best weight: 0.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 ASN C 193 GLN B 371 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.139832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.126089 restraints weight = 12774.868| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.92 r_work: 0.3546 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8979 Z= 0.299 Angle : 0.597 7.562 12172 Z= 0.304 Chirality : 0.044 0.161 1378 Planarity : 0.004 0.050 1549 Dihedral : 4.524 24.787 1232 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 5.49 % Allowed : 24.58 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.13 (0.25), residues: 1111 helix: 1.60 (0.27), residues: 373 sheet: -0.60 (0.30), residues: 270 loop : -0.66 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 151 HIS 0.004 0.001 HIS E 35 PHE 0.016 0.002 PHE E 68 TYR 0.010 0.002 TYR B 253 ARG 0.013 0.001 ARG B 280 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 211 time to evaluate : 1.021 Fit side-chains REVERT: A 78 VAL cc_start: 0.7551 (OUTLIER) cc_final: 0.7291 (p) REVERT: A 101 LEU cc_start: 0.5716 (OUTLIER) cc_final: 0.5128 (tp) REVERT: A 217 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7876 (ptpp) REVERT: A 279 VAL cc_start: 0.7977 (OUTLIER) cc_final: 0.7711 (m) REVERT: A 313 SER cc_start: 0.8022 (m) cc_final: 0.7642 (t) REVERT: C 86 LEU cc_start: 0.8721 (mm) cc_final: 0.8463 (mp) REVERT: C 167 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7887 (mmt180) REVERT: C 172 ASN cc_start: 0.8101 (t0) cc_final: 0.7734 (t0) REVERT: C 251 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.8101 (m-80) REVERT: C 324 VAL cc_start: 0.8544 (t) cc_final: 0.8314 (p) REVERT: C 335 LEU cc_start: 0.8018 (tt) cc_final: 0.7794 (tt) REVERT: E 71 SER cc_start: 0.8138 (OUTLIER) cc_final: 0.7704 (t) REVERT: E 166 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8224 (mt) REVERT: E 197 SER cc_start: 0.8139 (p) cc_final: 0.7911 (p) REVERT: B 216 LYS cc_start: 0.8252 (mmtt) cc_final: 0.7940 (tmtt) REVERT: B 274 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8260 (tppp) REVERT: B 283 ARG cc_start: 0.7575 (mtm-85) cc_final: 0.7345 (mtm-85) outliers start: 52 outliers final: 29 residues processed: 236 average time/residue: 1.0822 time to fit residues: 272.8026 Evaluate side-chains 243 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 205 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 167 ARG Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 251 PHE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 369 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 94 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 72 optimal weight: 0.2980 chunk 18 optimal weight: 0.5980 chunk 101 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN B 371 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.140094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.126582 restraints weight = 13028.242| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.96 r_work: 0.3561 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8979 Z= 0.237 Angle : 0.575 9.715 12172 Z= 0.289 Chirality : 0.043 0.187 1378 Planarity : 0.004 0.056 1549 Dihedral : 4.481 28.057 1232 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.85 % Allowed : 25.53 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.22 (0.25), residues: 1111 helix: 1.79 (0.28), residues: 365 sheet: -0.62 (0.30), residues: 277 loop : -0.60 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 151 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE E 68 TYR 0.013 0.001 TYR E 190 ARG 0.014 0.001 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 206 time to evaluate : 1.056 Fit side-chains REVERT: A 80 MET cc_start: 0.5654 (mtm) cc_final: 0.5332 (mtm) REVERT: A 101 LEU cc_start: 0.5655 (OUTLIER) cc_final: 0.5081 (tp) REVERT: A 217 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7917 (ptpp) REVERT: A 279 VAL cc_start: 0.7896 (OUTLIER) cc_final: 0.7644 (m) REVERT: A 313 SER cc_start: 0.8039 (m) cc_final: 0.7647 (t) REVERT: C 86 LEU cc_start: 0.8654 (mm) cc_final: 0.8385 (mp) REVERT: C 167 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7719 (mmt180) REVERT: C 172 ASN cc_start: 0.8086 (t0) cc_final: 0.7795 (t0) REVERT: C 217 VAL cc_start: 0.7901 (p) cc_final: 0.7661 (m) REVERT: C 251 PHE cc_start: 0.8537 (OUTLIER) cc_final: 0.8133 (m-80) REVERT: C 324 VAL cc_start: 0.8502 (t) cc_final: 0.8242 (p) REVERT: C 335 LEU cc_start: 0.7930 (tt) cc_final: 0.7719 (tt) REVERT: E 71 SER cc_start: 0.8120 (OUTLIER) cc_final: 0.7719 (t) REVERT: E 90 ASP cc_start: 0.8252 (m-30) cc_final: 0.8027 (m-30) REVERT: E 166 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8247 (mt) REVERT: E 197 SER cc_start: 0.8234 (p) cc_final: 0.8011 (p) REVERT: B 216 LYS cc_start: 0.8234 (mmtt) cc_final: 0.7914 (tmtt) REVERT: B 235 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7960 (mm) REVERT: B 274 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8261 (tppp) REVERT: B 283 ARG cc_start: 0.7538 (mtm-85) cc_final: 0.7308 (mtm-85) outliers start: 46 outliers final: 30 residues processed: 230 average time/residue: 1.1312 time to fit residues: 277.7211 Evaluate side-chains 240 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 201 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 167 ARG Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 251 PHE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 369 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 24 optimal weight: 0.0970 chunk 81 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 371 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.140005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.126566 restraints weight = 12970.669| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.94 r_work: 0.3564 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8979 Z= 0.233 Angle : 0.594 11.890 12172 Z= 0.293 Chirality : 0.044 0.264 1378 Planarity : 0.004 0.050 1549 Dihedral : 4.449 29.548 1232 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.43 % Allowed : 25.53 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.28 (0.25), residues: 1111 helix: 1.83 (0.28), residues: 365 sheet: -0.58 (0.29), residues: 287 loop : -0.57 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 151 HIS 0.004 0.001 HIS B 387 PHE 0.015 0.001 PHE B 340 TYR 0.012 0.001 TYR E 190 ARG 0.013 0.000 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 203 time to evaluate : 1.217 Fit side-chains REVERT: A 80 MET cc_start: 0.5733 (mtm) cc_final: 0.5427 (mtm) REVERT: A 101 LEU cc_start: 0.5653 (OUTLIER) cc_final: 0.5097 (tp) REVERT: A 137 ARG cc_start: 0.7925 (ptp-110) cc_final: 0.7696 (ptp-110) REVERT: A 217 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7912 (ptpp) REVERT: A 279 VAL cc_start: 0.7863 (OUTLIER) cc_final: 0.7626 (m) REVERT: A 313 SER cc_start: 0.8086 (m) cc_final: 0.7701 (t) REVERT: C 86 LEU cc_start: 0.8689 (mm) cc_final: 0.8424 (mp) REVERT: C 167 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7735 (mmt180) REVERT: C 172 ASN cc_start: 0.8072 (t0) cc_final: 0.7761 (t0) REVERT: C 217 VAL cc_start: 0.7891 (p) cc_final: 0.7653 (m) REVERT: C 251 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.8086 (m-80) REVERT: C 303 LEU cc_start: 0.8279 (mp) cc_final: 0.8022 (mp) REVERT: C 324 VAL cc_start: 0.8541 (t) cc_final: 0.8268 (p) REVERT: C 335 LEU cc_start: 0.7929 (tt) cc_final: 0.7575 (tp) REVERT: E 71 SER cc_start: 0.8161 (OUTLIER) cc_final: 0.7730 (t) REVERT: E 90 ASP cc_start: 0.8227 (m-30) cc_final: 0.7955 (m-30) REVERT: E 166 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8195 (mt) REVERT: E 197 SER cc_start: 0.8235 (p) cc_final: 0.8009 (p) REVERT: B 216 LYS cc_start: 0.8304 (mmtt) cc_final: 0.7967 (tmtt) REVERT: B 235 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7960 (mm) REVERT: B 274 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8265 (tppp) REVERT: B 283 ARG cc_start: 0.7568 (mtm-85) cc_final: 0.7328 (mtm-85) outliers start: 42 outliers final: 29 residues processed: 223 average time/residue: 1.2927 time to fit residues: 307.2615 Evaluate side-chains 239 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 201 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 167 ARG Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 251 PHE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 369 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 95 optimal weight: 0.0170 chunk 91 optimal weight: 0.2980 chunk 99 optimal weight: 0.7980 chunk 48 optimal weight: 0.4980 chunk 17 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 84 optimal weight: 0.0670 chunk 40 optimal weight: 0.5980 overall best weight: 0.2356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 371 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.142292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.128630 restraints weight = 12845.463| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.93 r_work: 0.3591 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8979 Z= 0.166 Angle : 0.574 11.411 12172 Z= 0.280 Chirality : 0.043 0.253 1378 Planarity : 0.004 0.056 1549 Dihedral : 4.333 38.173 1232 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.80 % Allowed : 26.79 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.44 (0.25), residues: 1111 helix: 1.98 (0.28), residues: 364 sheet: -0.46 (0.30), residues: 280 loop : -0.51 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 151 HIS 0.004 0.001 HIS B 387 PHE 0.013 0.001 PHE B 340 TYR 0.014 0.001 TYR E 190 ARG 0.015 0.000 ARG B 280 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 198 time to evaluate : 0.865 Fit side-chains REVERT: A 78 VAL cc_start: 0.7482 (OUTLIER) cc_final: 0.7277 (p) REVERT: A 217 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7863 (mtpm) REVERT: A 313 SER cc_start: 0.8026 (m) cc_final: 0.7632 (t) REVERT: C 86 LEU cc_start: 0.8601 (mm) cc_final: 0.8343 (mp) REVERT: C 167 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7585 (mmt180) REVERT: C 217 VAL cc_start: 0.7829 (p) cc_final: 0.7602 (m) REVERT: C 251 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.8034 (m-80) REVERT: C 303 LEU cc_start: 0.8160 (mp) cc_final: 0.7939 (mp) REVERT: C 335 LEU cc_start: 0.7824 (tt) cc_final: 0.7609 (tp) REVERT: E 71 SER cc_start: 0.8178 (OUTLIER) cc_final: 0.7705 (t) REVERT: E 166 LEU cc_start: 0.8603 (tt) cc_final: 0.8175 (mt) REVERT: E 197 SER cc_start: 0.8132 (p) cc_final: 0.7895 (p) REVERT: B 274 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8247 (tppp) REVERT: B 283 ARG cc_start: 0.7441 (mtm-85) cc_final: 0.7220 (mtm-85) REVERT: B 290 PHE cc_start: 0.7947 (m-10) cc_final: 0.7677 (m-10) REVERT: B 342 ARG cc_start: 0.7261 (ttp80) cc_final: 0.6761 (ttp80) outliers start: 36 outliers final: 27 residues processed: 216 average time/residue: 1.3871 time to fit residues: 318.3590 Evaluate side-chains 229 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 196 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 167 ARG Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 251 PHE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 340 ASP Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 276 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 0.0370 chunk 59 optimal weight: 0.5980 chunk 62 optimal weight: 0.1980 chunk 102 optimal weight: 1.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN B 371 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.141237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.127569 restraints weight = 12856.897| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 1.91 r_work: 0.3573 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8979 Z= 0.215 Angle : 0.585 11.456 12172 Z= 0.290 Chirality : 0.043 0.174 1378 Planarity : 0.004 0.056 1549 Dihedral : 4.368 33.622 1232 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.48 % Allowed : 27.74 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.44 (0.26), residues: 1111 helix: 1.96 (0.28), residues: 365 sheet: -0.50 (0.30), residues: 282 loop : -0.47 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 151 HIS 0.004 0.001 HIS B 387 PHE 0.013 0.001 PHE C 216 TYR 0.012 0.001 TYR E 190 ARG 0.015 0.000 ARG B 280 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7521.85 seconds wall clock time: 130 minutes 39.52 seconds (7839.52 seconds total)