Starting phenix.real_space_refine on Sat Dec 28 16:27:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ys6_34073/12_2024/7ys6_34073.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ys6_34073/12_2024/7ys6_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_34073/12_2024/7ys6_34073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ys6_34073/12_2024/7ys6_34073.map" model { file = "/net/cci-nas-00/data/ceres_data/7ys6_34073/12_2024/7ys6_34073.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ys6_34073/12_2024/7ys6_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 5.42, per 1000 atoms: 0.62 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: 3.01 Conformation dependent library (CDL) restraints added in 1.2 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: 1.02 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: 2.74 Time building geometry restraints manager: 2.65 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: 1.660 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.140 Find NCS groups from input model: 0.120 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: 0.000 Load rotamer database and sin/cos tables:13.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.130 ------------------------------------------------------------------------------- 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 : 0.971 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: 1.1131 time to fit residues: 269.9471 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 : 1.029 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 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 29.545 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 : 0.984 Fit side-chains REVERT: A 78 VAL cc_start: 0.7677 (m) cc_final: 0.7448 (p) REVERT: A 212 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7135 (mt) REVERT: C 36 ARG cc_start: 0.7088 (ttp80) cc_final: 0.6800 (ttp-170) REVERT: C 62 MET cc_start: 0.7881 (mtt) cc_final: 0.7665 (mtm) REVERT: C 154 ARG cc_start: 0.7932 (ttm110) cc_final: 0.7732 (ttm-80) REVERT: C 172 ASN cc_start: 0.8017 (t0) cc_final: 0.7765 (t0) REVERT: C 192 GLN cc_start: 0.8137 (mm-40) cc_final: 0.7873 (mm-40) REVERT: C 251 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.8070 (m-80) REVERT: C 260 THR cc_start: 0.8079 (m) cc_final: 0.7793 (p) REVERT: C 351 SER cc_start: 0.7224 (m) cc_final: 0.6952 (m) REVERT: E 71 SER cc_start: 0.7736 (OUTLIER) cc_final: 0.7406 (t) REVERT: E 166 LEU cc_start: 0.8455 (tt) cc_final: 0.8029 (mt) REVERT: E 197 SER cc_start: 0.8147 (p) cc_final: 0.7943 (p) REVERT: E 232 HIS cc_start: 0.8052 (OUTLIER) cc_final: 0.7843 (m-70) REVERT: B 216 LYS cc_start: 0.7948 (mmtt) cc_final: 0.7720 (mmtt) REVERT: B 340 PHE cc_start: 0.8155 (t80) cc_final: 0.7938 (t80) REVERT: B 356 ARG cc_start: 0.7238 (ttm110) cc_final: 0.6997 (ttp-110) REVERT: B 371 ASN cc_start: 0.8275 (m-40) cc_final: 0.8047 (m110) REVERT: B 373 ARG cc_start: 0.8121 (mtp85) cc_final: 0.7887 (mmm160) outliers start: 41 outliers final: 16 residues processed: 237 average time/residue: 1.1168 time to fit residues: 283.6533 Evaluate side-chains 223 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 193 SER Chi-restraints excluded: chain A residue 212 LEU 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 219 LEU Chi-restraints excluded: chain E residue 232 HIS 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 55 optimal weight: 0.3980 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 34 optimal weight: 0.2980 chunk 80 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 ASN B 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8979 Z= 0.217 Angle : 0.558 8.990 12172 Z= 0.285 Chirality : 0.042 0.200 1378 Planarity : 0.005 0.056 1549 Dihedral : 4.638 35.589 1232 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 5.17 % Allowed : 22.26 % Favored : 72.57 % 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: -0.24 (0.25), residues: 1111 helix: 1.14 (0.27), residues: 355 sheet: -0.63 (0.30), residues: 276 loop : -0.76 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.004 0.001 HIS E 35 PHE 0.011 0.002 PHE C 216 TYR 0.014 0.001 TYR E 190 ARG 0.011 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 260 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 211 time to evaluate : 0.956 Fit side-chains REVERT: A 78 VAL cc_start: 0.7671 (OUTLIER) cc_final: 0.7446 (p) REVERT: A 319 ILE cc_start: 0.6262 (mm) cc_final: 0.5862 (mm) REVERT: C 36 ARG cc_start: 0.6996 (ttp80) cc_final: 0.6613 (ttp-170) REVERT: C 39 ARG cc_start: 0.8115 (mtt180) cc_final: 0.7897 (mtt180) REVERT: C 154 ARG cc_start: 0.7953 (ttm110) cc_final: 0.7738 (ttm110) REVERT: C 167 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7878 (mmt180) REVERT: C 172 ASN cc_start: 0.7973 (t0) cc_final: 0.7705 (t0) REVERT: C 188 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.7435 (mm) REVERT: C 249 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8230 (tp) REVERT: C 251 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.8052 (m-80) REVERT: C 335 LEU cc_start: 0.7856 (tt) cc_final: 0.7550 (tt) REVERT: C 351 SER cc_start: 0.7247 (m) cc_final: 0.6952 (m) REVERT: E 71 SER cc_start: 0.7799 (OUTLIER) cc_final: 0.7409 (t) REVERT: E 83 MET cc_start: 0.7741 (mtm) cc_final: 0.7522 (mtp) REVERT: E 166 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8075 (mt) REVERT: E 197 SER cc_start: 0.8139 (p) cc_final: 0.7895 (p) REVERT: B 29 GLN cc_start: 0.7943 (tp40) cc_final: 0.7580 (tp-100) REVERT: B 216 LYS cc_start: 0.7945 (mmtt) cc_final: 0.7713 (mmtt) REVERT: B 274 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8184 (tppp) REVERT: B 286 SER cc_start: 0.8215 (OUTLIER) cc_final: 0.7969 (m) REVERT: B 356 ARG cc_start: 0.7201 (ttm110) cc_final: 0.6969 (ttp-110) outliers start: 49 outliers final: 17 residues processed: 236 average time/residue: 1.0835 time to fit residues: 274.0935 Evaluate side-chains 232 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 119 LEU Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 122 LEU 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 249 ILE 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 204 SER 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 286 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 193 GLN ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 ASN B 371 ASN B 387 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 8979 Z= 0.377 Angle : 0.630 8.705 12172 Z= 0.322 Chirality : 0.045 0.187 1378 Planarity : 0.005 0.055 1549 Dihedral : 4.760 26.827 1232 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 6.01 % Allowed : 21.10 % Favored : 72.89 % 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: -0.16 (0.25), residues: 1111 helix: 1.28 (0.28), residues: 366 sheet: -0.65 (0.30), residues: 277 loop : -0.79 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 314 HIS 0.008 0.002 HIS E 232 PHE 0.017 0.002 PHE A 277 TYR 0.014 0.002 TYR B 253 ARG 0.010 0.001 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 271 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 214 time to evaluate : 1.025 Fit side-chains REVERT: A 78 VAL cc_start: 0.7736 (OUTLIER) cc_final: 0.7477 (p) REVERT: A 269 THR cc_start: 0.7656 (m) cc_final: 0.7332 (m) REVERT: A 315 MET cc_start: 0.5920 (mmt) cc_final: 0.5706 (mmt) REVERT: C 146 ARG cc_start: 0.7046 (mtm180) cc_final: 0.6838 (mtm180) REVERT: C 167 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7906 (mmt180) REVERT: C 172 ASN cc_start: 0.7993 (t0) cc_final: 0.7520 (t0) REVERT: C 251 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.8033 (m-80) REVERT: C 335 LEU cc_start: 0.7948 (tt) cc_final: 0.7574 (tp) REVERT: E 71 SER cc_start: 0.7811 (OUTLIER) cc_final: 0.7430 (t) REVERT: E 83 MET cc_start: 0.7939 (mtm) cc_final: 0.7595 (mtp) REVERT: E 166 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8172 (mt) REVERT: E 197 SER cc_start: 0.8211 (p) cc_final: 0.7980 (p) REVERT: B 274 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8217 (ttpp) REVERT: B 342 ARG cc_start: 0.7264 (ttp80) cc_final: 0.6663 (ttp80) outliers start: 57 outliers final: 28 residues processed: 246 average time/residue: 1.1535 time to fit residues: 303.4902 Evaluate side-chains 241 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 207 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 119 LEU Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 272 ILE 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 127 ASN 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 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 226 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain B residue 25 MET 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 369 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 0 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 ASN C 283 HIS E 142 GLN B 292 ASN B 371 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8979 Z= 0.269 Angle : 0.596 10.213 12172 Z= 0.299 Chirality : 0.044 0.171 1378 Planarity : 0.004 0.053 1549 Dihedral : 4.561 24.353 1232 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 5.06 % Allowed : 23.84 % Favored : 71.10 % 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: 0.08 (0.25), residues: 1111 helix: 1.52 (0.28), residues: 367 sheet: -0.58 (0.30), residues: 277 loop : -0.65 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 314 HIS 0.004 0.001 HIS E 35 PHE 0.015 0.002 PHE C 216 TYR 0.013 0.001 TYR E 190 ARG 0.010 0.000 ARG A 137 *********************** 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 246 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 198 time to evaluate : 0.988 Fit side-chains REVERT: A 78 VAL cc_start: 0.7704 (OUTLIER) cc_final: 0.7479 (p) REVERT: A 269 THR cc_start: 0.7583 (OUTLIER) cc_final: 0.7274 (m) REVERT: A 272 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7400 (pt) REVERT: C 36 ARG cc_start: 0.7250 (ttp80) cc_final: 0.6796 (ttp80) REVERT: C 167 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7728 (mmt180) REVERT: C 172 ASN cc_start: 0.8067 (t0) cc_final: 0.7658 (t0) REVERT: C 251 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.8057 (m-80) REVERT: C 335 LEU cc_start: 0.7853 (tt) cc_final: 0.7599 (tt) REVERT: E 71 SER cc_start: 0.7821 (OUTLIER) cc_final: 0.7419 (t) REVERT: E 83 MET cc_start: 0.7826 (mtm) cc_final: 0.7615 (mtp) REVERT: E 166 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8193 (mt) REVERT: E 197 SER cc_start: 0.8189 (p) cc_final: 0.7978 (p) REVERT: B 34 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7676 (tppt) REVERT: B 274 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8206 (tppp) REVERT: B 342 ARG cc_start: 0.7218 (ttp80) cc_final: 0.6700 (ttp80) outliers start: 48 outliers final: 23 residues processed: 222 average time/residue: 1.2219 time to fit residues: 288.9230 Evaluate side-chains 226 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 122 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 276 MET 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 188 ILE Chi-restraints excluded: chain C residue 198 THR 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 51 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain B residue 34 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.0370 chunk 95 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 55 optimal weight: 0.2980 chunk 102 optimal weight: 0.4980 overall best weight: 0.3858 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8979 Z= 0.200 Angle : 0.561 9.227 12172 Z= 0.283 Chirality : 0.042 0.156 1378 Planarity : 0.004 0.053 1549 Dihedral : 4.428 29.842 1232 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.85 % Allowed : 24.89 % Favored : 70.25 % 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: 0.26 (0.25), residues: 1111 helix: 1.77 (0.28), residues: 366 sheet: -0.54 (0.30), residues: 277 loop : -0.57 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 151 HIS 0.002 0.001 HIS E 35 PHE 0.011 0.001 PHE B 222 TYR 0.015 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 246 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 200 time to evaluate : 0.939 Fit side-chains REVERT: A 78 VAL cc_start: 0.7689 (OUTLIER) cc_final: 0.7466 (p) REVERT: A 101 LEU cc_start: 0.5336 (OUTLIER) cc_final: 0.4801 (tp) REVERT: A 269 THR cc_start: 0.7528 (OUTLIER) cc_final: 0.7196 (m) REVERT: A 272 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.7355 (pt) REVERT: C 167 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7629 (mmt180) REVERT: C 172 ASN cc_start: 0.7990 (t0) cc_final: 0.7664 (t0) REVERT: C 217 VAL cc_start: 0.7728 (p) cc_final: 0.7478 (m) REVERT: C 251 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.8024 (m-80) REVERT: C 303 LEU cc_start: 0.8224 (mp) cc_final: 0.7981 (mp) REVERT: C 335 LEU cc_start: 0.7748 (tt) cc_final: 0.7493 (tt) REVERT: E 71 SER cc_start: 0.7880 (p) cc_final: 0.7452 (t) REVERT: E 83 MET cc_start: 0.7802 (mtm) cc_final: 0.7575 (mtp) REVERT: E 166 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8129 (mt) REVERT: E 168 SER cc_start: 0.7881 (p) cc_final: 0.7670 (p) REVERT: E 197 SER cc_start: 0.8161 (p) cc_final: 0.7942 (p) REVERT: B 235 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7988 (mm) REVERT: B 342 ARG cc_start: 0.7160 (ttp80) cc_final: 0.6699 (ttp80) REVERT: B 385 ARG cc_start: 0.7549 (mpt-90) cc_final: 0.7320 (mpt180) outliers start: 46 outliers final: 24 residues processed: 227 average time/residue: 1.2195 time to fit residues: 295.1311 Evaluate side-chains 230 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 122 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 276 MET 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 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 146 SER Chi-restraints excluded: chain E residue 166 LEU 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 276 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 ASN B 292 ASN B 371 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8979 Z= 0.335 Angle : 0.639 13.699 12172 Z= 0.320 Chirality : 0.045 0.244 1378 Planarity : 0.004 0.053 1549 Dihedral : 4.636 24.822 1232 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.75 % Allowed : 24.79 % Favored : 70.46 % 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: 0.12 (0.25), residues: 1111 helix: 1.61 (0.28), residues: 367 sheet: -0.56 (0.30), residues: 271 loop : -0.67 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 228 HIS 0.005 0.001 HIS E 232 PHE 0.017 0.002 PHE A 277 TYR 0.011 0.002 TYR B 253 ARG 0.013 0.001 ARG A 137 *********************** 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 247 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 202 time to evaluate : 0.920 Fit side-chains REVERT: A 78 VAL cc_start: 0.7703 (OUTLIER) cc_final: 0.7439 (p) REVERT: A 101 LEU cc_start: 0.5470 (OUTLIER) cc_final: 0.4918 (tp) REVERT: A 156 LEU cc_start: 0.7533 (tm) cc_final: 0.6924 (tp) REVERT: A 269 THR cc_start: 0.7626 (OUTLIER) cc_final: 0.7290 (m) REVERT: C 167 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7765 (mmt180) REVERT: C 172 ASN cc_start: 0.7998 (t0) cc_final: 0.7583 (t0) REVERT: C 251 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.8034 (m-80) REVERT: C 335 LEU cc_start: 0.7848 (tt) cc_final: 0.7520 (tt) REVERT: E 71 SER cc_start: 0.7897 (OUTLIER) cc_final: 0.7455 (t) REVERT: E 166 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8208 (mt) REVERT: E 197 SER cc_start: 0.8227 (p) cc_final: 0.8002 (p) REVERT: B 274 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8198 (tppp) REVERT: B 385 ARG cc_start: 0.7618 (mpt-90) cc_final: 0.7406 (mmt90) outliers start: 45 outliers final: 25 residues processed: 224 average time/residue: 1.2192 time to fit residues: 290.8760 Evaluate side-chains 230 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 197 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 269 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 276 MET 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 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 93 MET Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 172 THR 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 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 63 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 83 optimal weight: 0.0570 chunk 96 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 ASN C 127 ASN C 237 GLN B 371 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8979 Z= 0.240 Angle : 0.596 12.848 12172 Z= 0.298 Chirality : 0.043 0.250 1378 Planarity : 0.004 0.059 1549 Dihedral : 4.496 25.347 1232 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.11 % Allowed : 25.95 % 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: 0.24 (0.25), residues: 1111 helix: 1.73 (0.28), residues: 366 sheet: -0.54 (0.30), residues: 281 loop : -0.58 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 151 HIS 0.003 0.001 HIS E 35 PHE 0.013 0.001 PHE C 216 TYR 0.013 0.001 TYR E 190 ARG 0.013 0.000 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 234 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 195 time to evaluate : 1.070 Fit side-chains REVERT: A 78 VAL cc_start: 0.7674 (OUTLIER) cc_final: 0.7455 (p) REVERT: A 101 LEU cc_start: 0.5408 (OUTLIER) cc_final: 0.4830 (tp) REVERT: A 156 LEU cc_start: 0.7482 (tm) cc_final: 0.6880 (tp) REVERT: A 269 THR cc_start: 0.7513 (OUTLIER) cc_final: 0.7093 (m) REVERT: A 272 ILE cc_start: 0.7691 (OUTLIER) cc_final: 0.7473 (pt) REVERT: C 167 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7512 (mmt180) REVERT: C 172 ASN cc_start: 0.8052 (t0) cc_final: 0.7739 (t0) REVERT: C 217 VAL cc_start: 0.7766 (p) cc_final: 0.7523 (m) REVERT: C 251 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.8012 (m-80) REVERT: C 303 LEU cc_start: 0.8258 (mp) cc_final: 0.8015 (mp) REVERT: C 335 LEU cc_start: 0.7757 (tt) cc_final: 0.7504 (tt) REVERT: E 71 SER cc_start: 0.7842 (OUTLIER) cc_final: 0.7440 (t) REVERT: E 166 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8196 (mt) REVERT: E 197 SER cc_start: 0.8223 (p) cc_final: 0.8001 (p) REVERT: B 235 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7980 (mm) REVERT: B 274 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8182 (tppp) REVERT: B 385 ARG cc_start: 0.7630 (mpt-90) cc_final: 0.7402 (mpt180) outliers start: 39 outliers final: 27 residues processed: 215 average time/residue: 1.2860 time to fit residues: 293.7425 Evaluate side-chains 228 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 191 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 153 LEU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 276 MET 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 279 MET Chi-restraints excluded: chain C residue 285 ASN 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 166 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 192 MET 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 274 LYS Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 368 ASP 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 98 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 63 optimal weight: 0.0040 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 237 GLN B 371 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8979 Z= 0.232 Angle : 0.592 12.408 12172 Z= 0.297 Chirality : 0.043 0.234 1378 Planarity : 0.004 0.060 1549 Dihedral : 4.485 28.165 1232 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.22 % Allowed : 25.95 % Favored : 69.83 % 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: 0.27 (0.25), residues: 1111 helix: 1.78 (0.28), residues: 366 sheet: -0.57 (0.30), residues: 281 loop : -0.56 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 151 HIS 0.003 0.001 HIS E 35 PHE 0.013 0.001 PHE C 216 TYR 0.012 0.001 TYR E 190 ARG 0.015 0.000 ARG B 280 *********************** 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 233 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 193 time to evaluate : 1.141 Fit side-chains REVERT: A 78 VAL cc_start: 0.7672 (OUTLIER) cc_final: 0.7447 (p) REVERT: A 101 LEU cc_start: 0.5404 (OUTLIER) cc_final: 0.4841 (tp) REVERT: A 137 ARG cc_start: 0.7629 (ptp-110) cc_final: 0.7144 (ptp-110) REVERT: A 156 LEU cc_start: 0.7459 (tm) cc_final: 0.6874 (tp) REVERT: A 269 THR cc_start: 0.7540 (OUTLIER) cc_final: 0.7234 (m) REVERT: A 272 ILE cc_start: 0.7661 (OUTLIER) cc_final: 0.7414 (pt) REVERT: C 167 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7509 (mmt180) REVERT: C 172 ASN cc_start: 0.8051 (t0) cc_final: 0.7726 (t0) REVERT: C 217 VAL cc_start: 0.7774 (p) cc_final: 0.7534 (m) REVERT: C 236 ARG cc_start: 0.6999 (mtp85) cc_final: 0.6630 (mtp85) REVERT: C 237 GLN cc_start: 0.7652 (mt0) cc_final: 0.7353 (mt0) REVERT: C 251 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.7994 (m-80) REVERT: C 303 LEU cc_start: 0.8245 (mp) cc_final: 0.8009 (mp) REVERT: C 335 LEU cc_start: 0.7759 (tt) cc_final: 0.7506 (tt) REVERT: E 71 SER cc_start: 0.7864 (OUTLIER) cc_final: 0.7443 (t) REVERT: E 166 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8153 (mt) REVERT: E 197 SER cc_start: 0.8215 (p) cc_final: 0.7993 (p) REVERT: B 235 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7995 (mm) REVERT: B 385 ARG cc_start: 0.7673 (mpt-90) cc_final: 0.7464 (mpt180) REVERT: B 391 TYR cc_start: 0.8276 (m-80) cc_final: 0.8032 (m-10) outliers start: 40 outliers final: 31 residues processed: 212 average time/residue: 1.3157 time to fit residues: 296.8491 Evaluate side-chains 230 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 190 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 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 267 SER Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 276 MET 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 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 285 ASN 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 192 MET 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 236 GLN 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 49 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 0.3980 chunk 69 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8979 Z= 0.280 Angle : 0.620 12.090 12172 Z= 0.311 Chirality : 0.044 0.229 1378 Planarity : 0.004 0.057 1549 Dihedral : 4.561 24.747 1232 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.64 % Allowed : 25.63 % Favored : 69.73 % 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: 1.69 (0.28), residues: 367 sheet: -0.62 (0.29), residues: 282 loop : -0.52 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 151 HIS 0.004 0.001 HIS E 35 PHE 0.015 0.002 PHE C 216 TYR 0.011 0.001 TYR B 253 ARG 0.014 0.001 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 236 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 192 time to evaluate : 0.988 Fit side-chains REVERT: A 78 VAL cc_start: 0.7680 (OUTLIER) cc_final: 0.7436 (p) REVERT: A 101 LEU cc_start: 0.5432 (OUTLIER) cc_final: 0.4874 (tp) REVERT: A 212 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7730 (mm) REVERT: A 269 THR cc_start: 0.7551 (OUTLIER) cc_final: 0.7228 (m) REVERT: A 272 ILE cc_start: 0.7745 (OUTLIER) cc_final: 0.7446 (pt) REVERT: C 167 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7495 (mmt180) REVERT: C 172 ASN cc_start: 0.8065 (t0) cc_final: 0.7743 (t0) REVERT: C 236 ARG cc_start: 0.7006 (mtp85) cc_final: 0.6743 (mtp85) REVERT: C 251 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.8025 (m-80) REVERT: C 303 LEU cc_start: 0.8305 (mp) cc_final: 0.8066 (mp) REVERT: C 335 LEU cc_start: 0.7810 (tt) cc_final: 0.7512 (tt) REVERT: E 71 SER cc_start: 0.7827 (OUTLIER) cc_final: 0.7430 (t) REVERT: E 166 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8208 (mt) REVERT: E 197 SER cc_start: 0.8211 (p) cc_final: 0.7993 (p) REVERT: B 235 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7995 (mm) REVERT: B 274 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8189 (tppp) REVERT: B 385 ARG cc_start: 0.7624 (mpt-90) cc_final: 0.7415 (mpt180) REVERT: B 391 TYR cc_start: 0.8298 (m-80) cc_final: 0.8036 (m-10) outliers start: 44 outliers final: 29 residues processed: 214 average time/residue: 1.2930 time to fit residues: 294.5476 Evaluate side-chains 231 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 191 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 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 212 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 276 MET 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 192 MET 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 236 GLN Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 368 ASP 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 80 optimal weight: 0.0870 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 63 optimal weight: 0.0010 overall best weight: 0.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 237 GLN B 371 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.141045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.127793 restraints weight = 12755.782| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.91 r_work: 0.3588 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8979 Z= 0.209 Angle : 0.583 9.855 12172 Z= 0.293 Chirality : 0.042 0.145 1378 Planarity : 0.004 0.057 1549 Dihedral : 4.459 30.510 1232 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.80 % Allowed : 26.90 % Favored : 69.30 % 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: 0.33 (0.25), residues: 1111 helix: 1.81 (0.28), residues: 371 sheet: -0.49 (0.30), residues: 278 loop : -0.55 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 151 HIS 0.003 0.001 HIS B 357 PHE 0.013 0.001 PHE B 340 TYR 0.013 0.001 TYR E 190 ARG 0.014 0.001 ARG B 280 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4471.89 seconds wall clock time: 80 minutes 28.06 seconds (4828.06 seconds total)