Starting phenix.real_space_refine on Sat Aug 23 00:34:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ys6_34073/08_2025/7ys6_34073.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ys6_34073/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ys6_34073/08_2025/7ys6_34073.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ys6_34073/08_2025/7ys6_34073.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ys6_34073/08_2025/7ys6_34073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ys6_34073/08_2025/7ys6_34073.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.61, per 1000 atoms: 0.18 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: 0.56 Conformation dependent library (CDL) restraints added in 271.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.31 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: 0.95 Time building geometry restraints manager: 0.80 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: 0.900 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.140 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.750 ------------------------------------------------------------------------------- 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 8980 Z= 0.441 Angle : 1.108 11.431 12174 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.023 0.001 ARG C 236 TYR 0.018 0.002 TYR E 103 PHE 0.031 0.002 PHE A 277 TRP 0.016 0.001 TRP A 166 HIS 0.006 0.001 HIS B 357 Details of bonding type rmsd covalent geometry : bond 0.00712 ( 8979) covalent geometry : angle 1.10792 (12172) SS BOND : bond 0.00006 ( 1) SS BOND : angle 0.77922 ( 2) hydrogen bonds : bond 0.18428 ( 405) hydrogen bonds : angle 8.62593 ( 1176) *********************** 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 : 0.346 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: 0.5357 time to fit residues: 129.4403 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 : 0.332 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 HIS 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 = 0.3877 r_free = 0.3877 target = 0.144211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.130003 restraints weight = 12942.664| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.00 r_work: 0.3594 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8980 Z= 0.164 Angle : 0.610 8.522 12174 Z= 0.316 Chirality : 0.043 0.153 1378 Planarity : 0.005 0.051 1549 Dihedral : 4.867 36.670 1233 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.11 % Allowed : 21.94 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.24), residues: 1111 helix: -0.04 (0.25), residues: 352 sheet: -0.69 (0.30), residues: 290 loop : -0.90 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 385 TYR 0.015 0.002 TYR E 190 PHE 0.017 0.002 PHE B 212 TRP 0.014 0.002 TRP E 47 HIS 0.004 0.001 HIS C 108 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 8979) covalent geometry : angle 0.61029 (12172) SS BOND : bond 0.00603 ( 1) SS BOND : angle 0.19870 ( 2) hydrogen bonds : bond 0.04080 ( 405) hydrogen bonds : angle 5.26070 ( 1176) *********************** 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 262 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 223 time to evaluate : 0.335 Fit side-chains REVERT: A 108 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7769 (ttp) REVERT: C 62 MET cc_start: 0.7932 (mtt) cc_final: 0.7705 (mtm) REVERT: C 137 ILE cc_start: 0.7550 (mm) cc_final: 0.7344 (mp) REVERT: C 146 ARG cc_start: 0.7611 (ttm170) cc_final: 0.7371 (mtm180) REVERT: C 172 ASN cc_start: 0.8144 (t0) cc_final: 0.7941 (t0) REVERT: C 192 GLN cc_start: 0.8268 (mm-40) cc_final: 0.8046 (mm-40) REVERT: C 201 THR cc_start: 0.8248 (p) cc_final: 0.8045 (p) REVERT: C 251 PHE cc_start: 0.8596 (OUTLIER) cc_final: 0.8170 (m-80) REVERT: C 314 TRP cc_start: 0.8340 (m100) cc_final: 0.8133 (m100) REVERT: E 71 SER cc_start: 0.7991 (OUTLIER) cc_final: 0.7616 (t) REVERT: E 166 LEU cc_start: 0.8461 (tt) cc_final: 0.8048 (mt) REVERT: E 197 SER cc_start: 0.8166 (p) cc_final: 0.7932 (p) REVERT: E 214 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7407 (tp) REVERT: E 238 THR cc_start: 0.8609 (OUTLIER) cc_final: 0.8402 (p) REVERT: B 28 LYS cc_start: 0.8342 (ptmt) cc_final: 0.8099 (ptmt) REVERT: B 34 LYS cc_start: 0.7874 (tppt) cc_final: 0.7649 (tppt) REVERT: B 216 LYS cc_start: 0.8221 (mmtt) cc_final: 0.7853 (mmtt) REVERT: B 274 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8027 (tptp) REVERT: B 331 ASP cc_start: 0.4245 (t70) cc_final: 0.3891 (t70) REVERT: B 340 PHE cc_start: 0.7988 (t80) cc_final: 0.7759 (t80) REVERT: B 356 ARG cc_start: 0.7465 (ttm110) cc_final: 0.7165 (ttp-110) REVERT: B 373 ARG cc_start: 0.8157 (mtp85) cc_final: 0.7950 (mmp80) REVERT: B 374 ARG cc_start: 0.8253 (mtt-85) cc_final: 0.8023 (mtt180) REVERT: B 380 ARG cc_start: 0.7827 (ttp80) cc_final: 0.7618 (ttp-110) outliers start: 39 outliers final: 17 residues processed: 242 average time/residue: 0.5207 time to fit residues: 134.9254 Evaluate side-chains 229 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 119 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 198 THR Chi-restraints excluded: chain C residue 251 PHE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 93 MET 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 E residue 238 THR 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 274 LYS Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 301 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 102 optimal weight: 0.0470 chunk 25 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 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 = 0.3857 r_free = 0.3857 target = 0.142337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.128349 restraints weight = 12675.359| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.93 r_work: 0.3588 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8980 Z= 0.148 Angle : 0.570 9.195 12174 Z= 0.292 Chirality : 0.043 0.210 1378 Planarity : 0.004 0.055 1549 Dihedral : 4.594 33.660 1232 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 5.59 % Allowed : 21.10 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.25), residues: 1111 helix: 1.17 (0.27), residues: 355 sheet: -0.56 (0.31), residues: 276 loop : -0.77 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 342 TYR 0.013 0.001 TYR E 190 PHE 0.012 0.002 PHE C 216 TRP 0.013 0.001 TRP E 47 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 8979) covalent geometry : angle 0.57010 (12172) SS BOND : bond 0.00470 ( 1) SS BOND : angle 0.64514 ( 2) hydrogen bonds : bond 0.03682 ( 405) hydrogen bonds : angle 4.77173 ( 1176) *********************** 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 267 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 214 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.5655 (mtm) cc_final: 0.5454 (mtm) REVERT: A 108 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7742 (ttp) REVERT: A 319 ILE cc_start: 0.6354 (mm) cc_final: 0.5873 (mm) REVERT: C 62 MET cc_start: 0.7937 (mtt) cc_final: 0.7735 (mtm) REVERT: C 146 ARG cc_start: 0.7549 (ttm170) cc_final: 0.7339 (mtm180) REVERT: C 167 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8103 (mmt180) REVERT: C 172 ASN cc_start: 0.8097 (t0) cc_final: 0.7825 (t0) REVERT: C 201 THR cc_start: 0.8290 (p) cc_final: 0.8077 (p) REVERT: C 249 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8268 (tp) REVERT: C 251 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.8110 (m-80) REVERT: C 335 LEU cc_start: 0.8100 (tt) cc_final: 0.7829 (tt) REVERT: E 71 SER cc_start: 0.8057 (OUTLIER) cc_final: 0.7660 (t) REVERT: E 166 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8125 (mt) REVERT: E 197 SER cc_start: 0.8168 (p) cc_final: 0.7948 (p) REVERT: E 214 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7385 (tp) REVERT: B 27 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6935 (mt-10) REVERT: B 28 LYS cc_start: 0.8372 (ptmt) cc_final: 0.8145 (ptmt) REVERT: B 29 GLN cc_start: 0.7901 (tp40) cc_final: 0.7468 (tp-100) REVERT: B 216 LYS cc_start: 0.8255 (mmtt) cc_final: 0.7893 (mmtt) REVERT: B 286 SER cc_start: 0.8310 (p) cc_final: 0.8047 (m) REVERT: B 340 PHE cc_start: 0.7964 (t80) cc_final: 0.7764 (t80) outliers start: 53 outliers final: 19 residues processed: 242 average time/residue: 0.5315 time to fit residues: 137.5869 Evaluate side-chains 230 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 204 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 198 THR Chi-restraints excluded: chain C residue 249 ILE 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 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 192 MET Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain B residue 222 PHE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 79 optimal weight: 0.4980 chunk 89 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 192 GLN B 292 ASN B 371 ASN B 387 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.139650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.125869 restraints weight = 12718.850| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.92 r_work: 0.3546 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 8980 Z= 0.194 Angle : 0.590 8.220 12174 Z= 0.301 Chirality : 0.044 0.162 1378 Planarity : 0.004 0.054 1549 Dihedral : 4.630 30.874 1232 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 5.06 % Allowed : 22.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.25), residues: 1111 helix: 1.49 (0.28), residues: 361 sheet: -0.55 (0.30), residues: 277 loop : -0.71 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 280 TYR 0.012 0.002 TYR E 175 PHE 0.014 0.002 PHE A 277 TRP 0.013 0.002 TRP C 314 HIS 0.006 0.001 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 8979) covalent geometry : angle 0.59045 (12172) SS BOND : bond 0.00484 ( 1) SS BOND : angle 0.63583 ( 2) hydrogen bonds : bond 0.03862 ( 405) hydrogen bonds : angle 4.76851 ( 1176) *********************** 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 255 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 207 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 108 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7757 (ttp) REVERT: A 156 LEU cc_start: 0.7304 (tt) cc_final: 0.6994 (tp) REVERT: A 272 ILE cc_start: 0.7849 (OUTLIER) cc_final: 0.7477 (pt) REVERT: C 62 MET cc_start: 0.8005 (mtt) cc_final: 0.7788 (mtm) REVERT: C 146 ARG cc_start: 0.7578 (ttm170) cc_final: 0.7365 (mtm180) REVERT: C 167 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8081 (mmt180) REVERT: C 172 ASN cc_start: 0.8166 (t0) cc_final: 0.7733 (t0) REVERT: C 249 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8275 (tp) REVERT: C 251 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.8160 (m-80) REVERT: C 335 LEU cc_start: 0.8095 (tt) cc_final: 0.7885 (tt) REVERT: E 71 SER cc_start: 0.8079 (OUTLIER) cc_final: 0.7665 (t) REVERT: E 166 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8218 (mt) REVERT: E 192 MET cc_start: 0.7199 (OUTLIER) cc_final: 0.6919 (ptm) REVERT: E 197 SER cc_start: 0.8191 (p) cc_final: 0.7972 (p) REVERT: B 28 LYS cc_start: 0.8348 (ptmt) cc_final: 0.8121 (ptmt) REVERT: B 34 LYS cc_start: 0.7940 (tppt) cc_final: 0.7594 (tppt) REVERT: B 216 LYS cc_start: 0.8235 (mmtt) cc_final: 0.7952 (tmtt) outliers start: 48 outliers final: 24 residues processed: 232 average time/residue: 0.5862 time to fit residues: 144.6837 Evaluate side-chains 233 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 198 THR Chi-restraints excluded: chain C residue 249 ILE 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 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 146 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 192 MET 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 242 THR 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 108 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 81 optimal weight: 0.4980 chunk 43 optimal weight: 0.0020 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 14 optimal weight: 0.0570 overall best weight: 0.3706 ------------------------------------------------------------------------------- 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 B 371 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.141670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.127875 restraints weight = 12777.852| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.93 r_work: 0.3583 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8980 Z= 0.122 Angle : 0.547 8.226 12174 Z= 0.279 Chirality : 0.042 0.157 1378 Planarity : 0.004 0.053 1549 Dihedral : 4.468 34.182 1232 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.17 % Allowed : 23.10 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.25), residues: 1111 helix: 1.75 (0.28), residues: 366 sheet: -0.48 (0.30), residues: 276 loop : -0.64 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 137 TYR 0.015 0.001 TYR E 190 PHE 0.011 0.001 PHE C 216 TRP 0.011 0.001 TRP B 234 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8979) covalent geometry : angle 0.54713 (12172) SS BOND : bond 0.00379 ( 1) SS BOND : angle 0.42625 ( 2) hydrogen bonds : bond 0.03368 ( 405) hydrogen bonds : angle 4.57213 ( 1176) *********************** 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 249 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 200 time to evaluate : 0.362 Fit side-chains REVERT: A 108 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7705 (ttp) REVERT: A 156 LEU cc_start: 0.7275 (tt) cc_final: 0.6962 (tp) REVERT: A 217 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7993 (ptpp) REVERT: A 269 THR cc_start: 0.7843 (OUTLIER) cc_final: 0.7531 (m) REVERT: A 272 ILE cc_start: 0.7665 (OUTLIER) cc_final: 0.7357 (pt) REVERT: C 62 MET cc_start: 0.8017 (mtt) cc_final: 0.7806 (mtm) REVERT: C 86 LEU cc_start: 0.8608 (mm) cc_final: 0.8367 (mt) REVERT: C 167 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7906 (mmt180) REVERT: C 172 ASN cc_start: 0.8095 (t0) cc_final: 0.7798 (t0) REVERT: C 205 MET cc_start: 0.8074 (mmm) cc_final: 0.7812 (mmm) REVERT: C 249 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8214 (tp) REVERT: C 251 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.8088 (m-80) REVERT: C 325 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8076 (mt) REVERT: E 71 SER cc_start: 0.8127 (OUTLIER) cc_final: 0.7705 (t) REVERT: E 166 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8215 (mt) REVERT: E 168 SER cc_start: 0.7863 (p) cc_final: 0.7652 (p) REVERT: E 197 SER cc_start: 0.8147 (p) cc_final: 0.7920 (p) REVERT: B 34 LYS cc_start: 0.7912 (tppt) cc_final: 0.7513 (tppt) REVERT: B 216 LYS cc_start: 0.8223 (mmtt) cc_final: 0.7919 (tmtt) REVERT: B 274 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8276 (tppp) outliers start: 49 outliers final: 23 residues processed: 227 average time/residue: 0.5803 time to fit residues: 140.2150 Evaluate side-chains 228 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 194 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 217 LYS 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 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 245 ASP Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 251 PHE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 325 LEU 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 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 242 THR Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 276 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 28 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 14 optimal weight: 0.0980 chunk 47 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 80 optimal weight: 0.4980 chunk 97 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.140394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.126684 restraints weight = 12848.725| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.91 r_work: 0.3561 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8980 Z= 0.160 Angle : 0.587 10.403 12174 Z= 0.294 Chirality : 0.043 0.157 1378 Planarity : 0.004 0.052 1549 Dihedral : 4.465 29.312 1232 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 5.91 % Allowed : 22.68 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.25), residues: 1111 helix: 1.68 (0.28), residues: 372 sheet: -0.54 (0.31), residues: 272 loop : -0.64 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 137 TYR 0.012 0.001 TYR E 190 PHE 0.014 0.002 PHE C 216 TRP 0.012 0.001 TRP A 151 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 8979) covalent geometry : angle 0.58654 (12172) SS BOND : bond 0.00408 ( 1) SS BOND : angle 0.50362 ( 2) hydrogen bonds : bond 0.03569 ( 405) hydrogen bonds : angle 4.59305 ( 1176) *********************** 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 260 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 204 time to evaluate : 0.367 Fit side-chains REVERT: A 101 LEU cc_start: 0.5650 (OUTLIER) cc_final: 0.5070 (tp) REVERT: A 156 LEU cc_start: 0.7371 (tt) cc_final: 0.7028 (tp) REVERT: A 204 ILE cc_start: 0.7611 (mt) cc_final: 0.7407 (tt) REVERT: A 217 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7874 (ptpp) REVERT: A 269 THR cc_start: 0.7865 (OUTLIER) cc_final: 0.7590 (m) REVERT: A 272 ILE cc_start: 0.7808 (OUTLIER) cc_final: 0.7425 (pt) REVERT: A 315 MET cc_start: 0.6478 (mmp) cc_final: 0.6256 (mmp) REVERT: A 319 ILE cc_start: 0.7625 (pt) cc_final: 0.7203 (pt) REVERT: A 324 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.6838 (mtt) REVERT: C 36 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.7099 (mtp180) REVERT: C 62 MET cc_start: 0.8058 (mtt) cc_final: 0.7841 (mtm) REVERT: C 86 LEU cc_start: 0.8662 (mm) cc_final: 0.8419 (mp) REVERT: C 167 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7937 (mmt180) REVERT: C 172 ASN cc_start: 0.8102 (t0) cc_final: 0.7794 (t0) REVERT: C 205 MET cc_start: 0.8081 (mmm) cc_final: 0.7848 (mmm) REVERT: C 249 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8238 (tp) REVERT: C 251 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.8143 (m-80) REVERT: C 303 LEU cc_start: 0.8254 (mp) cc_final: 0.8021 (mp) REVERT: C 321 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7420 (ttp80) REVERT: E 71 SER cc_start: 0.8153 (OUTLIER) cc_final: 0.7710 (t) REVERT: E 166 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8228 (mt) REVERT: E 168 SER cc_start: 0.8016 (p) cc_final: 0.7803 (p) REVERT: E 197 SER cc_start: 0.8116 (p) cc_final: 0.7889 (p) REVERT: B 34 LYS cc_start: 0.7903 (tppt) cc_final: 0.7493 (tppt) REVERT: B 216 LYS cc_start: 0.8239 (mmtt) cc_final: 0.7931 (tmtt) REVERT: B 274 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8279 (ttpp) REVERT: B 283 ARG cc_start: 0.7621 (mtm-85) cc_final: 0.7392 (mtm-85) REVERT: B 342 ARG cc_start: 0.7274 (ttp80) cc_final: 0.6732 (ttp80) outliers start: 56 outliers final: 30 residues processed: 235 average time/residue: 0.5896 time to fit residues: 147.4434 Evaluate side-chains 243 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 200 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 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 269 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain C residue 36 ARG Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 63 ARG 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 249 ILE 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 C residue 321 ARG 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 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 28 LYS 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 242 THR 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 12 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 89 optimal weight: 0.4980 chunk 76 optimal weight: 0.0000 chunk 53 optimal weight: 0.5980 chunk 84 optimal weight: 0.3980 chunk 74 optimal weight: 0.9980 chunk 100 optimal weight: 0.0970 overall best weight: 0.3182 ------------------------------------------------------------------------------- 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 B 371 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.142017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.128350 restraints weight = 12832.454| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.91 r_work: 0.3586 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8980 Z= 0.114 Angle : 0.550 9.369 12174 Z= 0.276 Chirality : 0.042 0.147 1378 Planarity : 0.004 0.052 1549 Dihedral : 4.374 37.585 1232 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.54 % Allowed : 25.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.25), residues: 1111 helix: 1.93 (0.28), residues: 371 sheet: -0.53 (0.30), residues: 277 loop : -0.52 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 137 TYR 0.015 0.001 TYR E 190 PHE 0.011 0.001 PHE B 340 TRP 0.016 0.001 TRP A 151 HIS 0.003 0.001 HIS E 232 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8979) covalent geometry : angle 0.55049 (12172) SS BOND : bond 0.00443 ( 1) SS BOND : angle 0.44315 ( 2) hydrogen bonds : bond 0.03229 ( 405) hydrogen bonds : angle 4.44302 ( 1176) *********************** 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 242 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 199 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 156 LEU cc_start: 0.7318 (tt) cc_final: 0.7031 (tp) REVERT: A 217 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7844 (ptpp) REVERT: A 269 THR cc_start: 0.7798 (OUTLIER) cc_final: 0.7317 (m) REVERT: A 319 ILE cc_start: 0.7489 (pt) cc_final: 0.7081 (pt) REVERT: A 324 MET cc_start: 0.7002 (OUTLIER) cc_final: 0.6681 (mtt) REVERT: C 36 ARG cc_start: 0.7529 (ttp-170) cc_final: 0.7027 (mtp180) REVERT: C 62 MET cc_start: 0.8028 (mtt) cc_final: 0.7807 (mtm) REVERT: C 86 LEU cc_start: 0.8620 (mm) cc_final: 0.8360 (mt) REVERT: C 167 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7713 (mmt180) REVERT: C 172 ASN cc_start: 0.8073 (t0) cc_final: 0.7795 (t0) REVERT: C 192 GLN cc_start: 0.8348 (mm-40) cc_final: 0.8125 (mm110) REVERT: C 205 MET cc_start: 0.8054 (mmm) cc_final: 0.7807 (mmm) REVERT: C 249 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.8194 (tp) REVERT: C 251 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.8145 (m-80) REVERT: C 321 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7338 (ttp80) REVERT: C 325 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8104 (mt) REVERT: E 71 SER cc_start: 0.8172 (p) cc_final: 0.7711 (t) REVERT: E 166 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8178 (mt) REVERT: E 197 SER cc_start: 0.8104 (p) cc_final: 0.7871 (p) REVERT: B 34 LYS cc_start: 0.7884 (tppt) cc_final: 0.7488 (tppt) REVERT: B 216 LYS cc_start: 0.8231 (mmtt) cc_final: 0.7911 (tmtt) REVERT: B 235 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7919 (mm) REVERT: B 274 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8245 (tppp) REVERT: B 283 ARG cc_start: 0.7536 (mtm-85) cc_final: 0.7315 (mtm-85) REVERT: B 342 ARG cc_start: 0.7253 (ttp80) cc_final: 0.6783 (ttp80) outliers start: 43 outliers final: 26 residues processed: 227 average time/residue: 0.5829 time to fit residues: 140.7163 Evaluate side-chains 236 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 199 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 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 217 LYS Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 63 ARG 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 249 ILE 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 C residue 321 ARG Chi-restraints excluded: chain C residue 325 LEU 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 28 LYS Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 305 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 100 optimal weight: 0.2980 chunk 34 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 104 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 14 optimal weight: 0.0980 chunk 67 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 51 optimal weight: 0.3980 chunk 74 optimal weight: 0.7980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 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 = 0.3847 r_free = 0.3847 target = 0.141502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.127773 restraints weight = 12794.269| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.93 r_work: 0.3575 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8980 Z= 0.127 Angle : 0.556 8.864 12174 Z= 0.279 Chirality : 0.042 0.156 1378 Planarity : 0.004 0.051 1549 Dihedral : 4.351 34.486 1232 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.11 % Allowed : 25.42 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.25), residues: 1111 helix: 1.93 (0.28), residues: 372 sheet: -0.51 (0.30), residues: 272 loop : -0.52 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 280 TYR 0.012 0.001 TYR E 190 PHE 0.012 0.001 PHE A 277 TRP 0.020 0.001 TRP A 151 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8979) covalent geometry : angle 0.55625 (12172) SS BOND : bond 0.00393 ( 1) SS BOND : angle 0.53351 ( 2) hydrogen bonds : bond 0.03284 ( 405) hydrogen bonds : angle 4.43546 ( 1176) *********************** 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 233 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 194 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 101 LEU cc_start: 0.5717 (OUTLIER) cc_final: 0.5157 (tp) REVERT: A 156 LEU cc_start: 0.7349 (tt) cc_final: 0.7059 (tp) REVERT: A 217 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7893 (ptpp) REVERT: A 324 MET cc_start: 0.7027 (OUTLIER) cc_final: 0.6696 (mtt) REVERT: C 36 ARG cc_start: 0.7532 (ttp-170) cc_final: 0.7113 (mtp180) REVERT: C 86 LEU cc_start: 0.8673 (mm) cc_final: 0.8406 (mp) REVERT: C 167 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7780 (mmt180) REVERT: C 172 ASN cc_start: 0.8081 (t0) cc_final: 0.7790 (t0) REVERT: C 205 MET cc_start: 0.8047 (mmm) cc_final: 0.7806 (mmm) REVERT: C 249 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8221 (tp) REVERT: C 251 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.8110 (m-80) REVERT: C 321 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7365 (ttp80) REVERT: C 339 ASP cc_start: 0.7082 (m-30) cc_final: 0.6860 (m-30) REVERT: E 71 SER cc_start: 0.8182 (p) cc_final: 0.7710 (t) REVERT: E 90 ASP cc_start: 0.8184 (m-30) cc_final: 0.7875 (m-30) REVERT: E 166 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8190 (mt) REVERT: E 197 SER cc_start: 0.8114 (p) cc_final: 0.7879 (p) REVERT: B 34 LYS cc_start: 0.7902 (tppt) cc_final: 0.7476 (tppt) REVERT: B 216 LYS cc_start: 0.8310 (mmtt) cc_final: 0.7979 (tmtt) REVERT: B 235 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7931 (mm) REVERT: B 283 ARG cc_start: 0.7593 (mtm-85) cc_final: 0.7373 (mtm-85) REVERT: B 342 ARG cc_start: 0.7278 (ttp80) cc_final: 0.6808 (ttp80) outliers start: 39 outliers final: 27 residues processed: 218 average time/residue: 0.6182 time to fit residues: 143.0697 Evaluate side-chains 229 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 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 217 LYS Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 63 ARG 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 249 ILE Chi-restraints excluded: chain C residue 251 PHE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 321 ARG 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 28 LYS Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 305 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 89 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 36 optimal weight: 0.0470 chunk 49 optimal weight: 0.0010 chunk 44 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 21 optimal weight: 0.2980 chunk 66 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 48 optimal weight: 0.0770 overall best weight: 0.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 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 = 0.3870 r_free = 0.3870 target = 0.143371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.129719 restraints weight = 12842.056| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.93 r_work: 0.3600 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8980 Z= 0.104 Angle : 0.546 8.506 12174 Z= 0.273 Chirality : 0.041 0.132 1378 Planarity : 0.004 0.055 1549 Dihedral : 4.262 38.920 1232 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.27 % Allowed : 26.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.26), residues: 1111 helix: 2.06 (0.28), residues: 371 sheet: -0.41 (0.30), residues: 275 loop : -0.42 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 280 TYR 0.015 0.001 TYR E 190 PHE 0.010 0.001 PHE A 277 TRP 0.023 0.001 TRP A 151 HIS 0.003 0.001 HIS E 232 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 8979) covalent geometry : angle 0.54572 (12172) SS BOND : bond 0.00437 ( 1) SS BOND : angle 0.42495 ( 2) hydrogen bonds : bond 0.03063 ( 405) hydrogen bonds : angle 4.36810 ( 1176) *********************** 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 225 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 194 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 79 VAL cc_start: 0.7120 (t) cc_final: 0.6869 (p) REVERT: A 156 LEU cc_start: 0.7288 (tt) cc_final: 0.7007 (tp) REVERT: C 36 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.7099 (mtp180) REVERT: C 86 LEU cc_start: 0.8615 (mm) cc_final: 0.8365 (mp) REVERT: C 144 LYS cc_start: 0.8579 (mmtp) cc_final: 0.8286 (mttm) REVERT: C 172 ASN cc_start: 0.8016 (t0) cc_final: 0.7767 (t0) REVERT: C 205 MET cc_start: 0.8015 (mmm) cc_final: 0.7768 (mmm) REVERT: C 251 PHE cc_start: 0.8586 (OUTLIER) cc_final: 0.8167 (m-80) REVERT: E 71 SER cc_start: 0.8169 (p) cc_final: 0.7662 (t) REVERT: E 166 LEU cc_start: 0.8559 (tt) cc_final: 0.8134 (mt) REVERT: E 197 SER cc_start: 0.8092 (p) cc_final: 0.7840 (p) REVERT: B 34 LYS cc_start: 0.7850 (tppt) cc_final: 0.7426 (tppt) REVERT: B 216 LYS cc_start: 0.8240 (mmtt) cc_final: 0.7936 (tmtt) REVERT: B 342 ARG cc_start: 0.7224 (ttp80) cc_final: 0.6813 (ttp80) REVERT: B 368 ASP cc_start: 0.7315 (m-30) cc_final: 0.7037 (m-30) outliers start: 31 outliers final: 19 residues processed: 211 average time/residue: 0.6311 time to fit residues: 141.3882 Evaluate side-chains 210 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET 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 C residue 36 ARG Chi-restraints excluded: chain C residue 49 GLN 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 D residue 6 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 88 SER 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 28 LYS Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 305 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 36 optimal weight: 0.9990 chunk 52 optimal weight: 0.0370 chunk 25 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 41 optimal weight: 0.0670 chunk 44 optimal weight: 0.8980 chunk 76 optimal weight: 0.0370 chunk 54 optimal weight: 0.6980 chunk 10 optimal weight: 0.0070 chunk 16 optimal weight: 0.5980 overall best weight: 0.1492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 GLN C 127 ASN B 59 GLN B 371 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.144829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.131141 restraints weight = 12869.572| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.94 r_work: 0.3621 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8980 Z= 0.099 Angle : 0.542 9.434 12174 Z= 0.269 Chirality : 0.041 0.138 1378 Planarity : 0.004 0.059 1549 Dihedral : 4.192 40.303 1232 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.43 % Allowed : 27.53 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.26), residues: 1111 helix: 2.05 (0.28), residues: 377 sheet: -0.44 (0.31), residues: 277 loop : -0.38 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 280 TYR 0.014 0.001 TYR E 190 PHE 0.010 0.001 PHE B 340 TRP 0.026 0.001 TRP A 151 HIS 0.002 0.001 HIS E 232 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 8979) covalent geometry : angle 0.54179 (12172) SS BOND : bond 0.00448 ( 1) SS BOND : angle 0.50631 ( 2) hydrogen bonds : bond 0.03010 ( 405) hydrogen bonds : angle 4.29439 ( 1176) ********************** 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 217 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 194 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 79 VAL cc_start: 0.7004 (t) cc_final: 0.6762 (p) REVERT: A 101 LEU cc_start: 0.5621 (OUTLIER) cc_final: 0.5086 (tp) REVERT: C 36 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7064 (mtp180) REVERT: C 86 LEU cc_start: 0.8623 (mm) cc_final: 0.8389 (mp) REVERT: C 144 LYS cc_start: 0.8575 (mmtp) cc_final: 0.8300 (mttm) REVERT: C 172 ASN cc_start: 0.7950 (t0) cc_final: 0.7728 (t0) REVERT: C 205 MET cc_start: 0.7900 (mmm) cc_final: 0.7676 (mmm) REVERT: C 251 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.8136 (m-80) REVERT: C 321 ARG cc_start: 0.7357 (ttp-110) cc_final: 0.6990 (ttp80) REVERT: E 71 SER cc_start: 0.8156 (p) cc_final: 0.7653 (t) REVERT: E 166 LEU cc_start: 0.8565 (tt) cc_final: 0.8139 (mt) REVERT: E 197 SER cc_start: 0.8092 (p) cc_final: 0.7837 (p) REVERT: B 34 LYS cc_start: 0.7848 (tppt) cc_final: 0.7410 (tppt) REVERT: B 342 ARG cc_start: 0.7168 (ttp80) cc_final: 0.6771 (ttp80) outliers start: 23 outliers final: 17 residues processed: 208 average time/residue: 0.5802 time to fit residues: 128.3527 Evaluate side-chains 209 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 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 C residue 36 ARG Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 127 ASN 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 D residue 6 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 305 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 25 optimal weight: 0.0870 chunk 104 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 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 = 0.3841 r_free = 0.3841 target = 0.141011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.127321 restraints weight = 12705.212| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.93 r_work: 0.3568 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8980 Z= 0.171 Angle : 0.585 8.778 12174 Z= 0.295 Chirality : 0.043 0.151 1378 Planarity : 0.004 0.054 1549 Dihedral : 4.351 30.577 1232 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.06 % Allowed : 27.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.26), residues: 1111 helix: 2.02 (0.28), residues: 373 sheet: -0.52 (0.30), residues: 273 loop : -0.39 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 280 TYR 0.013 0.002 TYR B 253 PHE 0.014 0.002 PHE C 216 TRP 0.032 0.002 TRP A 151 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 8979) covalent geometry : angle 0.58512 (12172) SS BOND : bond 0.00317 ( 1) SS BOND : angle 0.68173 ( 2) hydrogen bonds : bond 0.03474 ( 405) hydrogen bonds : angle 4.48386 ( 1176) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3759.42 seconds wall clock time: 64 minutes 53.88 seconds (3893.88 seconds total)