Starting phenix.real_space_refine on Sat Dec 28 03:13:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hk5_34846/12_2024/8hk5_34846.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hk5_34846/12_2024/8hk5_34846.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hk5_34846/12_2024/8hk5_34846.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hk5_34846/12_2024/8hk5_34846.map" model { file = "/net/cci-nas-00/data/ceres_data/8hk5_34846/12_2024/8hk5_34846.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hk5_34846/12_2024/8hk5_34846.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.032 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 57 5.16 5 C 4861 2.51 5 N 1303 2.21 5 O 1383 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7604 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2321 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 14, 'TRANS': 278} Chain: "B" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 573 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 1809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1809 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Chain: "D" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2509 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 322} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 356 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 43} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'PLM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.63, per 1000 atoms: 0.61 Number of scatterers: 7604 At special positions: 0 Unit cell: (84.048, 99.704, 147.496, 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 57 16.00 O 1383 8.00 N 1303 7.00 C 4861 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 47 " distance=1.99 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 54 " distance=2.02 Simple disulfide: pdb=" SG CYS B 34 " - pdb=" SG CYS B 55 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 1.1 seconds 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1830 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 9 sheets defined 47.6% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 34 through 66 Processing helix chain 'A' and resid 70 through 88 removed outlier: 4.331A pdb=" N TRP A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE A 75 " --> pdb=" O ASN A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 98 removed outlier: 3.606A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 140 Proline residue: A 113 - end of helix Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 149 through 174 removed outlier: 3.591A pdb=" N ALA A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 195 through 211 Processing helix chain 'A' and resid 211 through 231 Processing helix chain 'A' and resid 237 through 266 removed outlier: 4.393A pdb=" N LEU A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Proline residue: A 257 - end of helix Processing helix chain 'A' and resid 272 through 290 removed outlier: 3.697A pdb=" N LEU A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LEU A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 304 removed outlier: 3.938A pdb=" N CYS A 294 " --> pdb=" O TYR A 290 " (cutoff:3.500A) Proline residue: A 297 - end of helix Processing helix chain 'A' and resid 306 through 314 removed outlier: 3.706A pdb=" N ARG A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 13 removed outlier: 3.605A pdb=" N ILE B 9 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR B 13 " --> pdb=" O ILE B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 27 Processing helix chain 'B' and resid 33 through 40 removed outlier: 4.399A pdb=" N ARG B 40 " --> pdb=" O GLN B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 63 Processing helix chain 'C' and resid 6 through 33 removed outlier: 4.135A pdb=" N ALA C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 53 Processing helix chain 'C' and resid 207 through 216 removed outlier: 4.248A pdb=" N ILE C 212 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N HIS C 213 " --> pdb=" O LYS C 210 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS C 214 " --> pdb=" O TRP C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 232 removed outlier: 3.714A pdb=" N LEU C 232 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 255 Processing helix chain 'C' and resid 270 through 279 removed outlier: 3.644A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.665A pdb=" N ILE C 285 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 310 Processing helix chain 'C' and resid 330 through 351 Processing helix chain 'D' and resid 14 through 26 Processing helix chain 'D' and resid 29 through 34 removed outlier: 3.962A pdb=" N ILE D 33 " --> pdb=" O THR D 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 25 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.548A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 180 Processing sheet with id=AA2, first strand: chain 'C' and resid 185 through 191 removed outlier: 6.976A pdb=" N LYS C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ILE C 222 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N CYS C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU C 39 " --> pdb=" O CYS C 224 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N ALA C 226 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 47 through 51 removed outlier: 4.012A pdb=" N ARG D 49 " --> pdb=" O ILE D 338 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS D 317 " --> pdb=" O GLY D 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 58 through 63 removed outlier: 3.632A pdb=" N ALA D 60 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER D 74 " --> pdb=" O LYS D 78 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU D 79 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA D 92 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE D 81 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 100 through 105 removed outlier: 7.193A pdb=" N GLY D 115 " --> pdb=" O MET D 101 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N CYS D 103 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA D 113 " --> pdb=" O CYS D 103 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N TYR D 105 " --> pdb=" O TYR D 111 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N TYR D 111 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N CYS D 121 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLU D 138 " --> pdb=" O CYS D 121 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE D 123 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG D 134 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 146 through 151 removed outlier: 3.927A pdb=" N THR D 165 " --> pdb=" O SER D 161 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASP D 170 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLN D 176 " --> pdb=" O ASP D 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 187 through 192 removed outlier: 6.795A pdb=" N GLY D 202 " --> pdb=" O MET D 188 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU D 190 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL D 200 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LEU D 192 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LEU D 198 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN D 220 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ASP D 212 " --> pdb=" O CYS D 218 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N CYS D 218 " --> pdb=" O ASP D 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 229 through 234 removed outlier: 6.421A pdb=" N GLY D 244 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ILE D 232 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA D 242 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N PHE D 234 " --> pdb=" O ALA D 240 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ALA D 240 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASP D 254 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLU D 260 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 273 through 278 removed outlier: 6.420A pdb=" N GLY D 288 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL D 276 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU D 286 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N PHE D 278 " --> pdb=" O LEU D 284 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LEU D 284 " --> pdb=" O PHE D 278 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASP D 298 " --> pdb=" O ARG D 304 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ARG D 304 " --> pdb=" O ASP D 298 " (cutoff:3.500A) 399 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.25 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1239 1.31 - 1.44: 2067 1.44 - 1.57: 4372 1.57 - 1.70: 0 1.70 - 1.83: 76 Bond restraints: 7754 Sorted by residual: bond pdb=" CA TYR B 23 " pdb=" C TYR B 23 " ideal model delta sigma weight residual 1.524 1.462 0.061 1.29e-02 6.01e+03 2.24e+01 bond pdb=" C CYS B 34 " pdb=" O CYS B 34 " ideal model delta sigma weight residual 1.237 1.187 0.050 1.16e-02 7.43e+03 1.86e+01 bond pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 1.459 1.407 0.052 1.23e-02 6.61e+03 1.78e+01 bond pdb=" N ASP D 291 " pdb=" CA ASP D 291 " ideal model delta sigma weight residual 1.462 1.417 0.045 1.15e-02 7.56e+03 1.53e+01 bond pdb=" N ARG B 37 " pdb=" CA ARG B 37 " ideal model delta sigma weight residual 1.459 1.414 0.046 1.20e-02 6.94e+03 1.44e+01 ... (remaining 7749 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 10306 1.47 - 2.95: 135 2.95 - 4.42: 46 4.42 - 5.89: 3 5.89 - 7.37: 5 Bond angle restraints: 10495 Sorted by residual: angle pdb=" N GLU A 180 " pdb=" CA GLU A 180 " pdb=" C GLU A 180 " ideal model delta sigma weight residual 109.24 101.90 7.34 1.63e+00 3.76e-01 2.03e+01 angle pdb=" N TYR B 23 " pdb=" CA TYR B 23 " pdb=" C TYR B 23 " ideal model delta sigma weight residual 111.36 106.58 4.78 1.09e+00 8.42e-01 1.92e+01 angle pdb=" O GLU B 32 " pdb=" C GLU B 32 " pdb=" N THR B 33 " ideal model delta sigma weight residual 123.19 118.62 4.57 1.30e+00 5.92e-01 1.24e+01 angle pdb=" CA GLU B 32 " pdb=" C GLU B 32 " pdb=" N THR B 33 " ideal model delta sigma weight residual 115.63 120.52 -4.89 1.51e+00 4.39e-01 1.05e+01 angle pdb=" CA CYS B 55 " pdb=" CB CYS B 55 " pdb=" SG CYS B 55 " ideal model delta sigma weight residual 114.40 121.77 -7.37 2.30e+00 1.89e-01 1.03e+01 ... (remaining 10490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.04: 4293 16.04 - 32.08: 278 32.08 - 48.12: 51 48.12 - 64.17: 13 64.17 - 80.21: 7 Dihedral angle restraints: 4642 sinusoidal: 1826 harmonic: 2816 Sorted by residual: dihedral pdb=" CA PHE A 182 " pdb=" C PHE A 182 " pdb=" N PRO A 183 " pdb=" CA PRO A 183 " ideal model delta harmonic sigma weight residual 180.00 161.88 18.12 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 54 " pdb=" CB CYS B 54 " ideal model delta sinusoidal sigma weight residual -86.00 -112.86 26.86 1 1.00e+01 1.00e-02 1.04e+01 dihedral pdb=" CG ARG B 37 " pdb=" CD ARG B 37 " pdb=" NE ARG B 37 " pdb=" CZ ARG B 37 " ideal model delta sinusoidal sigma weight residual 180.00 137.02 42.98 2 1.50e+01 4.44e-03 9.92e+00 ... (remaining 4639 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1075 0.064 - 0.128: 128 0.128 - 0.192: 4 0.192 - 0.256: 0 0.256 - 0.320: 2 Chirality restraints: 1209 Sorted by residual: chirality pdb=" CA ASP B 24 " pdb=" N ASP B 24 " pdb=" C ASP B 24 " pdb=" CB ASP B 24 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CA CYS B 22 " pdb=" N CYS B 22 " pdb=" C CYS B 22 " pdb=" CB CYS B 22 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CB THR C 329 " pdb=" CA THR C 329 " pdb=" OG1 THR C 329 " pdb=" CG2 THR C 329 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.90e-01 ... (remaining 1206 not shown) Planarity restraints: 1319 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 310 " -0.192 9.50e-02 1.11e+02 8.61e-02 4.55e+00 pdb=" NE ARG A 310 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 310 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 310 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 310 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 21 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.14e+00 pdb=" C CYS B 21 " 0.025 2.00e-02 2.50e+03 pdb=" O CYS B 21 " -0.009 2.00e-02 2.50e+03 pdb=" N CYS B 22 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 32 " 0.006 2.00e-02 2.50e+03 1.14e-02 1.29e+00 pdb=" C GLU B 32 " -0.020 2.00e-02 2.50e+03 pdb=" O GLU B 32 " 0.007 2.00e-02 2.50e+03 pdb=" N THR B 33 " 0.007 2.00e-02 2.50e+03 ... (remaining 1316 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 91 2.64 - 3.20: 7100 3.20 - 3.77: 11623 3.77 - 4.33: 16324 4.33 - 4.90: 26972 Nonbonded interactions: 62110 Sorted by model distance: nonbonded pdb=" OG SER D 281 " pdb=" OD2 ASP G 48 " model vdw 2.073 3.040 nonbonded pdb=" OG SER D 147 " pdb=" O MET D 188 " model vdw 2.208 3.040 nonbonded pdb=" OG1 THR D 274 " pdb=" OD1 ASP D 290 " model vdw 2.231 3.040 nonbonded pdb=" OD1 ASP C 251 " pdb=" ND2 ASN C 255 " model vdw 2.243 3.120 nonbonded pdb=" OH TYR A 300 " pdb=" NH1 ARG A 310 " model vdw 2.249 3.120 ... (remaining 62105 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: 0.680 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: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.960 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 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 : 0.003 0.061 7754 Z= 0.194 Angle : 0.505 7.367 10495 Z= 0.307 Chirality : 0.040 0.320 1209 Planarity : 0.003 0.086 1319 Dihedral : 11.846 80.207 2803 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 0.24 % Allowed : 4.63 % Favored : 95.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.26), residues: 955 helix: 0.58 (0.24), residues: 436 sheet: -0.04 (0.38), residues: 189 loop : -1.36 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 74 HIS 0.001 0.000 HIS A 101 PHE 0.015 0.001 PHE D 234 TYR 0.005 0.000 TYR C 296 ARG 0.002 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 232 time to evaluate : 0.886 Fit side-chains revert: symmetry clash REVERT: A 228 ARG cc_start: 0.8147 (tpp80) cc_final: 0.7915 (tpp80) REVERT: A 298 ILE cc_start: 0.8483 (mt) cc_final: 0.8230 (mp) REVERT: C 209 LYS cc_start: 0.7878 (ttpt) cc_final: 0.7553 (ttpt) REVERT: D 82 TRP cc_start: 0.8506 (m100) cc_final: 0.8273 (m100) REVERT: D 86 THR cc_start: 0.8091 (p) cc_final: 0.7834 (p) REVERT: D 217 MET cc_start: 0.5944 (ttm) cc_final: 0.5647 (ttm) REVERT: D 273 ILE cc_start: 0.7134 (mt) cc_final: 0.6924 (mt) REVERT: D 303 ASP cc_start: 0.6706 (m-30) cc_final: 0.6455 (m-30) outliers start: 2 outliers final: 0 residues processed: 234 average time/residue: 1.0135 time to fit residues: 252.7936 Evaluate side-chains 179 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN A 194 HIS B 67 HIS D 142 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7754 Z= 0.287 Angle : 0.593 7.739 10495 Z= 0.306 Chirality : 0.043 0.142 1209 Planarity : 0.004 0.033 1319 Dihedral : 4.557 46.812 1069 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.31 % Allowed : 14.98 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.27), residues: 955 helix: 1.45 (0.24), residues: 436 sheet: 0.33 (0.37), residues: 189 loop : -0.79 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 169 HIS 0.011 0.002 HIS B 67 PHE 0.019 0.002 PHE D 253 TYR 0.020 0.002 TYR A 258 ARG 0.007 0.001 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 191 time to evaluate : 0.847 Fit side-chains REVERT: A 265 MET cc_start: 0.7829 (mtt) cc_final: 0.7622 (mtt) REVERT: C 29 LYS cc_start: 0.8117 (tppp) cc_final: 0.7837 (mtpp) REVERT: C 197 LYS cc_start: 0.7855 (tttt) cc_final: 0.7619 (tttm) REVERT: C 209 LYS cc_start: 0.7855 (ttpt) cc_final: 0.7515 (ttpt) REVERT: C 216 GLU cc_start: 0.7214 (tt0) cc_final: 0.7013 (tt0) REVERT: C 334 PHE cc_start: 0.8242 (t80) cc_final: 0.7933 (t80) REVERT: D 136 SER cc_start: 0.8332 (t) cc_final: 0.8099 (p) REVERT: D 197 ARG cc_start: 0.7180 (mtp85) cc_final: 0.6960 (mtp180) REVERT: D 270 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7879 (pp) REVERT: D 303 ASP cc_start: 0.6793 (m-30) cc_final: 0.6497 (m-30) outliers start: 19 outliers final: 4 residues processed: 201 average time/residue: 1.0762 time to fit residues: 230.4659 Evaluate side-chains 183 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 178 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 270 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 HIS C 188 HIS C 269 ASN D 230 ASN D 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7754 Z= 0.206 Angle : 0.544 7.569 10495 Z= 0.277 Chirality : 0.042 0.145 1209 Planarity : 0.004 0.072 1319 Dihedral : 4.438 44.147 1069 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.05 % Allowed : 18.39 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.27), residues: 955 helix: 1.86 (0.24), residues: 432 sheet: 0.41 (0.37), residues: 192 loop : -0.67 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 74 HIS 0.008 0.001 HIS B 67 PHE 0.013 0.002 PHE C 196 TYR 0.014 0.002 TYR A 258 ARG 0.009 0.001 ARG D 304 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 0.927 Fit side-chains REVERT: A 236 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7315 (ttp80) REVERT: A 265 MET cc_start: 0.7801 (mtt) cc_final: 0.7575 (mtt) REVERT: A 272 SER cc_start: 0.8481 (t) cc_final: 0.8160 (p) REVERT: C 29 LYS cc_start: 0.8099 (tppp) cc_final: 0.7882 (mtpp) REVERT: C 197 LYS cc_start: 0.7892 (tttt) cc_final: 0.7587 (tttm) REVERT: C 209 LYS cc_start: 0.7836 (ttpt) cc_final: 0.7500 (ttpt) REVERT: C 216 GLU cc_start: 0.7222 (tt0) cc_final: 0.7004 (tt0) REVERT: C 308 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7307 (mt-10) REVERT: D 136 SER cc_start: 0.8361 (t) cc_final: 0.8136 (p) REVERT: D 163 ASP cc_start: 0.7404 (p0) cc_final: 0.7148 (p0) REVERT: D 197 ARG cc_start: 0.7216 (mtp85) cc_final: 0.7009 (mtp180) REVERT: D 303 ASP cc_start: 0.6711 (m-30) cc_final: 0.6397 (m-30) outliers start: 25 outliers final: 12 residues processed: 198 average time/residue: 1.1482 time to fit residues: 240.9730 Evaluate side-chains 186 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 173 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 237 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 ASN C 188 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7754 Z= 0.209 Angle : 0.528 7.217 10495 Z= 0.272 Chirality : 0.041 0.144 1209 Planarity : 0.004 0.039 1319 Dihedral : 4.405 42.332 1069 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.41 % Allowed : 18.51 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.27), residues: 955 helix: 1.99 (0.24), residues: 432 sheet: 0.47 (0.36), residues: 191 loop : -0.62 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 74 HIS 0.003 0.001 HIS D 62 PHE 0.014 0.002 PHE A 182 TYR 0.015 0.002 TYR A 258 ARG 0.011 0.001 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 0.891 Fit side-chains REVERT: A 236 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7331 (ttp80) REVERT: A 265 MET cc_start: 0.7787 (mtt) cc_final: 0.7485 (mtt) REVERT: A 272 SER cc_start: 0.8492 (t) cc_final: 0.8155 (p) REVERT: A 276 LEU cc_start: 0.7726 (mm) cc_final: 0.7505 (mt) REVERT: A 298 ILE cc_start: 0.8519 (mt) cc_final: 0.8252 (mp) REVERT: B 29 ASN cc_start: 0.7716 (t0) cc_final: 0.7459 (t0) REVERT: C 29 LYS cc_start: 0.8152 (tppp) cc_final: 0.7920 (mtpp) REVERT: C 197 LYS cc_start: 0.7889 (tttt) cc_final: 0.7605 (tttm) REVERT: C 209 LYS cc_start: 0.7827 (ttpt) cc_final: 0.7486 (ttpt) REVERT: C 216 GLU cc_start: 0.7208 (tt0) cc_final: 0.6980 (tt0) REVERT: C 308 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7255 (mt-10) REVERT: D 136 SER cc_start: 0.8342 (t) cc_final: 0.8115 (p) REVERT: D 197 ARG cc_start: 0.7233 (mtp85) cc_final: 0.6983 (mtp180) REVERT: D 290 ASP cc_start: 0.6412 (m-30) cc_final: 0.5991 (m-30) REVERT: D 303 ASP cc_start: 0.6693 (m-30) cc_final: 0.6340 (m-30) outliers start: 28 outliers final: 16 residues processed: 196 average time/residue: 1.1339 time to fit residues: 235.7185 Evaluate side-chains 195 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 234 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7754 Z= 0.333 Angle : 0.589 7.476 10495 Z= 0.305 Chirality : 0.044 0.146 1209 Planarity : 0.004 0.045 1319 Dihedral : 4.719 40.743 1069 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.51 % Allowed : 17.54 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.27), residues: 955 helix: 1.85 (0.24), residues: 430 sheet: 0.35 (0.37), residues: 183 loop : -0.62 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 74 HIS 0.005 0.002 HIS C 322 PHE 0.017 0.002 PHE D 235 TYR 0.020 0.002 TYR A 258 ARG 0.008 0.001 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 0.894 Fit side-chains REVERT: A 92 LEU cc_start: 0.8112 (mp) cc_final: 0.7887 (mt) REVERT: A 236 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7467 (ttp80) REVERT: A 265 MET cc_start: 0.7863 (mtt) cc_final: 0.7594 (mtt) REVERT: A 272 SER cc_start: 0.8542 (t) cc_final: 0.8222 (p) REVERT: A 276 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7660 (mt) REVERT: A 279 LYS cc_start: 0.8007 (mmmm) cc_final: 0.7726 (mmmm) REVERT: C 29 LYS cc_start: 0.8186 (tppp) cc_final: 0.7931 (mtpp) REVERT: C 197 LYS cc_start: 0.7892 (tttt) cc_final: 0.7612 (tttm) REVERT: C 209 LYS cc_start: 0.7850 (ttpt) cc_final: 0.7514 (ttpt) REVERT: C 308 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7340 (mt-10) REVERT: C 330 LYS cc_start: 0.7589 (mttt) cc_final: 0.7304 (mtmm) REVERT: D 136 SER cc_start: 0.8437 (t) cc_final: 0.8179 (p) REVERT: D 290 ASP cc_start: 0.6442 (m-30) cc_final: 0.6043 (m-30) REVERT: D 303 ASP cc_start: 0.6729 (m-30) cc_final: 0.6368 (m-30) outliers start: 37 outliers final: 18 residues processed: 206 average time/residue: 1.1550 time to fit residues: 252.3550 Evaluate side-chains 192 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 237 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 53 optimal weight: 0.0980 chunk 22 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 ASN C 188 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7754 Z= 0.328 Angle : 0.581 7.361 10495 Z= 0.302 Chirality : 0.043 0.141 1209 Planarity : 0.004 0.044 1319 Dihedral : 4.745 38.264 1069 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.38 % Allowed : 18.76 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.27), residues: 955 helix: 1.78 (0.24), residues: 430 sheet: 0.37 (0.38), residues: 182 loop : -0.68 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 74 HIS 0.005 0.001 HIS C 322 PHE 0.018 0.002 PHE D 235 TYR 0.018 0.002 TYR A 258 ARG 0.007 0.001 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 176 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8124 (mp) cc_final: 0.7894 (mt) REVERT: A 236 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7474 (ttp80) REVERT: A 272 SER cc_start: 0.8566 (t) cc_final: 0.8211 (p) REVERT: A 279 LYS cc_start: 0.7995 (mmmm) cc_final: 0.7717 (mmmm) REVERT: C 29 LYS cc_start: 0.8174 (tppp) cc_final: 0.7903 (mtpp) REVERT: C 197 LYS cc_start: 0.7891 (tttt) cc_final: 0.7618 (tttm) REVERT: C 209 LYS cc_start: 0.7855 (ttpt) cc_final: 0.7513 (ttpt) REVERT: C 330 LYS cc_start: 0.7587 (mttt) cc_final: 0.7377 (mttp) REVERT: D 136 SER cc_start: 0.8439 (t) cc_final: 0.8191 (p) REVERT: D 290 ASP cc_start: 0.6452 (m-30) cc_final: 0.6086 (m-30) REVERT: D 303 ASP cc_start: 0.6639 (m-30) cc_final: 0.6275 (m-30) outliers start: 36 outliers final: 20 residues processed: 192 average time/residue: 1.1302 time to fit residues: 230.3387 Evaluate side-chains 196 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 237 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 90 optimal weight: 0.0980 chunk 56 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 ASN C 188 HIS D 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7754 Z= 0.196 Angle : 0.538 7.493 10495 Z= 0.280 Chirality : 0.041 0.142 1209 Planarity : 0.004 0.041 1319 Dihedral : 4.472 35.504 1069 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 4.02 % Allowed : 19.98 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.27), residues: 955 helix: 1.96 (0.25), residues: 431 sheet: 0.26 (0.37), residues: 184 loop : -0.63 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 74 HIS 0.002 0.001 HIS C 322 PHE 0.016 0.002 PHE A 275 TYR 0.013 0.002 TYR D 59 ARG 0.007 0.001 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 183 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8066 (mp) cc_final: 0.7838 (mt) REVERT: A 236 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7360 (ttp80) REVERT: A 272 SER cc_start: 0.8527 (t) cc_final: 0.8215 (p) REVERT: C 29 LYS cc_start: 0.8155 (tppp) cc_final: 0.7876 (mtpp) REVERT: C 188 HIS cc_start: 0.7876 (OUTLIER) cc_final: 0.7591 (m170) REVERT: C 197 LYS cc_start: 0.7854 (tttt) cc_final: 0.7604 (mtpp) REVERT: C 209 LYS cc_start: 0.7815 (ttpt) cc_final: 0.7474 (ttpt) REVERT: C 247 MET cc_start: 0.7811 (mtp) cc_final: 0.7535 (mtt) REVERT: C 309 ASP cc_start: 0.6826 (m-30) cc_final: 0.6339 (m-30) REVERT: C 330 LYS cc_start: 0.7534 (mttt) cc_final: 0.7299 (mttm) REVERT: D 270 ILE cc_start: 0.8146 (tp) cc_final: 0.7867 (mm) REVERT: D 290 ASP cc_start: 0.6536 (m-30) cc_final: 0.6181 (m-30) REVERT: D 303 ASP cc_start: 0.6599 (m-30) cc_final: 0.6237 (m-30) outliers start: 33 outliers final: 18 residues processed: 200 average time/residue: 1.0882 time to fit residues: 232.3964 Evaluate side-chains 194 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 188 HIS Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 ASN D 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7754 Z= 0.288 Angle : 0.572 7.616 10495 Z= 0.299 Chirality : 0.042 0.142 1209 Planarity : 0.004 0.043 1319 Dihedral : 4.552 34.172 1069 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.14 % Allowed : 20.22 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.27), residues: 955 helix: 1.88 (0.24), residues: 431 sheet: 0.38 (0.38), residues: 182 loop : -0.68 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 74 HIS 0.013 0.002 HIS C 188 PHE 0.022 0.002 PHE C 336 TYR 0.015 0.002 TYR A 258 ARG 0.006 0.001 ARG D 150 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8102 (mp) cc_final: 0.7872 (mt) REVERT: A 236 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7356 (ttp80) REVERT: A 272 SER cc_start: 0.8520 (t) cc_final: 0.8204 (p) REVERT: A 279 LYS cc_start: 0.7976 (mmmm) cc_final: 0.7707 (mmmm) REVERT: C 29 LYS cc_start: 0.8200 (tppp) cc_final: 0.7911 (mtpp) REVERT: C 186 GLU cc_start: 0.6535 (pt0) cc_final: 0.6178 (pt0) REVERT: C 188 HIS cc_start: 0.7898 (m170) cc_final: 0.7103 (m-70) REVERT: C 197 LYS cc_start: 0.7867 (tttt) cc_final: 0.7410 (tttm) REVERT: C 209 LYS cc_start: 0.7832 (ttpt) cc_final: 0.7493 (ttpt) REVERT: C 308 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7399 (mt-10) REVERT: C 309 ASP cc_start: 0.6837 (m-30) cc_final: 0.6333 (m-30) REVERT: C 330 LYS cc_start: 0.7566 (mttt) cc_final: 0.7325 (mttm) REVERT: D 210 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7818 (tp) REVERT: D 270 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7907 (mm) REVERT: D 290 ASP cc_start: 0.6552 (m-30) cc_final: 0.6230 (m-30) REVERT: D 303 ASP cc_start: 0.6612 (m-30) cc_final: 0.6252 (m-30) outliers start: 34 outliers final: 18 residues processed: 196 average time/residue: 1.0744 time to fit residues: 223.8801 Evaluate side-chains 199 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 ASN D 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7754 Z= 0.233 Angle : 0.567 7.647 10495 Z= 0.296 Chirality : 0.042 0.161 1209 Planarity : 0.004 0.041 1319 Dihedral : 4.500 31.836 1069 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.29 % Allowed : 21.19 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.27), residues: 955 helix: 1.87 (0.24), residues: 431 sheet: 0.27 (0.37), residues: 184 loop : -0.67 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 74 HIS 0.003 0.001 HIS C 322 PHE 0.020 0.002 PHE C 336 TYR 0.018 0.002 TYR C 320 ARG 0.004 0.000 ARG D 150 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 178 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8092 (mp) cc_final: 0.7857 (mt) REVERT: A 134 ARG cc_start: 0.8128 (mtt180) cc_final: 0.7905 (mtt180) REVERT: A 236 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.6820 (ttp80) REVERT: A 272 SER cc_start: 0.8516 (t) cc_final: 0.8299 (p) REVERT: C 29 LYS cc_start: 0.8170 (tppp) cc_final: 0.7867 (mtpp) REVERT: C 186 GLU cc_start: 0.6541 (pt0) cc_final: 0.6126 (pt0) REVERT: C 197 LYS cc_start: 0.7870 (tttt) cc_final: 0.7460 (tttm) REVERT: C 209 LYS cc_start: 0.7815 (ttpt) cc_final: 0.7485 (ttpt) REVERT: C 308 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7276 (mt-10) REVERT: C 330 LYS cc_start: 0.7547 (mttt) cc_final: 0.7306 (mttm) REVERT: D 210 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7824 (tp) REVERT: D 270 ILE cc_start: 0.8173 (tp) cc_final: 0.7904 (mm) REVERT: D 290 ASP cc_start: 0.6549 (m-30) cc_final: 0.6215 (m-30) REVERT: D 303 ASP cc_start: 0.6599 (m-30) cc_final: 0.6246 (m-30) REVERT: G 21 MET cc_start: 0.6106 (mtp) cc_final: 0.5822 (mtp) outliers start: 27 outliers final: 19 residues processed: 194 average time/residue: 1.1341 time to fit residues: 233.2750 Evaluate side-chains 193 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 74 optimal weight: 0.0010 chunk 7 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 59 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 110 ASN D 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7754 Z= 0.256 Angle : 0.575 7.691 10495 Z= 0.300 Chirality : 0.042 0.141 1209 Planarity : 0.004 0.045 1319 Dihedral : 4.534 29.547 1069 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.29 % Allowed : 21.32 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.27), residues: 955 helix: 1.85 (0.24), residues: 432 sheet: 0.28 (0.37), residues: 184 loop : -0.65 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 74 HIS 0.003 0.001 HIS D 225 PHE 0.020 0.002 PHE C 336 TYR 0.014 0.002 TYR C 320 ARG 0.010 0.001 ARG A 200 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 179 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8108 (mp) cc_final: 0.7877 (mt) REVERT: A 236 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.6826 (ttp80) REVERT: A 272 SER cc_start: 0.8577 (t) cc_final: 0.8274 (p) REVERT: C 29 LYS cc_start: 0.8163 (tppp) cc_final: 0.7874 (mtpp) REVERT: C 186 GLU cc_start: 0.6551 (pt0) cc_final: 0.6252 (pt0) REVERT: C 197 LYS cc_start: 0.7860 (tttt) cc_final: 0.7471 (tttm) REVERT: C 209 LYS cc_start: 0.7806 (ttpt) cc_final: 0.7482 (ttpt) REVERT: C 216 GLU cc_start: 0.7295 (tt0) cc_final: 0.7015 (tt0) REVERT: C 247 MET cc_start: 0.7789 (mtp) cc_final: 0.7545 (mtt) REVERT: C 309 ASP cc_start: 0.6781 (m-30) cc_final: 0.6248 (m-30) REVERT: C 318 GLU cc_start: 0.6736 (pm20) cc_final: 0.6513 (pm20) REVERT: C 330 LYS cc_start: 0.7556 (mttt) cc_final: 0.7329 (mttm) REVERT: D 210 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7842 (tp) REVERT: D 270 ILE cc_start: 0.8186 (tp) cc_final: 0.7909 (mm) REVERT: D 290 ASP cc_start: 0.6559 (m-30) cc_final: 0.6247 (m-30) REVERT: D 303 ASP cc_start: 0.6620 (m-30) cc_final: 0.6255 (m-30) REVERT: G 21 MET cc_start: 0.6123 (mtp) cc_final: 0.5856 (mtp) outliers start: 27 outliers final: 18 residues processed: 194 average time/residue: 1.1384 time to fit residues: 234.1334 Evaluate side-chains 195 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 31 optimal weight: 0.4980 chunk 76 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.135579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.118866 restraints weight = 10151.570| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.79 r_work: 0.3445 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7754 Z= 0.234 Angle : 0.580 9.999 10495 Z= 0.298 Chirality : 0.042 0.176 1209 Planarity : 0.004 0.039 1319 Dihedral : 4.493 27.300 1069 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.56 % Allowed : 22.78 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.27), residues: 955 helix: 1.85 (0.25), residues: 432 sheet: 0.19 (0.37), residues: 185 loop : -0.57 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 258 HIS 0.003 0.001 HIS D 225 PHE 0.019 0.002 PHE C 336 TYR 0.013 0.002 TYR A 258 ARG 0.010 0.000 ARG D 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3847.39 seconds wall clock time: 69 minutes 26.99 seconds (4166.99 seconds total)