Starting phenix.real_space_refine on Thu Jul 2 07:19:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8kh4_37236/07_2026/8kh4_37236.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kh4_37236/07_2026/8kh4_37236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8kh4_37236/07_2026/8kh4_37236.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kh4_37236/07_2026/8kh4_37236.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kh4_37236/07_2026/8kh4_37236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kh4_37236/07_2026/8kh4_37236.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8kh4_37236/07_2026/8kh4_37236.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8kh4_37236/07_2026/8kh4_37236.cif" } resolution = 3.1 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= 0.118 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 51 5.16 5 C 4814 2.51 5 N 1286 2.21 5 O 1370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7521 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2048 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 10, 'TRANS': 255} Chain breaks: 1 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 3, 'ARG:plan': 2, 'GLU:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 1809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1809 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 4, 'ASN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 57 Chain: "C" Number of atoms: 2435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 336, 2425 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 5, 'GLN:plan1': 6, 'ARG:plan': 9, 'GLU:plan': 5, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 113 Conformer: "B" Number of residues, atoms: 336, 2425 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 5, 'GLN:plan1': 6, 'ARG:plan': 9, 'GLU:plan': 5, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 113 bond proxies already assigned to first conformer: 2458 Chain: "E" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 936 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 265 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 1, 'TRANS': 42} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.79, per 1000 atoms: 0.24 Number of scatterers: 7521 At special positions: 0 Unit cell: (72.36, 95.04, 126.36, 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 51 16.00 O 1370 8.00 N 1286 7.00 C 4814 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 178 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 107 " 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: 0.63 Conformation dependent library (CDL) restraints added in 351.2 milliseconds 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1886 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 11 sheets defined 43.4% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 27 through 55 removed outlier: 3.838A pdb=" N ILE A 39 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS A 55 " --> pdb=" O THR A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 59 Processing helix chain 'A' and resid 60 through 80 Processing helix chain 'A' and resid 80 through 91 Processing helix chain 'A' and resid 96 through 131 removed outlier: 3.655A pdb=" N GLY A 119 " --> pdb=" O MET A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 139 Processing helix chain 'A' and resid 140 through 160 removed outlier: 3.593A pdb=" N TRP A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 165 Processing helix chain 'A' and resid 185 through 197 Processing helix chain 'A' and resid 197 through 219 removed outlier: 3.815A pdb=" N PHE A 201 " --> pdb=" O ALA A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 297 removed outlier: 3.683A pdb=" N PHE A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 302 through 327 removed outlier: 4.122A pdb=" N ALA A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Proline residue: A 321 - end of helix removed outlier: 3.550A pdb=" N TRP A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'B' and resid 13 through 39 removed outlier: 3.691A pdb=" N ALA B 39 " --> pdb=" O GLN B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 60 removed outlier: 3.658A pdb=" N MET B 60 " --> pdb=" O ILE B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 279 Processing helix chain 'B' and resid 293 through 304 Processing helix chain 'B' and resid 307 through 312 removed outlier: 4.039A pdb=" N TYR B 311 " --> pdb=" O LYS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 318 Processing helix chain 'B' and resid 331 through 352 removed outlier: 3.683A pdb=" N ILE B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER B 352 " --> pdb=" O ILE B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 391 Processing helix chain 'C' and resid 6 through 26 Processing helix chain 'C' and resid 29 through 35 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.739A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.563A pdb=" N THR E 91 " --> pdb=" O PRO E 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 24 Processing helix chain 'D' and resid 29 through 45 Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing sheet with id=AA1, first strand: chain 'A' and resid 169 through 172 removed outlier: 3.657A pdb=" N VAL A 179 " --> pdb=" O GLU A 170 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP A 172 " --> pdb=" O MET A 177 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET A 177 " --> pdb=" O ASP A 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 210 through 214 removed outlier: 9.660A pdb=" N ALA B 243 " --> pdb=" O THR B 40 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG B 42 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ILE B 245 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU B 44 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N VAL B 247 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU B 46 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ASP B 249 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE B 244 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N PHE B 290 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N PHE B 246 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASN B 292 " --> pdb=" O PHE B 246 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL B 248 " --> pdb=" O ASN B 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 52 removed outlier: 3.625A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL C 327 " --> pdb=" O TRP C 339 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.692A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 4.555A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.579A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 7.112A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.737A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP C 254 " --> pdb=" O GLN C 259 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.747A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.833A pdb=" N GLY E 10 " --> pdb=" O THR E 125 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N MET E 34 " --> pdb=" O ASP E 50 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASP E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 1212 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: 1.13 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1208 1.29 - 1.42: 2106 1.42 - 1.56: 4303 1.56 - 1.69: 3 1.69 - 1.83: 73 Bond restraints: 7693 Sorted by residual: bond pdb=" CA PHE A 201 " pdb=" C PHE A 201 " ideal model delta sigma weight residual 1.524 1.415 0.109 1.29e-02 6.01e+03 7.08e+01 bond pdb=" CA SER A 62 " pdb=" C SER A 62 " ideal model delta sigma weight residual 1.524 1.426 0.098 1.26e-02 6.30e+03 6.04e+01 bond pdb=" CA VAL A 179 " pdb=" C VAL A 179 " ideal model delta sigma weight residual 1.523 1.427 0.096 1.27e-02 6.20e+03 5.74e+01 bond pdb=" C PHE A 201 " pdb=" O PHE A 201 " ideal model delta sigma weight residual 1.237 1.156 0.080 1.19e-02 7.06e+03 4.57e+01 bond pdb=" N VAL A 179 " pdb=" CA VAL A 179 " ideal model delta sigma weight residual 1.459 1.377 0.082 1.25e-02 6.40e+03 4.26e+01 ... (remaining 7688 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 10227 2.70 - 5.40: 217 5.40 - 8.10: 39 8.10 - 10.79: 14 10.79 - 13.49: 6 Bond angle restraints: 10503 Sorted by residual: angle pdb=" N ARG A 213 " pdb=" CA ARG A 213 " pdb=" C ARG A 213 " ideal model delta sigma weight residual 111.07 100.56 10.51 1.07e+00 8.73e-01 9.65e+01 angle pdb=" N ILE A 211 " pdb=" CA ILE A 211 " pdb=" C ILE A 211 " ideal model delta sigma weight residual 110.62 102.37 8.25 1.02e+00 9.61e-01 6.55e+01 angle pdb=" N ALA D 34 " pdb=" CA ALA D 34 " pdb=" C ALA D 34 " ideal model delta sigma weight residual 111.28 102.51 8.77 1.09e+00 8.42e-01 6.47e+01 angle pdb=" N TYR D 40 " pdb=" CA TYR D 40 " pdb=" C TYR D 40 " ideal model delta sigma weight residual 111.28 102.91 8.37 1.09e+00 8.42e-01 5.90e+01 angle pdb=" C PHE A 199 " pdb=" N PRO A 200 " pdb=" CA PRO A 200 " ideal model delta sigma weight residual 119.05 110.58 8.47 1.11e+00 8.12e-01 5.82e+01 ... (remaining 10498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.19: 4273 24.19 - 48.38: 186 48.38 - 72.57: 13 72.57 - 96.76: 5 96.76 - 120.95: 1 Dihedral angle restraints: 4478 sinusoidal: 1558 harmonic: 2920 Sorted by residual: dihedral pdb=" CB CYS E 99 " pdb=" SG CYS E 99 " pdb=" SG CYS E 107 " pdb=" CB CYS E 107 " ideal model delta sinusoidal sigma weight residual -86.00 -2.52 -83.48 1 1.00e+01 1.00e-02 8.51e+01 dihedral pdb=" C ASN A 63 " pdb=" N ASN A 63 " pdb=" CA ASN A 63 " pdb=" CB ASN A 63 " ideal model delta harmonic sigma weight residual -122.60 -138.96 16.36 0 2.50e+00 1.60e-01 4.28e+01 dihedral pdb=" N ASN A 63 " pdb=" C ASN A 63 " pdb=" CA ASN A 63 " pdb=" CB ASN A 63 " ideal model delta harmonic sigma weight residual 122.80 139.06 -16.26 0 2.50e+00 1.60e-01 4.23e+01 ... (remaining 4475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.163: 1181 0.163 - 0.327: 29 0.327 - 0.490: 7 0.490 - 0.653: 4 0.653 - 0.817: 2 Chirality restraints: 1223 Sorted by residual: chirality pdb=" CA ASN A 63 " pdb=" N ASN A 63 " pdb=" C ASN A 63 " pdb=" CB ASN A 63 " both_signs ideal model delta sigma weight residual False 2.51 1.69 0.82 2.00e-01 2.50e+01 1.67e+01 chirality pdb=" CA ALA A 219 " pdb=" N ALA A 219 " pdb=" C ALA A 219 " pdb=" CB ALA A 219 " both_signs ideal model delta sigma weight residual False 2.48 1.77 0.72 2.00e-01 2.50e+01 1.28e+01 chirality pdb=" CA PHE A 174 " pdb=" N PHE A 174 " pdb=" C PHE A 174 " pdb=" CB PHE A 174 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.06e+01 ... (remaining 1220 not shown) Planarity restraints: 1324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " 0.066 5.00e-02 4.00e+02 9.76e-02 1.53e+01 pdb=" N PRO C 236 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 213 " -0.018 2.00e-02 2.50e+03 3.44e-02 1.19e+01 pdb=" C ARG A 213 " 0.060 2.00e-02 2.50e+03 pdb=" O ARG A 213 " -0.022 2.00e-02 2.50e+03 pdb=" N VAL A 214 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 57 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.07e+00 pdb=" C TYR A 57 " -0.052 2.00e-02 2.50e+03 pdb=" O TYR A 57 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU A 58 " 0.017 2.00e-02 2.50e+03 ... (remaining 1321 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 128 2.62 - 3.19: 6873 3.19 - 3.76: 12272 3.76 - 4.33: 16918 4.33 - 4.90: 28357 Nonbonded interactions: 64548 Sorted by model distance: nonbonded pdb=" CD2 LEU A 61 " pdb=" CB ALA A 144 " model vdw 2.049 3.880 nonbonded pdb=" OG SER C 74 " pdb=" OD1 ASP C 76 " model vdw 2.150 3.040 nonbonded pdb=" O ILE C 58 " pdb=" OG SER C 316 " model vdw 2.180 3.040 nonbonded pdb=" N VAL A 179 " pdb=" O VAL A 179 " model vdw 2.218 2.496 nonbonded pdb=" NH1 ARG B 228 " pdb=" OD1 ASP C 186 " model vdw 2.219 3.120 ... (remaining 64543 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=0.38 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: 0.350 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.490 Find NCS groups from input model: 0.040 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:0.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 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 : 0.009 0.109 7696 Z= 0.635 Angle : 1.017 13.493 10509 Z= 0.633 Chirality : 0.081 0.817 1223 Planarity : 0.007 0.098 1324 Dihedral : 13.589 120.945 2583 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.40 % Allowed : 1.48 % Favored : 98.12 % Cbeta Deviations : 0.95 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.62 (0.27), residues: 988 helix: 1.63 (0.26), residues: 402 sheet: 0.16 (0.35), residues: 204 loop : -0.73 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 72 TYR 0.025 0.002 TYR C 85 PHE 0.028 0.002 PHE A 65 TRP 0.026 0.002 TRP C 99 HIS 0.007 0.002 HIS D 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00893 / 0.64 ( 7693) covalent geometry : angle 1.01418 / 0.63 (10503) SS BOND : bond 0.00782 / 0.41 ( 3) SS BOND : angle 3.09228 / 1.64 ( 6) hydrogen bonds : bond 0.12467 / 7.96 ( 420) hydrogen bonds : angle 6.80101 / 4.94 ( 1212) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 167 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 327 TRP cc_start: 0.8058 (OUTLIER) cc_final: 0.6682 (m-10) REVERT: B 34 LYS cc_start: 0.7829 (ttpt) cc_final: 0.7618 (tttt) REVERT: B 280 ARG cc_start: 0.8064 (tpt90) cc_final: 0.7821 (ttt90) REVERT: B 317 ARG cc_start: 0.7751 (ptp90) cc_final: 0.7476 (ptp90) REVERT: C 101 MET cc_start: 0.8895 (mtp) cc_final: 0.8644 (mtp) REVERT: C 290 ASP cc_start: 0.6802 (m-30) cc_final: 0.6572 (m-30) REVERT: E 60 TYR cc_start: 0.7386 (m-80) cc_final: 0.7036 (m-80) REVERT: E 80 TYR cc_start: 0.7486 (m-80) cc_final: 0.7066 (m-80) outliers start: 3 outliers final: 0 residues processed: 170 average time/residue: 0.0678 time to fit residues: 15.7376 Evaluate side-chains 150 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 23 ASN C 88 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 ASN E 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.192345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.157188 restraints weight = 17551.872| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 3.39 r_work: 0.3717 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3857 r_free = 0.3857 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3856 r_free = 0.3856 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.3856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7696 Z= 0.155 Angle : 0.628 10.526 10509 Z= 0.330 Chirality : 0.045 0.275 1223 Planarity : 0.005 0.076 1324 Dihedral : 6.364 110.782 1093 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.08 % Allowed : 9.96 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.82 (0.27), residues: 988 helix: 1.92 (0.26), residues: 394 sheet: 0.10 (0.33), residues: 222 loop : -0.63 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 304 TYR 0.029 0.002 TYR C 85 PHE 0.018 0.002 PHE B 212 TRP 0.022 0.002 TRP C 99 HIS 0.005 0.001 HIS C 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 ( 7693) covalent geometry : angle 0.62667 / 0.33 (10503) SS BOND : bond 0.00130 / 0.06 ( 3) SS BOND : angle 1.84648 / 1.05 ( 6) hydrogen bonds : bond 0.04228 / 2.86 ( 420) hydrogen bonds : angle 5.31799 / 3.88 ( 1212) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 156 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 MET cc_start: 0.7639 (mtp) cc_final: 0.7425 (mtm) REVERT: A 327 TRP cc_start: 0.7907 (OUTLIER) cc_final: 0.7191 (m-10) REVERT: B 266 LEU cc_start: 0.8642 (tp) cc_final: 0.8280 (tp) REVERT: B 274 LYS cc_start: 0.7865 (tttp) cc_final: 0.7584 (ttmt) REVERT: B 280 ARG cc_start: 0.8255 (tpt90) cc_final: 0.7954 (ttt90) REVERT: C 101 MET cc_start: 0.8887 (mtp) cc_final: 0.8681 (mtp) REVERT: E 80 TYR cc_start: 0.7722 (m-80) cc_final: 0.7169 (m-80) REVERT: E 115 TYR cc_start: 0.8079 (t80) cc_final: 0.7873 (t80) outliers start: 8 outliers final: 4 residues processed: 160 average time/residue: 0.0701 time to fit residues: 15.5612 Evaluate side-chains 150 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 145 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 327 TRP Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 284 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 9 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.193749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.157954 restraints weight = 18488.365| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 3.66 r_work: 0.3696 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3834 r_free = 0.3834 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3834 r_free = 0.3834 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7696 Z= 0.151 Angle : 0.598 11.106 10509 Z= 0.312 Chirality : 0.044 0.163 1223 Planarity : 0.005 0.070 1324 Dihedral : 6.223 111.838 1093 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.21 % Allowed : 13.06 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.84 (0.27), residues: 988 helix: 2.06 (0.26), residues: 390 sheet: 0.06 (0.33), residues: 219 loop : -0.69 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 304 TYR 0.027 0.002 TYR C 85 PHE 0.016 0.002 PHE B 212 TRP 0.014 0.002 TRP C 169 HIS 0.006 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 7693) covalent geometry : angle 0.59686 / 0.31 (10503) SS BOND : bond 0.00078 / 0.03 ( 3) SS BOND : angle 1.57971 / 0.88 ( 6) hydrogen bonds : bond 0.03966 / 2.67 ( 420) hydrogen bonds : angle 5.09870 / 3.72 ( 1212) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 156 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 280 MET cc_start: 0.7643 (mtp) cc_final: 0.7417 (mtm) REVERT: A 327 TRP cc_start: 0.7908 (OUTLIER) cc_final: 0.7206 (m-10) REVERT: B 266 LEU cc_start: 0.8672 (tp) cc_final: 0.8364 (tp) REVERT: B 274 LYS cc_start: 0.7855 (tttp) cc_final: 0.7620 (ttmt) REVERT: B 280 ARG cc_start: 0.8333 (tpt90) cc_final: 0.7945 (ttt90) REVERT: E 50 ASP cc_start: 0.8722 (OUTLIER) cc_final: 0.8199 (p0) REVERT: E 80 TYR cc_start: 0.7753 (m-80) cc_final: 0.7236 (m-80) REVERT: E 94 TYR cc_start: 0.7290 (m-80) cc_final: 0.6383 (m-80) REVERT: E 115 TYR cc_start: 0.8102 (t80) cc_final: 0.7886 (t80) REVERT: D 38 MET cc_start: 0.6707 (mtm) cc_final: 0.6432 (mtp) outliers start: 9 outliers final: 5 residues processed: 161 average time/residue: 0.0672 time to fit residues: 14.8386 Evaluate side-chains 145 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 327 TRP Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 95 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 91 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 40 optimal weight: 0.0000 chunk 74 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 23 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN E 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.194374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.160749 restraints weight = 19310.964| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 4.13 r_work: 0.3673 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3812 r_free = 0.3812 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3812 r_free = 0.3812 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7696 Z= 0.137 Angle : 0.576 11.265 10509 Z= 0.299 Chirality : 0.043 0.163 1223 Planarity : 0.005 0.068 1324 Dihedral : 6.149 112.795 1093 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.15 % Allowed : 14.54 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.95 (0.27), residues: 988 helix: 2.17 (0.27), residues: 392 sheet: 0.06 (0.32), residues: 222 loop : -0.64 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 38 TYR 0.023 0.002 TYR C 85 PHE 0.015 0.001 PHE B 222 TRP 0.012 0.001 TRP C 169 HIS 0.005 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 7693) covalent geometry : angle 0.57508 / 0.30 (10503) SS BOND : bond 0.00095 / 0.04 ( 3) SS BOND : angle 1.35779 / 0.76 ( 6) hydrogen bonds : bond 0.03779 / 2.54 ( 420) hydrogen bonds : angle 4.94390 / 3.60 ( 1212) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: A 280 MET cc_start: 0.7738 (mtp) cc_final: 0.7497 (mtm) REVERT: A 327 TRP cc_start: 0.7896 (OUTLIER) cc_final: 0.7139 (m-10) REVERT: B 266 LEU cc_start: 0.8642 (tp) cc_final: 0.8340 (tp) REVERT: B 274 LYS cc_start: 0.7921 (tttp) cc_final: 0.7685 (ttmt) REVERT: B 280 ARG cc_start: 0.8362 (tpt90) cc_final: 0.7947 (ttt90) REVERT: C 111 TYR cc_start: 0.8368 (m-80) cc_final: 0.8139 (m-80) REVERT: E 50 ASP cc_start: 0.8714 (p0) cc_final: 0.8191 (p0) REVERT: E 80 TYR cc_start: 0.7754 (m-80) cc_final: 0.7224 (m-80) REVERT: D 38 MET cc_start: 0.6696 (mtm) cc_final: 0.6430 (mtp) outliers start: 16 outliers final: 9 residues processed: 153 average time/residue: 0.0644 time to fit residues: 13.7640 Evaluate side-chains 146 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 TRP Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain E residue 95 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 15 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 0.0270 chunk 64 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN E 74 ASN E 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.192490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.159436 restraints weight = 22180.992| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 5.39 r_work: 0.3607 rms_B_bonded: 5.38 restraints_weight: 2.0000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3749 r_free = 0.3749 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3749 r_free = 0.3749 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7696 Z= 0.149 Angle : 0.582 11.579 10509 Z= 0.302 Chirality : 0.043 0.175 1223 Planarity : 0.005 0.068 1324 Dihedral : 6.153 112.317 1093 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.42 % Allowed : 14.94 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.27), residues: 988 helix: 2.42 (0.27), residues: 382 sheet: -0.05 (0.32), residues: 233 loop : -0.67 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 314 TYR 0.024 0.002 TYR C 85 PHE 0.015 0.001 PHE B 212 TRP 0.012 0.002 TRP C 169 HIS 0.005 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 7693) covalent geometry : angle 0.58122 / 0.30 (10503) SS BOND : bond 0.00089 / 0.04 ( 3) SS BOND : angle 1.29781 / 0.71 ( 6) hydrogen bonds : bond 0.03759 / 2.54 ( 420) hydrogen bonds : angle 4.88801 / 3.56 ( 1212) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 VAL cc_start: 0.8625 (m) cc_final: 0.8248 (p) REVERT: A 140 THR cc_start: 0.6544 (OUTLIER) cc_final: 0.6330 (t) REVERT: A 327 TRP cc_start: 0.7957 (OUTLIER) cc_final: 0.7043 (m-10) REVERT: B 266 LEU cc_start: 0.8714 (tp) cc_final: 0.8427 (tp) REVERT: B 274 LYS cc_start: 0.7970 (tttp) cc_final: 0.7719 (ttmt) REVERT: C 263 THR cc_start: 0.8233 (m) cc_final: 0.7964 (p) REVERT: E 50 ASP cc_start: 0.8733 (OUTLIER) cc_final: 0.8185 (p0) REVERT: E 80 TYR cc_start: 0.7812 (m-80) cc_final: 0.7294 (m-80) outliers start: 18 outliers final: 12 residues processed: 158 average time/residue: 0.0627 time to fit residues: 13.8147 Evaluate side-chains 156 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 TRP Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain C residue 85 TYR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 114 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 42 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 59 optimal weight: 0.0970 chunk 86 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 ASN E 77 ASN E 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.193984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.159078 restraints weight = 17461.956| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 3.50 r_work: 0.3711 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3848 r_free = 0.3848 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3848 r_free = 0.3848 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7696 Z= 0.135 Angle : 0.582 11.706 10509 Z= 0.303 Chirality : 0.043 0.165 1223 Planarity : 0.005 0.068 1324 Dihedral : 6.105 112.771 1093 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.69 % Allowed : 16.02 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.16 (0.27), residues: 988 helix: 2.49 (0.27), residues: 381 sheet: 0.28 (0.33), residues: 214 loop : -0.67 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 68 TYR 0.018 0.002 TYR C 85 PHE 0.015 0.001 PHE B 222 TRP 0.014 0.001 TRP C 211 HIS 0.004 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 7693) covalent geometry : angle 0.58147 / 0.30 (10503) SS BOND : bond 0.00089 / 0.04 ( 3) SS BOND : angle 1.15611 / 0.63 ( 6) hydrogen bonds : bond 0.03632 / 2.45 ( 420) hydrogen bonds : angle 4.82407 / 3.51 ( 1212) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 VAL cc_start: 0.8606 (m) cc_final: 0.8257 (p) REVERT: A 327 TRP cc_start: 0.7873 (OUTLIER) cc_final: 0.7030 (m-10) REVERT: A 338 MET cc_start: 0.7966 (mtp) cc_final: 0.7667 (mtp) REVERT: B 266 LEU cc_start: 0.8577 (tp) cc_final: 0.8276 (tp) REVERT: B 274 LYS cc_start: 0.7900 (tttp) cc_final: 0.7677 (ttmt) REVERT: E 50 ASP cc_start: 0.8689 (OUTLIER) cc_final: 0.8112 (p0) REVERT: E 80 TYR cc_start: 0.7759 (m-80) cc_final: 0.7282 (m-80) outliers start: 20 outliers final: 13 residues processed: 162 average time/residue: 0.0635 time to fit residues: 14.2783 Evaluate side-chains 156 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 TRP Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain B residue 253 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 95 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN E 84 ASN E 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.191388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.157694 restraints weight = 20450.665| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 4.50 r_work: 0.3631 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3775 r_free = 0.3775 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3775 r_free = 0.3775 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7696 Z= 0.159 Angle : 0.598 12.151 10509 Z= 0.311 Chirality : 0.043 0.168 1223 Planarity : 0.005 0.069 1324 Dihedral : 6.163 112.681 1093 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.42 % Allowed : 16.69 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.11 (0.27), residues: 988 helix: 2.44 (0.27), residues: 382 sheet: 0.07 (0.33), residues: 222 loop : -0.58 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 68 TYR 0.021 0.002 TYR C 85 PHE 0.014 0.002 PHE B 212 TRP 0.014 0.002 TRP C 169 HIS 0.006 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 7693) covalent geometry : angle 0.59773 / 0.31 (10503) SS BOND : bond 0.00094 / 0.04 ( 3) SS BOND : angle 1.25885 / 0.69 ( 6) hydrogen bonds : bond 0.03744 / 2.53 ( 420) hydrogen bonds : angle 4.85681 / 3.53 ( 1212) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 VAL cc_start: 0.8659 (m) cc_final: 0.8296 (p) REVERT: A 327 TRP cc_start: 0.7931 (OUTLIER) cc_final: 0.6954 (m-10) REVERT: A 338 MET cc_start: 0.8192 (mtp) cc_final: 0.7917 (mtp) REVERT: B 38 ARG cc_start: 0.7981 (ttp80) cc_final: 0.7163 (ttp80) REVERT: B 274 LYS cc_start: 0.7934 (tttp) cc_final: 0.7682 (ttmt) REVERT: E 50 ASP cc_start: 0.8709 (OUTLIER) cc_final: 0.8116 (p0) REVERT: E 80 TYR cc_start: 0.7782 (m-80) cc_final: 0.7244 (m-80) outliers start: 18 outliers final: 14 residues processed: 158 average time/residue: 0.0634 time to fit residues: 13.7844 Evaluate side-chains 155 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 TRP Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 95 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 82 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.193583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.155871 restraints weight = 12072.281| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.76 r_work: 0.3741 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3878 r_free = 0.3878 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3878 r_free = 0.3878 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7696 Z= 0.130 Angle : 0.576 12.015 10509 Z= 0.300 Chirality : 0.042 0.169 1223 Planarity : 0.005 0.068 1324 Dihedral : 6.095 112.701 1093 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.29 % Allowed : 16.96 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.17 (0.27), residues: 988 helix: 2.49 (0.27), residues: 382 sheet: 0.02 (0.33), residues: 223 loop : -0.50 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 72 TYR 0.017 0.001 TYR C 85 PHE 0.014 0.001 PHE B 212 TRP 0.012 0.001 TRP A 311 HIS 0.004 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 7693) covalent geometry : angle 0.57542 / 0.30 (10503) SS BOND : bond 0.00074 / 0.03 ( 3) SS BOND : angle 1.12377 / 0.61 ( 6) hydrogen bonds : bond 0.03579 / 2.41 ( 420) hydrogen bonds : angle 4.79336 / 3.47 ( 1212) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: A 134 VAL cc_start: 0.8606 (m) cc_final: 0.8259 (p) REVERT: A 327 TRP cc_start: 0.7853 (OUTLIER) cc_final: 0.6910 (m-10) REVERT: A 338 MET cc_start: 0.8114 (mtp) cc_final: 0.7814 (mtp) REVERT: B 38 ARG cc_start: 0.7841 (ttp80) cc_final: 0.7132 (ttp80) REVERT: B 266 LEU cc_start: 0.8424 (tp) cc_final: 0.8009 (tp) REVERT: B 274 LYS cc_start: 0.7839 (tttp) cc_final: 0.7617 (ttmt) REVERT: E 50 ASP cc_start: 0.8692 (OUTLIER) cc_final: 0.8047 (p0) REVERT: E 80 TYR cc_start: 0.7757 (m-80) cc_final: 0.7278 (m-80) outliers start: 17 outliers final: 14 residues processed: 155 average time/residue: 0.0647 time to fit residues: 13.9850 Evaluate side-chains 159 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 TRP Chi-restraints excluded: chain B residue 253 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain C residue 85 TYR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 95 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 26 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 94 optimal weight: 30.0000 chunk 83 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN E 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.182471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.140877 restraints weight = 18122.040| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 3.74 r_work: 0.3537 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3592 r_free = 0.3592 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3592 r_free = 0.3592 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7696 Z= 0.166 Angle : 0.610 12.551 10509 Z= 0.318 Chirality : 0.043 0.168 1223 Planarity : 0.005 0.068 1324 Dihedral : 6.198 112.658 1093 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.83 % Allowed : 17.09 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.27), residues: 988 helix: 2.43 (0.27), residues: 383 sheet: 0.01 (0.33), residues: 217 loop : -0.57 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 72 TYR 0.022 0.002 TYR C 85 PHE 0.015 0.002 PHE E 108 TRP 0.015 0.002 TRP C 169 HIS 0.006 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 ( 7693) covalent geometry : angle 0.60892 / 0.32 (10503) SS BOND : bond 0.00101 / 0.05 ( 3) SS BOND : angle 1.30112 / 0.71 ( 6) hydrogen bonds : bond 0.03774 / 2.56 ( 420) hydrogen bonds : angle 4.89372 / 3.55 ( 1212) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 134 VAL cc_start: 0.8425 (m) cc_final: 0.8012 (p) REVERT: A 327 TRP cc_start: 0.8033 (OUTLIER) cc_final: 0.6850 (m-10) REVERT: A 338 MET cc_start: 0.8245 (mtp) cc_final: 0.8002 (mtp) REVERT: B 266 LEU cc_start: 0.8518 (tp) cc_final: 0.8173 (tp) REVERT: B 274 LYS cc_start: 0.7622 (tttp) cc_final: 0.7350 (ttmt) REVERT: E 50 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.7979 (p0) REVERT: E 80 TYR cc_start: 0.7647 (m-80) cc_final: 0.7051 (m-80) outliers start: 21 outliers final: 16 residues processed: 155 average time/residue: 0.0669 time to fit residues: 14.5668 Evaluate side-chains 159 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 TRP Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 95 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 82 optimal weight: 0.0670 chunk 83 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 294 GLN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.193953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.161078 restraints weight = 16447.638| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 3.41 r_work: 0.3704 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3844 r_free = 0.3844 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3844 r_free = 0.3844 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7696 Z= 0.125 Angle : 0.576 12.199 10509 Z= 0.301 Chirality : 0.042 0.171 1223 Planarity : 0.005 0.068 1324 Dihedral : 6.074 112.647 1093 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.02 % Allowed : 17.90 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.27), residues: 988 helix: 2.52 (0.27), residues: 382 sheet: 0.09 (0.33), residues: 220 loop : -0.49 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 72 TYR 0.015 0.001 TYR C 85 PHE 0.014 0.001 PHE B 212 TRP 0.011 0.001 TRP A 311 HIS 0.004 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 7693) covalent geometry : angle 0.57559 / 0.30 (10503) SS BOND : bond 0.00067 / 0.03 ( 3) SS BOND : angle 1.07938 / 0.59 ( 6) hydrogen bonds : bond 0.03540 / 2.40 ( 420) hydrogen bonds : angle 4.79344 / 3.47 ( 1212) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 134 VAL cc_start: 0.8588 (m) cc_final: 0.8241 (p) REVERT: A 327 TRP cc_start: 0.7860 (OUTLIER) cc_final: 0.6906 (m-10) REVERT: A 338 MET cc_start: 0.8333 (mtp) cc_final: 0.8040 (mtp) REVERT: B 266 LEU cc_start: 0.8496 (tp) cc_final: 0.8094 (tp) REVERT: B 274 LYS cc_start: 0.7870 (tttp) cc_final: 0.7666 (ttmt) REVERT: E 50 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.8097 (p0) REVERT: E 80 TYR cc_start: 0.7782 (m-80) cc_final: 0.7323 (m-80) outliers start: 15 outliers final: 12 residues processed: 151 average time/residue: 0.0701 time to fit residues: 14.7794 Evaluate side-chains 153 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 TRP Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain C residue 85 TYR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 95 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 30.0000 chunk 78 optimal weight: 6.9990 chunk 42 optimal weight: 0.0980 chunk 73 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 294 GLN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.193568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.159260 restraints weight = 15001.152| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 3.13 r_work: 0.3710 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3848 r_free = 0.3848 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3848 r_free = 0.3848 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7696 Z= 0.137 Angle : 0.588 12.294 10509 Z= 0.307 Chirality : 0.043 0.175 1223 Planarity : 0.005 0.068 1324 Dihedral : 6.061 112.255 1093 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.02 % Allowed : 18.44 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.27), residues: 988 helix: 2.51 (0.27), residues: 382 sheet: 0.02 (0.33), residues: 219 loop : -0.48 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 72 TYR 0.017 0.002 TYR C 85 PHE 0.013 0.001 PHE B 212 TRP 0.011 0.001 TRP C 169 HIS 0.004 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 7693) covalent geometry : angle 0.58732 / 0.31 (10503) SS BOND : bond 0.00029 / 0.01 ( 3) SS BOND : angle 1.12662 / 0.61 ( 6) hydrogen bonds : bond 0.03589 / 2.43 ( 420) hydrogen bonds : angle 4.78790 / 3.47 ( 1212) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1665.70 seconds wall clock time: 29 minutes 10.86 seconds (1750.86 seconds total)