Starting phenix.real_space_refine on Wed Sep 17 11:27:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jvg_61838/09_2025/9jvg_61838.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jvg_61838/09_2025/9jvg_61838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jvg_61838/09_2025/9jvg_61838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jvg_61838/09_2025/9jvg_61838.map" model { file = "/net/cci-nas-00/data/ceres_data/9jvg_61838/09_2025/9jvg_61838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jvg_61838/09_2025/9jvg_61838.cif" } resolution = 2.76 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= -0.000 sd= 0.019 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 50 5.16 5 C 5335 2.51 5 N 1461 2.21 5 O 1550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8396 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1836 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 1 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 6, 'ARG:plan': 4, 'TYR:plan': 1, 'GLU:plan': 9, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 87 Chain: "R" Number of atoms: 2079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2079 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 281} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 322 Unresolved non-hydrogen angles: 410 Unresolved non-hydrogen dihedrals: 274 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'ASP:plan': 6, 'ARG:plan': 10, 'HIS:plan': 4, 'PHE:plan': 7, 'ASN:plan1': 4, 'TRP:plan': 2, 'GLU:plan': 7, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 195 Chain: "B" Number of atoms: 2439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2439 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 4, 'GLN:plan1': 5, 'ARG:plan': 8, 'ASN:plan1': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 114 Chain: "G" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 350 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "S" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1692 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 42 Time building chain proxies: 2.32, per 1000 atoms: 0.28 Number of scatterers: 8396 At special positions: 0 Unit cell: (86.92, 124.02, 126.14, 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 50 16.00 O 1550 8.00 N 1461 7.00 C 5335 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 92 " - pdb=" SG CYS R 170 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 491.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 13 sheets defined 37.2% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 6 through 38 removed outlier: 3.828A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 64 Processing helix chain 'A' and resid 245 through 249 removed outlier: 3.842A pdb=" N ASN A 249 " --> pdb=" O GLN A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.502A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.976A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 352 removed outlier: 4.452A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'R' and resid 20 through 50 removed outlier: 3.523A pdb=" N SER R 24 " --> pdb=" O LEU R 20 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE R 27 " --> pdb=" O PRO R 23 " (cutoff:3.500A) Proline residue: R 35 - end of helix Processing helix chain 'R' and resid 53 through 81 removed outlier: 3.757A pdb=" N TYR R 57 " --> pdb=" O GLU R 53 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA R 64 " --> pdb=" O ASN R 60 " (cutoff:3.500A) Proline residue: R 73 - end of helix Processing helix chain 'R' and resid 88 through 122 removed outlier: 3.852A pdb=" N CYS R 92 " --> pdb=" O GLY R 88 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS R 93 " --> pdb=" O PRO R 89 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU R 94 " --> pdb=" O GLY R 90 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE R 97 " --> pdb=" O LYS R 93 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ILE R 103 " --> pdb=" O PHE R 99 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N TYR R 104 " --> pdb=" O TYR R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 132 through 151 Processing helix chain 'R' and resid 152 through 157 removed outlier: 4.371A pdb=" N PHE R 156 " --> pdb=" O SER R 152 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N HIS R 157 " --> pdb=" O ALA R 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 152 through 157' Processing helix chain 'R' and resid 177 through 190 removed outlier: 3.573A pdb=" N ALA R 181 " --> pdb=" O GLU R 177 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TRP R 182 " --> pdb=" O ARG R 178 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR R 186 " --> pdb=" O TRP R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 209 Processing helix chain 'R' and resid 217 through 256 removed outlier: 3.583A pdb=" N LEU R 227 " --> pdb=" O LYS R 223 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE R 232 " --> pdb=" O ALA R 228 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL R 235 " --> pdb=" O LEU R 231 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU R 236 " --> pdb=" O ILE R 232 " (cutoff:3.500A) Proline residue: R 241 - end of helix removed outlier: 3.559A pdb=" N TYR R 253 " --> pdb=" O ARG R 249 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY R 255 " --> pdb=" O ALA R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 264 Processing helix chain 'R' and resid 265 through 276 removed outlier: 4.707A pdb=" N ALA R 269 " --> pdb=" O ARG R 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 280 Processing helix chain 'R' and resid 282 through 290 removed outlier: 3.648A pdb=" N ILE R 286 " --> pdb=" O VAL R 282 " (cutoff:3.500A) Processing helix chain 'R' and resid 292 through 304 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 12 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.814A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 218 through 224 removed outlier: 6.191A pdb=" N HIS A 41 " --> pdb=" O HIS A 230 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N PHE A 232 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A 43 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA A 253 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE A 254 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N PHE A 290 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE A 256 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ASN A 292 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL A 258 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.565A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.700A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.475A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.665A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.768A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.618A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 removed outlier: 6.241A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.956A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 4.054A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 158 through 160 Processing sheet with id=AB4, first strand: chain 'S' and resid 194 through 195 removed outlier: 6.562A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1203 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: 1.44 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1358 1.30 - 1.42: 2372 1.42 - 1.55: 4784 1.55 - 1.68: 0 1.68 - 1.81: 70 Bond restraints: 8584 Sorted by residual: bond pdb=" N ASP B 205 " pdb=" CA ASP B 205 " ideal model delta sigma weight residual 1.458 1.393 0.065 1.14e-02 7.69e+03 3.28e+01 bond pdb=" C CYS B 204 " pdb=" O CYS B 204 " ideal model delta sigma weight residual 1.236 1.167 0.069 1.33e-02 5.65e+03 2.71e+01 bond pdb=" C GLY B 202 " pdb=" O GLY B 202 " ideal model delta sigma weight residual 1.234 1.167 0.067 1.34e-02 5.57e+03 2.48e+01 bond pdb=" CA GLY B 202 " pdb=" C GLY B 202 " ideal model delta sigma weight residual 1.518 1.482 0.036 7.30e-03 1.88e+04 2.47e+01 bond pdb=" CA ASP B 205 " pdb=" CB ASP B 205 " ideal model delta sigma weight residual 1.530 1.467 0.063 1.39e-02 5.18e+03 2.05e+01 ... (remaining 8579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 11410 2.11 - 4.21: 260 4.21 - 6.32: 36 6.32 - 8.43: 6 8.43 - 10.54: 6 Bond angle restraints: 11718 Sorted by residual: angle pdb=" N GLN A 390 " pdb=" CA GLN A 390 " pdb=" C GLN A 390 " ideal model delta sigma weight residual 111.40 121.94 -10.54 1.22e+00 6.72e-01 7.46e+01 angle pdb=" C GLN A 390 " pdb=" CA GLN A 390 " pdb=" CB GLN A 390 " ideal model delta sigma weight residual 110.79 100.91 9.88 1.68e+00 3.54e-01 3.46e+01 angle pdb=" C PRO S 41 " pdb=" CA PRO S 41 " pdb=" CB PRO S 41 " ideal model delta sigma weight residual 111.56 120.59 -9.03 1.65e+00 3.67e-01 3.00e+01 angle pdb=" N PHE R 169 " pdb=" CA PHE R 169 " pdb=" C PHE R 169 " ideal model delta sigma weight residual 111.24 118.75 -7.51 1.38e+00 5.25e-01 2.96e+01 angle pdb=" CA ASN B 313 " pdb=" C ASN B 313 " pdb=" N ARG B 314 " ideal model delta sigma weight residual 115.63 121.90 -6.27 1.36e+00 5.41e-01 2.12e+01 ... (remaining 11713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.09: 4570 16.09 - 32.18: 342 32.18 - 48.26: 67 48.26 - 64.35: 10 64.35 - 80.44: 7 Dihedral angle restraints: 4996 sinusoidal: 1648 harmonic: 3348 Sorted by residual: dihedral pdb=" CB CYS R 92 " pdb=" SG CYS R 92 " pdb=" SG CYS R 170 " pdb=" CB CYS R 170 " ideal model delta sinusoidal sigma weight residual -86.00 -138.38 52.38 1 1.00e+01 1.00e-02 3.74e+01 dihedral pdb=" C VAL B 307 " pdb=" N VAL B 307 " pdb=" CA VAL B 307 " pdb=" CB VAL B 307 " ideal model delta harmonic sigma weight residual -122.00 -110.41 -11.59 0 2.50e+00 1.60e-01 2.15e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 157.09 22.91 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 4993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1201 0.080 - 0.160: 143 0.160 - 0.240: 7 0.240 - 0.320: 2 0.320 - 0.399: 3 Chirality restraints: 1356 Sorted by residual: chirality pdb=" CA ALA B 206 " pdb=" N ALA B 206 " pdb=" C ALA B 206 " pdb=" CB ALA B 206 " both_signs ideal model delta sigma weight residual False 2.48 2.09 0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb=" CA PRO S 41 " pdb=" N PRO S 41 " pdb=" C PRO S 41 " pdb=" CB PRO S 41 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" CA VAL B 307 " pdb=" N VAL B 307 " pdb=" C VAL B 307 " pdb=" CB VAL B 307 " both_signs ideal model delta sigma weight residual False 2.44 2.79 -0.35 2.00e-01 2.50e+01 3.04e+00 ... (remaining 1353 not shown) Planarity restraints: 1503 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 204 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.37e+00 pdb=" C CYS B 204 " 0.053 2.00e-02 2.50e+03 pdb=" O CYS B 204 " -0.020 2.00e-02 2.50e+03 pdb=" N ASP B 205 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " 0.019 2.00e-02 2.50e+03 1.64e-02 5.38e+00 pdb=" CG TYR B 59 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP R 85 " 0.011 2.00e-02 2.50e+03 2.31e-02 5.32e+00 pdb=" C TRP R 85 " -0.040 2.00e-02 2.50e+03 pdb=" O TRP R 85 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE R 86 " 0.013 2.00e-02 2.50e+03 ... (remaining 1500 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.30: 5 2.30 - 2.95: 3945 2.95 - 3.60: 12259 3.60 - 4.25: 19389 4.25 - 4.90: 33325 Nonbonded interactions: 68923 Sorted by model distance: nonbonded pdb=" CE2 TYR A 391 " pdb=" CB ALA R 120 " model vdw 1.644 3.760 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.096 3.040 nonbonded pdb=" NH1 ARG B 96 " pdb=" OE2 GLU B 138 " model vdw 2.198 3.120 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.255 3.040 nonbonded pdb=" NH2 ARG S 67 " pdb=" OD2 ASP S 90 " model vdw 2.289 3.120 ... (remaining 68918 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 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: 0.030 Set scattering table: 0.020 Process input model: 9.990 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 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 : 0.008 0.076 8586 Z= 0.386 Angle : 0.794 10.537 11722 Z= 0.458 Chirality : 0.054 0.399 1356 Planarity : 0.005 0.047 1503 Dihedral : 12.559 80.441 2830 Min Nonbonded Distance : 1.644 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.38 % Allowed : 0.50 % Favored : 99.12 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.25), residues: 1135 helix: 0.89 (0.27), residues: 373 sheet: -0.56 (0.31), residues: 267 loop : -1.46 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 256 TYR 0.041 0.002 TYR B 59 PHE 0.028 0.002 PHE B 151 TRP 0.014 0.002 TRP B 169 HIS 0.010 0.002 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00773 ( 8584) covalent geometry : angle 0.79387 (11718) SS BOND : bond 0.00407 ( 2) SS BOND : angle 0.84203 ( 4) hydrogen bonds : bond 0.17619 ( 421) hydrogen bonds : angle 7.36011 ( 1203) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 208 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: B 264 TYR cc_start: 0.6263 (m-80) cc_final: 0.5951 (m-80) REVERT: S 223 ASP cc_start: 0.7472 (m-30) cc_final: 0.7149 (t0) outliers start: 3 outliers final: 1 residues processed: 210 average time/residue: 0.5220 time to fit residues: 117.4816 Evaluate side-chains 120 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.1980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 ASN R 280 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN S 179 GLN S 231 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.135648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.113071 restraints weight = 15925.651| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.88 r_work: 0.3633 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8586 Z= 0.148 Angle : 0.608 10.345 11722 Z= 0.326 Chirality : 0.044 0.139 1356 Planarity : 0.005 0.057 1503 Dihedral : 4.755 46.861 1240 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.89 % Allowed : 13.57 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.25), residues: 1135 helix: 1.65 (0.28), residues: 372 sheet: -0.35 (0.31), residues: 272 loop : -1.16 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 67 TYR 0.037 0.002 TYR A 391 PHE 0.018 0.002 PHE R 99 TRP 0.024 0.002 TRP R 75 HIS 0.003 0.001 HIS R 271 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8584) covalent geometry : angle 0.60803 (11718) SS BOND : bond 0.00146 ( 2) SS BOND : angle 0.98277 ( 4) hydrogen bonds : bond 0.04455 ( 421) hydrogen bonds : angle 5.07653 ( 1203) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: R 125 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8391 (mp) REVERT: R 131 ARG cc_start: 0.8373 (mtm110) cc_final: 0.7844 (mtm110) REVERT: R 132 ARG cc_start: 0.7297 (mtp-110) cc_final: 0.6952 (mtt180) REVERT: B 264 TYR cc_start: 0.6613 (m-80) cc_final: 0.5979 (m-80) REVERT: G 38 MET cc_start: 0.6629 (tmm) cc_final: 0.6416 (tpt) REVERT: S 93 MET cc_start: 0.8274 (ttp) cc_final: 0.8029 (ttp) REVERT: S 223 ASP cc_start: 0.7509 (m-30) cc_final: 0.6848 (t0) REVERT: S 231 GLN cc_start: 0.7076 (OUTLIER) cc_final: 0.6819 (pp30) REVERT: S 245 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7835 (mm) outliers start: 31 outliers final: 10 residues processed: 157 average time/residue: 0.5212 time to fit residues: 87.8336 Evaluate side-chains 122 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 216 THR Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 135 SER Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 231 GLN Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 9 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 75 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN R 60 ASN B 75 GLN B 88 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.134728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.111745 restraints weight = 15814.166| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.87 r_work: 0.3620 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8586 Z= 0.142 Angle : 0.571 9.505 11722 Z= 0.304 Chirality : 0.042 0.139 1356 Planarity : 0.004 0.048 1503 Dihedral : 4.331 19.186 1238 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.27 % Allowed : 15.58 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.25), residues: 1135 helix: 1.75 (0.28), residues: 377 sheet: -0.37 (0.31), residues: 276 loop : -1.11 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 18 TYR 0.026 0.002 TYR A 391 PHE 0.016 0.001 PHE R 276 TRP 0.018 0.002 TRP R 75 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8584) covalent geometry : angle 0.57088 (11718) SS BOND : bond 0.00176 ( 2) SS BOND : angle 0.96425 ( 4) hydrogen bonds : bond 0.04092 ( 421) hydrogen bonds : angle 4.75784 ( 1203) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.357 Fit side-chains REVERT: R 132 ARG cc_start: 0.7397 (mtp-110) cc_final: 0.7029 (mtt180) REVERT: R 183 MET cc_start: 0.8264 (tpp) cc_final: 0.8031 (tpp) REVERT: R 215 SER cc_start: 0.8640 (OUTLIER) cc_final: 0.8398 (t) REVERT: R 280 ASN cc_start: 0.7853 (t0) cc_final: 0.7422 (t0) REVERT: B 217 MET cc_start: 0.8558 (pmm) cc_final: 0.8273 (pmt) REVERT: B 264 TYR cc_start: 0.6415 (m-80) cc_final: 0.5915 (m-80) REVERT: S 223 ASP cc_start: 0.7485 (m-30) cc_final: 0.6834 (t0) REVERT: S 245 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7576 (mp) outliers start: 26 outliers final: 10 residues processed: 142 average time/residue: 0.4928 time to fit residues: 75.5667 Evaluate side-chains 120 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 215 SER Chi-restraints excluded: chain R residue 216 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 36 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 21 optimal weight: 0.0270 chunk 59 optimal weight: 0.6980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN R 184 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN S 231 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.135149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.112220 restraints weight = 16063.459| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.90 r_work: 0.3626 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8586 Z= 0.127 Angle : 0.564 11.526 11722 Z= 0.294 Chirality : 0.042 0.139 1356 Planarity : 0.004 0.052 1503 Dihedral : 4.159 18.738 1238 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.27 % Allowed : 16.08 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.25), residues: 1135 helix: 1.69 (0.27), residues: 387 sheet: -0.49 (0.31), residues: 277 loop : -1.16 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 18 TYR 0.020 0.002 TYR A 391 PHE 0.013 0.001 PHE R 99 TRP 0.020 0.002 TRP R 42 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8584) covalent geometry : angle 0.56347 (11718) SS BOND : bond 0.00128 ( 2) SS BOND : angle 1.04122 ( 4) hydrogen bonds : bond 0.03731 ( 421) hydrogen bonds : angle 4.53679 ( 1203) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.372 Fit side-chains REVERT: A 392 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8675 (mp0) REVERT: R 59 MET cc_start: 0.8427 (mmm) cc_final: 0.8030 (mtp) REVERT: R 183 MET cc_start: 0.8295 (tpp) cc_final: 0.8044 (tpp) REVERT: R 215 SER cc_start: 0.8618 (OUTLIER) cc_final: 0.8385 (t) REVERT: R 280 ASN cc_start: 0.7780 (t0) cc_final: 0.7405 (t0) REVERT: B 217 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8268 (pmt) REVERT: B 221 THR cc_start: 0.8039 (OUTLIER) cc_final: 0.7719 (m) REVERT: B 264 TYR cc_start: 0.6280 (m-80) cc_final: 0.5885 (m-80) REVERT: G 28 ILE cc_start: 0.7244 (OUTLIER) cc_final: 0.6629 (tp) REVERT: S 38 ARG cc_start: 0.7617 (ptp90) cc_final: 0.7259 (ptp-170) REVERT: S 93 MET cc_start: 0.8092 (ttp) cc_final: 0.7741 (ttp) REVERT: S 158 SER cc_start: 0.8495 (p) cc_final: 0.8286 (t) REVERT: S 223 ASP cc_start: 0.7512 (m-30) cc_final: 0.6906 (t0) REVERT: S 245 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7418 (mp) outliers start: 34 outliers final: 18 residues processed: 149 average time/residue: 0.4834 time to fit residues: 78.0133 Evaluate side-chains 136 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 215 SER Chi-restraints excluded: chain R residue 216 THR Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 135 SER Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 100 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN R 102 ASN R 184 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN S 194 ASN S 231 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.133913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.110946 restraints weight = 16027.589| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.88 r_work: 0.3605 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8586 Z= 0.140 Angle : 0.556 11.305 11722 Z= 0.293 Chirality : 0.043 0.183 1356 Planarity : 0.004 0.055 1503 Dihedral : 4.123 18.715 1238 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.77 % Allowed : 17.21 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.25), residues: 1135 helix: 1.76 (0.27), residues: 388 sheet: -0.54 (0.31), residues: 277 loop : -1.17 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 18 TYR 0.020 0.002 TYR A 391 PHE 0.012 0.001 PHE R 99 TRP 0.022 0.002 TRP R 42 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8584) covalent geometry : angle 0.55615 (11718) SS BOND : bond 0.00165 ( 2) SS BOND : angle 1.03358 ( 4) hydrogen bonds : bond 0.03729 ( 421) hydrogen bonds : angle 4.47465 ( 1203) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 0.339 Fit side-chains REVERT: R 50 GLN cc_start: 0.8967 (mm-40) cc_final: 0.8649 (mm-40) REVERT: R 59 MET cc_start: 0.8351 (mmm) cc_final: 0.8019 (mtp) REVERT: R 63 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7518 (mp) REVERT: R 183 MET cc_start: 0.8147 (tpp) cc_final: 0.7926 (tpp) REVERT: R 215 SER cc_start: 0.8632 (OUTLIER) cc_final: 0.8407 (t) REVERT: R 280 ASN cc_start: 0.7799 (t0) cc_final: 0.7574 (t0) REVERT: B 96 ARG cc_start: 0.8551 (mtt180) cc_final: 0.7959 (mmp80) REVERT: B 130 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7376 (mp0) REVERT: B 217 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8353 (pmt) REVERT: B 264 TYR cc_start: 0.6396 (m-80) cc_final: 0.5936 (m-80) REVERT: G 27 ARG cc_start: 0.8541 (mpt180) cc_final: 0.8216 (mpt180) REVERT: G 28 ILE cc_start: 0.7148 (OUTLIER) cc_final: 0.6603 (tp) REVERT: G 48 ASP cc_start: 0.6522 (t0) cc_final: 0.5456 (t70) REVERT: S 38 ARG cc_start: 0.7697 (ptp90) cc_final: 0.7357 (ptp-170) REVERT: S 93 MET cc_start: 0.8132 (ttp) cc_final: 0.7816 (ttp) REVERT: S 223 ASP cc_start: 0.7575 (m-30) cc_final: 0.6985 (t0) REVERT: S 245 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7453 (mp) outliers start: 38 outliers final: 18 residues processed: 153 average time/residue: 0.4798 time to fit residues: 79.0779 Evaluate side-chains 144 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 215 SER Chi-restraints excluded: chain R residue 216 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 135 SER Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 0.0060 chunk 22 optimal weight: 0.6980 chunk 71 optimal weight: 0.0000 chunk 37 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 102 ASN R 184 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN S 231 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.136143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.113374 restraints weight = 15843.135| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.88 r_work: 0.3641 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8586 Z= 0.110 Angle : 0.528 8.751 11722 Z= 0.279 Chirality : 0.042 0.133 1356 Planarity : 0.004 0.056 1503 Dihedral : 3.943 18.194 1238 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.52 % Allowed : 19.60 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.25), residues: 1135 helix: 1.87 (0.27), residues: 386 sheet: -0.58 (0.31), residues: 277 loop : -1.04 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 18 TYR 0.020 0.001 TYR B 59 PHE 0.010 0.001 PHE R 99 TRP 0.024 0.001 TRP R 42 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 8584) covalent geometry : angle 0.52753 (11718) SS BOND : bond 0.00198 ( 2) SS BOND : angle 0.75445 ( 4) hydrogen bonds : bond 0.03372 ( 421) hydrogen bonds : angle 4.38752 ( 1203) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.330 Fit side-chains REVERT: A 347 ARG cc_start: 0.8528 (ptp90) cc_final: 0.8310 (mtm-85) REVERT: R 59 MET cc_start: 0.8420 (mmm) cc_final: 0.8128 (mtp) REVERT: R 63 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7444 (mp) REVERT: R 183 MET cc_start: 0.8042 (tpp) cc_final: 0.7834 (tpp) REVERT: R 215 SER cc_start: 0.8598 (OUTLIER) cc_final: 0.8375 (t) REVERT: B 96 ARG cc_start: 0.8508 (mtt180) cc_final: 0.7973 (mmp80) REVERT: B 217 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8240 (pmt) REVERT: B 264 TYR cc_start: 0.6354 (m-80) cc_final: 0.5906 (m-80) REVERT: G 27 ARG cc_start: 0.8605 (mpt180) cc_final: 0.8236 (mpt180) REVERT: G 28 ILE cc_start: 0.7089 (OUTLIER) cc_final: 0.6592 (tp) REVERT: S 18 ARG cc_start: 0.6684 (ttt90) cc_final: 0.6307 (ttt90) REVERT: S 38 ARG cc_start: 0.7721 (ptp90) cc_final: 0.7397 (ptp-170) REVERT: S 93 MET cc_start: 0.8096 (ttp) cc_final: 0.7738 (ttp) REVERT: S 113 GLN cc_start: 0.7689 (mm110) cc_final: 0.7472 (mm-40) REVERT: S 223 ASP cc_start: 0.7583 (m-30) cc_final: 0.7014 (t0) REVERT: S 245 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7403 (mp) outliers start: 28 outliers final: 11 residues processed: 156 average time/residue: 0.4669 time to fit residues: 78.1557 Evaluate side-chains 129 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 215 SER Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 135 SER Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 17 optimal weight: 0.9990 chunk 68 optimal weight: 0.0000 chunk 102 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 184 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN S 194 ASN S 231 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.135174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.112409 restraints weight = 16078.278| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.91 r_work: 0.3625 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8586 Z= 0.125 Angle : 0.552 9.901 11722 Z= 0.291 Chirality : 0.042 0.132 1356 Planarity : 0.004 0.060 1503 Dihedral : 3.963 18.118 1238 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.40 % Allowed : 19.72 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.25), residues: 1135 helix: 1.98 (0.27), residues: 385 sheet: -0.51 (0.31), residues: 274 loop : -1.07 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 18 TYR 0.015 0.001 TYR A 391 PHE 0.012 0.001 PHE R 99 TRP 0.025 0.002 TRP R 42 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8584) covalent geometry : angle 0.55193 (11718) SS BOND : bond 0.00244 ( 2) SS BOND : angle 0.75182 ( 4) hydrogen bonds : bond 0.03419 ( 421) hydrogen bonds : angle 4.36419 ( 1203) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 0.308 Fit side-chains REVERT: A 347 ARG cc_start: 0.8530 (ptp90) cc_final: 0.8300 (mtm-85) REVERT: R 59 MET cc_start: 0.8380 (mmm) cc_final: 0.8109 (mtp) REVERT: R 63 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7502 (mp) REVERT: R 183 MET cc_start: 0.8058 (tpp) cc_final: 0.7852 (tpp) REVERT: R 215 SER cc_start: 0.8601 (OUTLIER) cc_final: 0.8385 (t) REVERT: B 96 ARG cc_start: 0.8491 (mtt180) cc_final: 0.7984 (mmp80) REVERT: B 217 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8286 (pmt) REVERT: B 264 TYR cc_start: 0.6334 (m-80) cc_final: 0.5887 (m-80) REVERT: G 27 ARG cc_start: 0.8601 (mpt180) cc_final: 0.8199 (mpt180) REVERT: G 28 ILE cc_start: 0.7064 (OUTLIER) cc_final: 0.6544 (tp) REVERT: G 48 ASP cc_start: 0.6477 (t0) cc_final: 0.5365 (t70) REVERT: S 93 MET cc_start: 0.8117 (ttp) cc_final: 0.7722 (ttp) REVERT: S 223 ASP cc_start: 0.7570 (m-30) cc_final: 0.7016 (t0) REVERT: S 234 GLU cc_start: 0.8798 (pt0) cc_final: 0.8434 (pt0) REVERT: S 245 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7356 (mp) outliers start: 35 outliers final: 19 residues processed: 144 average time/residue: 0.4975 time to fit residues: 76.8305 Evaluate side-chains 139 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 215 SER Chi-restraints excluded: chain R residue 216 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 135 SER Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 231 GLN Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 52 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 29 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 108 optimal weight: 0.0370 chunk 103 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.8462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 184 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN S 231 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.133715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.110719 restraints weight = 16055.216| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.89 r_work: 0.3604 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8586 Z= 0.145 Angle : 0.572 9.350 11722 Z= 0.303 Chirality : 0.042 0.134 1356 Planarity : 0.004 0.062 1503 Dihedral : 4.063 18.303 1238 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.89 % Allowed : 20.60 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.25), residues: 1135 helix: 2.01 (0.27), residues: 384 sheet: -0.59 (0.32), residues: 265 loop : -1.06 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 18 TYR 0.017 0.002 TYR R 270 PHE 0.014 0.001 PHE R 99 TRP 0.027 0.002 TRP R 42 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8584) covalent geometry : angle 0.57166 (11718) SS BOND : bond 0.00179 ( 2) SS BOND : angle 0.88654 ( 4) hydrogen bonds : bond 0.03590 ( 421) hydrogen bonds : angle 4.40592 ( 1203) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.357 Fit side-chains REVERT: A 347 ARG cc_start: 0.8545 (ptp90) cc_final: 0.8269 (mtm-85) REVERT: R 59 MET cc_start: 0.8371 (mmm) cc_final: 0.8118 (mtp) REVERT: R 63 ILE cc_start: 0.7752 (OUTLIER) cc_final: 0.7511 (mp) REVERT: R 183 MET cc_start: 0.7987 (tpp) cc_final: 0.7786 (tpp) REVERT: R 215 SER cc_start: 0.8621 (OUTLIER) cc_final: 0.8407 (t) REVERT: B 96 ARG cc_start: 0.8502 (mtt180) cc_final: 0.7983 (mmp80) REVERT: B 101 MET cc_start: 0.9086 (ptp) cc_final: 0.8864 (ptm) REVERT: B 217 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8332 (pmt) REVERT: B 264 TYR cc_start: 0.6507 (m-80) cc_final: 0.6033 (m-80) REVERT: G 27 ARG cc_start: 0.8593 (mpt180) cc_final: 0.8218 (mpt180) REVERT: G 28 ILE cc_start: 0.7091 (OUTLIER) cc_final: 0.6575 (tp) REVERT: G 48 ASP cc_start: 0.6569 (t0) cc_final: 0.5458 (t70) REVERT: S 93 MET cc_start: 0.8101 (ttp) cc_final: 0.7720 (ttp) REVERT: S 223 ASP cc_start: 0.7616 (m-30) cc_final: 0.7052 (t0) REVERT: S 234 GLU cc_start: 0.8810 (pt0) cc_final: 0.8483 (pt0) REVERT: S 245 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7433 (mp) outliers start: 31 outliers final: 19 residues processed: 143 average time/residue: 0.4990 time to fit residues: 76.7166 Evaluate side-chains 139 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 215 SER Chi-restraints excluded: chain R residue 216 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 231 GLN Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN R 184 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN S 186 GLN S 194 ASN ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.132685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.109575 restraints weight = 16072.418| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.91 r_work: 0.3584 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8586 Z= 0.162 Angle : 0.580 7.675 11722 Z= 0.309 Chirality : 0.043 0.152 1356 Planarity : 0.004 0.065 1503 Dihedral : 4.158 18.404 1238 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.52 % Allowed : 21.48 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.25), residues: 1135 helix: 1.99 (0.27), residues: 384 sheet: -0.64 (0.32), residues: 270 loop : -1.03 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 18 TYR 0.017 0.002 TYR A 391 PHE 0.014 0.001 PHE R 99 TRP 0.028 0.002 TRP R 42 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 8584) covalent geometry : angle 0.58038 (11718) SS BOND : bond 0.00209 ( 2) SS BOND : angle 0.87067 ( 4) hydrogen bonds : bond 0.03790 ( 421) hydrogen bonds : angle 4.49660 ( 1203) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 0.314 Fit side-chains REVERT: A 347 ARG cc_start: 0.8557 (ptp90) cc_final: 0.8288 (mtm-85) REVERT: R 59 MET cc_start: 0.8477 (mmm) cc_final: 0.8232 (mtp) REVERT: R 215 SER cc_start: 0.8642 (OUTLIER) cc_final: 0.8432 (t) REVERT: B 96 ARG cc_start: 0.8456 (mtt180) cc_final: 0.7932 (mmp80) REVERT: B 217 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8339 (pmt) REVERT: B 264 TYR cc_start: 0.6597 (m-80) cc_final: 0.6080 (m-80) REVERT: G 27 ARG cc_start: 0.8580 (mpt180) cc_final: 0.8196 (mpt180) REVERT: G 28 ILE cc_start: 0.7110 (OUTLIER) cc_final: 0.6593 (tp) REVERT: G 48 ASP cc_start: 0.6599 (t0) cc_final: 0.5581 (t70) REVERT: S 93 MET cc_start: 0.8180 (ttp) cc_final: 0.7900 (ttp) REVERT: S 223 ASP cc_start: 0.7603 (m-30) cc_final: 0.7007 (t0) REVERT: S 234 GLU cc_start: 0.8869 (pt0) cc_final: 0.8566 (pt0) REVERT: S 245 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7476 (mp) outliers start: 28 outliers final: 19 residues processed: 137 average time/residue: 0.4756 time to fit residues: 70.1350 Evaluate side-chains 136 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 215 SER Chi-restraints excluded: chain R residue 216 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 70 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 14 optimal weight: 0.2980 chunk 81 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 40 optimal weight: 0.0870 chunk 59 optimal weight: 0.2980 chunk 65 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 184 ASN S 39 GLN S 186 GLN ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.134935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.112046 restraints weight = 15912.358| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.90 r_work: 0.3630 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8586 Z= 0.119 Angle : 0.566 7.655 11722 Z= 0.297 Chirality : 0.042 0.136 1356 Planarity : 0.004 0.066 1503 Dihedral : 4.012 18.652 1238 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.02 % Allowed : 22.49 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.25), residues: 1135 helix: 2.00 (0.27), residues: 382 sheet: -0.60 (0.31), residues: 270 loop : -1.02 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 18 TYR 0.019 0.001 TYR R 270 PHE 0.011 0.001 PHE R 99 TRP 0.032 0.002 TRP R 42 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 8584) covalent geometry : angle 0.56549 (11718) SS BOND : bond 0.00220 ( 2) SS BOND : angle 0.77397 ( 4) hydrogen bonds : bond 0.03468 ( 421) hydrogen bonds : angle 4.45074 ( 1203) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.406 Fit side-chains REVERT: A 347 ARG cc_start: 0.8529 (ptp90) cc_final: 0.8259 (mtm-85) REVERT: R 50 GLN cc_start: 0.8972 (mm-40) cc_final: 0.8573 (mm-40) REVERT: R 59 MET cc_start: 0.8447 (mmm) cc_final: 0.8182 (mtp) REVERT: R 215 SER cc_start: 0.8597 (OUTLIER) cc_final: 0.8382 (t) REVERT: B 96 ARG cc_start: 0.8502 (mtt180) cc_final: 0.7975 (mmp80) REVERT: B 217 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8317 (pmt) REVERT: B 264 TYR cc_start: 0.6602 (m-80) cc_final: 0.6053 (m-80) REVERT: G 27 ARG cc_start: 0.8578 (mpt180) cc_final: 0.8201 (mpt180) REVERT: G 28 ILE cc_start: 0.7029 (OUTLIER) cc_final: 0.6490 (tp) REVERT: G 48 ASP cc_start: 0.6500 (t0) cc_final: 0.5433 (t70) REVERT: S 93 MET cc_start: 0.8087 (ttp) cc_final: 0.7861 (ttp) REVERT: S 223 ASP cc_start: 0.7572 (m-30) cc_final: 0.7028 (t0) REVERT: S 234 GLU cc_start: 0.8805 (pt0) cc_final: 0.8527 (pt0) REVERT: S 245 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7425 (mp) outliers start: 24 outliers final: 15 residues processed: 140 average time/residue: 0.4963 time to fit residues: 74.9229 Evaluate side-chains 136 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 215 SER Chi-restraints excluded: chain R residue 216 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 110 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 184 ASN S 39 GLN S 186 GLN S 194 ASN ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.133851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.110919 restraints weight = 16014.780| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.90 r_work: 0.3611 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8586 Z= 0.141 Angle : 0.578 7.563 11722 Z= 0.303 Chirality : 0.043 0.142 1356 Planarity : 0.004 0.067 1503 Dihedral : 4.041 19.510 1238 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.39 % Allowed : 23.12 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.25), residues: 1135 helix: 2.00 (0.27), residues: 382 sheet: -0.61 (0.32), residues: 270 loop : -1.03 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 18 TYR 0.020 0.001 TYR B 59 PHE 0.013 0.001 PHE R 99 TRP 0.030 0.002 TRP R 42 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 8584) covalent geometry : angle 0.57776 (11718) SS BOND : bond 0.00184 ( 2) SS BOND : angle 0.84604 ( 4) hydrogen bonds : bond 0.03573 ( 421) hydrogen bonds : angle 4.47382 ( 1203) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3666.01 seconds wall clock time: 63 minutes 8.12 seconds (3788.12 seconds total)