Starting phenix.real_space_refine on Sun May 11 20:26:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jvg_61838/05_2025/9jvg_61838.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jvg_61838/05_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_61838/05_2025/9jvg_61838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jvg_61838/05_2025/9jvg_61838.map" model { file = "/net/cci-nas-00/data/ceres_data/9jvg_61838/05_2025/9jvg_61838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jvg_61838/05_2025/9jvg_61838.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'TYR:plan': 1, 'GLU:plan': 9, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 6} 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, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 2, 'HIS:plan': 4, 'PHE:plan': 7, 'GLU:plan': 7, 'ARG:plan': 10} 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: {'GLN:plan1': 5, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 8} 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, 'GLU:plan': 4, 'ARG:plan': 2, '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: 5.25, per 1000 atoms: 0.63 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: 2.14 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.02 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: 2.61 Time building geometry restraints manager: 2.38 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: 1.420 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: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.310 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.430 ------------------------------------------------------------------------------- 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 : 10.65 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (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 TRP 0.014 0.002 TRP B 169 HIS 0.010 0.002 HIS B 142 PHE 0.028 0.002 PHE B 151 TYR 0.041 0.002 TYR B 59 ARG 0.006 0.001 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.17619 ( 421) hydrogen bonds : angle 7.36011 ( 1203) SS BOND : bond 0.00407 ( 2) SS BOND : angle 0.84203 ( 4) covalent geometry : bond 0.00773 ( 8584) covalent geometry : angle 0.79387 (11718) *********************** 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 : 0.931 Fit side-chains revert: symmetry clash REVERT: A 34 LYS cc_start: 0.8163 (ttmt) cc_final: 0.7963 (ttmm) REVERT: B 264 TYR cc_start: 0.6263 (m-80) cc_final: 0.5948 (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: 0.9717 time to fit residues: 219.3393 Evaluate side-chains 122 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 94 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 0.0770 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 = 0.4078 r_free = 0.4078 target = 0.135960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.113457 restraints weight = 15945.936| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.89 r_work: 0.3639 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2092 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= 0.147 Angle : 0.607 10.275 11722 Z= 0.325 Chirality : 0.043 0.138 1356 Planarity : 0.005 0.057 1503 Dihedral : 4.740 44.949 1240 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.15 % Allowed : 12.81 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.25), residues: 1135 helix: 1.64 (0.28), residues: 372 sheet: -0.34 (0.31), residues: 272 loop : -1.16 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 75 HIS 0.003 0.001 HIS S 35 PHE 0.018 0.002 PHE R 276 TYR 0.036 0.002 TYR A 391 ARG 0.006 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04612 ( 421) hydrogen bonds : angle 5.11678 ( 1203) SS BOND : bond 0.00141 ( 2) SS BOND : angle 0.92447 ( 4) covalent geometry : bond 0.00328 ( 8584) covalent geometry : angle 0.60726 (11718) *********************** 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: 33 poor density : 138 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: R 116 ASP cc_start: 0.8653 (t0) cc_final: 0.8382 (t0) REVERT: R 125 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8389 (mp) REVERT: R 131 ARG cc_start: 0.8379 (mtm110) cc_final: 0.7844 (mtm110) REVERT: R 132 ARG cc_start: 0.7283 (mtp-110) cc_final: 0.6935 (mtt180) REVERT: R 215 SER cc_start: 0.8645 (OUTLIER) cc_final: 0.8373 (t) REVERT: B 264 TYR cc_start: 0.6585 (m-80) cc_final: 0.5873 (m-80) REVERT: G 38 MET cc_start: 0.6631 (tmm) cc_final: 0.6264 (tpt) REVERT: S 93 MET cc_start: 0.8284 (ttp) cc_final: 0.7964 (ttp) REVERT: S 223 ASP cc_start: 0.7511 (m-30) cc_final: 0.6855 (t0) REVERT: S 245 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7841 (mm) outliers start: 33 outliers final: 10 residues processed: 156 average time/residue: 0.9898 time to fit residues: 166.5426 Evaluate side-chains 124 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 215 SER 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 245 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 25 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 13 optimal weight: 0.2980 chunk 91 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 104 optimal weight: 0.0970 chunk 90 optimal weight: 0.0470 chunk 100 optimal weight: 0.2980 overall best weight: 0.2876 ------------------------------------------------------------------------------- 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 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN 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 S 231 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.138439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.115844 restraints weight = 15966.702| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.91 r_work: 0.3682 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8586 Z= 0.110 Angle : 0.560 11.687 11722 Z= 0.292 Chirality : 0.042 0.136 1356 Planarity : 0.004 0.045 1503 Dihedral : 4.124 18.503 1238 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.39 % Allowed : 15.20 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.25), residues: 1135 helix: 1.91 (0.27), residues: 368 sheet: -0.38 (0.30), residues: 271 loop : -1.05 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 75 HIS 0.004 0.001 HIS S 35 PHE 0.013 0.001 PHE R 99 TYR 0.024 0.001 TYR A 391 ARG 0.005 0.000 ARG S 18 Details of bonding type rmsd hydrogen bonds : bond 0.03758 ( 421) hydrogen bonds : angle 4.64746 ( 1203) SS BOND : bond 0.00302 ( 2) SS BOND : angle 0.83232 ( 4) covalent geometry : bond 0.00242 ( 8584) covalent geometry : angle 0.55981 (11718) *********************** 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 166 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 1.048 Fit side-chains REVERT: R 59 MET cc_start: 0.8369 (mmm) cc_final: 0.8122 (mmm) REVERT: R 63 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7473 (mp) REVERT: R 132 ARG cc_start: 0.7271 (mtp-110) cc_final: 0.6956 (mtt180) REVERT: R 183 MET cc_start: 0.8075 (tpp) cc_final: 0.7825 (tpp) REVERT: R 215 SER cc_start: 0.8550 (OUTLIER) cc_final: 0.8305 (t) REVERT: B 217 MET cc_start: 0.8482 (pmm) cc_final: 0.8168 (pmt) REVERT: B 221 THR cc_start: 0.7945 (t) cc_final: 0.7624 (m) REVERT: B 264 TYR cc_start: 0.6417 (m-80) cc_final: 0.6061 (m-80) REVERT: S 93 MET cc_start: 0.8184 (ttp) cc_final: 0.7846 (ttp) REVERT: S 223 ASP cc_start: 0.7485 (m-30) cc_final: 0.6902 (t0) outliers start: 27 outliers final: 9 residues processed: 156 average time/residue: 0.9165 time to fit residues: 154.8497 Evaluate side-chains 122 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 63 ILE Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 215 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 135 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 45 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 89 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 90 optimal weight: 0.0980 chunk 59 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 279 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.135958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.113144 restraints weight = 15910.880| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.90 r_work: 0.3641 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2965 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= 0.130 Angle : 0.568 11.632 11722 Z= 0.293 Chirality : 0.043 0.300 1356 Planarity : 0.004 0.051 1503 Dihedral : 4.074 18.164 1238 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.64 % Allowed : 17.21 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.25), residues: 1135 helix: 1.92 (0.27), residues: 378 sheet: -0.49 (0.31), residues: 272 loop : -1.06 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 42 HIS 0.005 0.001 HIS S 35 PHE 0.012 0.001 PHE R 99 TYR 0.017 0.001 TYR R 270 ARG 0.005 0.000 ARG S 18 Details of bonding type rmsd hydrogen bonds : bond 0.03703 ( 421) hydrogen bonds : angle 4.50892 ( 1203) SS BOND : bond 0.00143 ( 2) SS BOND : angle 0.93621 ( 4) covalent geometry : bond 0.00299 ( 8584) covalent geometry : angle 0.56823 (11718) *********************** 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 156 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.978 Fit side-chains REVERT: R 59 MET cc_start: 0.8533 (mmm) cc_final: 0.8243 (mmm) REVERT: R 63 ILE cc_start: 0.7993 (OUTLIER) cc_final: 0.7504 (mp) REVERT: R 132 ARG cc_start: 0.7374 (mtp-110) cc_final: 0.7000 (mtt180) REVERT: R 215 SER cc_start: 0.8605 (OUTLIER) cc_final: 0.8371 (t) REVERT: R 280 ASN cc_start: 0.7654 (t0) cc_final: 0.7317 (t0) REVERT: B 217 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8261 (pmt) REVERT: B 264 TYR cc_start: 0.6544 (m-80) cc_final: 0.6088 (m-80) REVERT: B 269 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8412 (tt) REVERT: G 28 ILE cc_start: 0.7254 (OUTLIER) cc_final: 0.6673 (tp) REVERT: G 38 MET cc_start: 0.6615 (tmm) cc_final: 0.6246 (tpt) REVERT: S 158 SER cc_start: 0.8484 (p) cc_final: 0.8275 (t) REVERT: S 223 ASP cc_start: 0.7495 (m-30) cc_final: 0.6811 (t0) outliers start: 29 outliers final: 12 residues processed: 143 average time/residue: 0.8941 time to fit residues: 139.1215 Evaluate side-chains 133 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 R residue 236 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 269 ILE 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 21 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 117 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 6 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 30 optimal weight: 0.0670 chunk 106 optimal weight: 0.6980 chunk 32 optimal weight: 0.3980 chunk 46 optimal weight: 0.7980 chunk 95 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.136442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.113552 restraints weight = 15912.646| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.92 r_work: 0.3649 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8586 Z= 0.115 Angle : 0.546 11.155 11722 Z= 0.282 Chirality : 0.042 0.318 1356 Planarity : 0.004 0.053 1503 Dihedral : 3.958 17.966 1238 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.15 % Allowed : 18.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.25), residues: 1135 helix: 2.00 (0.27), residues: 378 sheet: -0.50 (0.31), residues: 272 loop : -1.01 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 42 HIS 0.004 0.001 HIS S 35 PHE 0.011 0.001 PHE R 99 TYR 0.014 0.001 TYR B 59 ARG 0.005 0.000 ARG S 18 Details of bonding type rmsd hydrogen bonds : bond 0.03497 ( 421) hydrogen bonds : angle 4.40825 ( 1203) SS BOND : bond 0.00369 ( 2) SS BOND : angle 0.88042 ( 4) covalent geometry : bond 0.00264 ( 8584) covalent geometry : angle 0.54587 (11718) *********************** 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 161 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.905 Fit side-chains revert: symmetry clash REVERT: R 59 MET cc_start: 0.8597 (mmm) cc_final: 0.8286 (mmm) REVERT: R 63 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7497 (mp) REVERT: R 132 ARG cc_start: 0.7375 (mtp-110) cc_final: 0.7011 (mtt180) REVERT: R 215 SER cc_start: 0.8555 (OUTLIER) cc_final: 0.8325 (t) REVERT: R 280 ASN cc_start: 0.7745 (t0) cc_final: 0.7495 (t0) REVERT: B 96 ARG cc_start: 0.8471 (mtt180) cc_final: 0.8241 (mtt180) REVERT: B 217 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8244 (pmt) REVERT: B 221 THR cc_start: 0.8010 (t) cc_final: 0.7690 (m) REVERT: B 264 TYR cc_start: 0.6701 (m-80) cc_final: 0.6130 (m-80) REVERT: B 269 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8386 (tt) REVERT: G 28 ILE cc_start: 0.7215 (OUTLIER) cc_final: 0.6704 (tp) REVERT: S 38 ARG cc_start: 0.7638 (ptp90) cc_final: 0.7288 (ptp-170) REVERT: S 93 MET cc_start: 0.8142 (ttp) cc_final: 0.7823 (ttp) REVERT: S 223 ASP cc_start: 0.7488 (m-30) cc_final: 0.6840 (t0) outliers start: 33 outliers final: 9 residues processed: 147 average time/residue: 0.9290 time to fit residues: 147.7022 Evaluate side-chains 133 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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 R residue 216 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 28 ILE 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 210 THR Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 1 optimal weight: 0.2980 chunk 24 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 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 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN ** 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 = 0.4059 r_free = 0.4059 target = 0.134480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.111449 restraints weight = 15817.720| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.90 r_work: 0.3615 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3299 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= 0.140 Angle : 0.574 10.950 11722 Z= 0.296 Chirality : 0.044 0.361 1356 Planarity : 0.004 0.055 1503 Dihedral : 4.036 18.153 1238 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.15 % Allowed : 20.10 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.25), residues: 1135 helix: 2.02 (0.27), residues: 379 sheet: -0.56 (0.31), residues: 274 loop : -0.94 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 42 HIS 0.004 0.001 HIS S 35 PHE 0.011 0.001 PHE R 99 TYR 0.016 0.002 TYR R 270 ARG 0.007 0.000 ARG S 18 Details of bonding type rmsd hydrogen bonds : bond 0.03662 ( 421) hydrogen bonds : angle 4.41825 ( 1203) SS BOND : bond 0.00180 ( 2) SS BOND : angle 0.96594 ( 4) covalent geometry : bond 0.00326 ( 8584) covalent geometry : angle 0.57431 (11718) *********************** 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 158 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.973 Fit side-chains REVERT: R 59 MET cc_start: 0.8614 (mmm) cc_final: 0.8270 (mmm) REVERT: R 63 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7529 (mp) REVERT: R 132 ARG cc_start: 0.7443 (mtp-110) cc_final: 0.7045 (mtt180) REVERT: R 215 SER cc_start: 0.8621 (OUTLIER) cc_final: 0.8401 (t) REVERT: R 280 ASN cc_start: 0.7832 (t0) cc_final: 0.7615 (t0) REVERT: B 96 ARG cc_start: 0.8514 (mtt180) cc_final: 0.7949 (mmp80) REVERT: B 217 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8315 (pmt) REVERT: B 264 TYR cc_start: 0.6668 (m-80) cc_final: 0.6124 (m-80) REVERT: B 269 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8407 (tt) REVERT: G 28 ILE cc_start: 0.7144 (OUTLIER) cc_final: 0.6619 (tp) REVERT: G 38 MET cc_start: 0.6589 (tmm) cc_final: 0.6330 (tpt) REVERT: S 18 ARG cc_start: 0.6666 (ttt90) cc_final: 0.6285 (ttt90) REVERT: S 93 MET cc_start: 0.8131 (ttp) cc_final: 0.7890 (ttp) REVERT: S 113 GLN cc_start: 0.7711 (mm110) cc_final: 0.7457 (mm-40) REVERT: S 137 ASP cc_start: 0.7425 (p0) cc_final: 0.7170 (p0) REVERT: S 223 ASP cc_start: 0.7560 (m-30) cc_final: 0.6894 (t0) outliers start: 33 outliers final: 18 residues processed: 147 average time/residue: 0.9595 time to fit residues: 152.3655 Evaluate side-chains 133 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 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 217 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 269 ILE 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 21 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 20 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 30 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 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 = 0.4061 r_free = 0.4061 target = 0.134732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.111770 restraints weight = 15953.906| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.91 r_work: 0.3622 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8586 Z= 0.129 Angle : 0.576 12.679 11722 Z= 0.293 Chirality : 0.044 0.406 1356 Planarity : 0.004 0.060 1503 Dihedral : 3.982 18.193 1238 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.89 % Allowed : 20.85 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.25), residues: 1135 helix: 2.04 (0.27), residues: 380 sheet: -0.61 (0.32), residues: 264 loop : -0.91 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 42 HIS 0.003 0.001 HIS R 271 PHE 0.010 0.001 PHE R 99 TYR 0.014 0.001 TYR B 59 ARG 0.006 0.000 ARG S 18 Details of bonding type rmsd hydrogen bonds : bond 0.03563 ( 421) hydrogen bonds : angle 4.40758 ( 1203) SS BOND : bond 0.00273 ( 2) SS BOND : angle 0.70492 ( 4) covalent geometry : bond 0.00300 ( 8584) covalent geometry : angle 0.57577 (11718) *********************** 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 151 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 0.885 Fit side-chains REVERT: R 50 GLN cc_start: 0.8888 (mm-40) cc_final: 0.8533 (mm-40) REVERT: R 63 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7715 (mt) REVERT: R 215 SER cc_start: 0.8616 (OUTLIER) cc_final: 0.8397 (t) REVERT: B 96 ARG cc_start: 0.8502 (mtt180) cc_final: 0.7977 (mmp80) REVERT: B 217 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8307 (pmt) REVERT: B 264 TYR cc_start: 0.6704 (m-80) cc_final: 0.6112 (m-80) REVERT: B 298 ASP cc_start: 0.7260 (t70) cc_final: 0.6932 (t70) REVERT: G 28 ILE cc_start: 0.7117 (OUTLIER) cc_final: 0.6627 (tp) REVERT: G 38 MET cc_start: 0.6697 (tmm) cc_final: 0.6419 (tpt) REVERT: S 18 ARG cc_start: 0.6713 (ttt90) cc_final: 0.6373 (ttt90) REVERT: S 223 ASP cc_start: 0.7555 (m-30) cc_final: 0.7029 (t0) REVERT: S 234 GLU cc_start: 0.8812 (pt0) cc_final: 0.8518 (pt0) outliers start: 31 outliers final: 19 residues processed: 142 average time/residue: 0.8773 time to fit residues: 135.6064 Evaluate side-chains 137 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 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 239 ASN 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 63 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 233 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 60 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 80 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 108 optimal weight: 0.0980 chunk 79 optimal weight: 0.5980 chunk 23 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 184 ASN B 220 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN S 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.135607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.112653 restraints weight = 16048.277| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.91 r_work: 0.3637 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3548 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= 0.120 Angle : 0.581 11.507 11722 Z= 0.296 Chirality : 0.044 0.386 1356 Planarity : 0.004 0.059 1503 Dihedral : 3.949 18.776 1238 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.14 % Allowed : 21.48 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.25), residues: 1135 helix: 2.06 (0.27), residues: 378 sheet: -0.59 (0.32), residues: 264 loop : -0.88 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 42 HIS 0.003 0.001 HIS S 35 PHE 0.010 0.001 PHE B 151 TYR 0.018 0.001 TYR S 95 ARG 0.006 0.000 ARG S 18 Details of bonding type rmsd hydrogen bonds : bond 0.03470 ( 421) hydrogen bonds : angle 4.34736 ( 1203) SS BOND : bond 0.00190 ( 2) SS BOND : angle 0.93330 ( 4) covalent geometry : bond 0.00276 ( 8584) covalent geometry : angle 0.58123 (11718) *********************** 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 145 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.984 Fit side-chains REVERT: R 50 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8524 (mm-40) REVERT: R 63 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7574 (mp) REVERT: R 215 SER cc_start: 0.8601 (OUTLIER) cc_final: 0.8393 (t) REVERT: B 96 ARG cc_start: 0.8487 (mtt180) cc_final: 0.7983 (mmp80) REVERT: B 217 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8288 (pmt) REVERT: B 239 ASN cc_start: 0.7137 (OUTLIER) cc_final: 0.6726 (t0) REVERT: B 264 TYR cc_start: 0.6709 (m-80) cc_final: 0.6143 (m-80) REVERT: B 298 ASP cc_start: 0.7476 (t70) cc_final: 0.7166 (t70) REVERT: G 28 ILE cc_start: 0.7060 (OUTLIER) cc_final: 0.6546 (tp) REVERT: G 38 MET cc_start: 0.6512 (tmm) cc_final: 0.5741 (tpt) REVERT: G 42 GLU cc_start: 0.6323 (pp20) cc_final: 0.6098 (pm20) REVERT: S 18 ARG cc_start: 0.6720 (ttt90) cc_final: 0.6373 (ttt90) REVERT: S 223 ASP cc_start: 0.7564 (m-30) cc_final: 0.7063 (t0) REVERT: S 234 GLU cc_start: 0.8796 (pt0) cc_final: 0.8528 (pt0) outliers start: 25 outliers final: 18 residues processed: 137 average time/residue: 0.9326 time to fit residues: 138.7577 Evaluate side-chains 133 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 279 ASN 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 61 MET Chi-restraints excluded: chain B residue 97 SER 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 239 ASN 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 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 233 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 3.9990 chunk 39 optimal weight: 0.0030 chunk 104 optimal weight: 0.4980 chunk 92 optimal weight: 0.9990 chunk 29 optimal weight: 0.0980 chunk 68 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 48 optimal weight: 0.0370 chunk 45 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.2468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 184 ASN B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 194 ASN ** 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 = 0.4097 r_free = 0.4097 target = 0.137411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.114615 restraints weight = 16022.896| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.92 r_work: 0.3668 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8586 Z= 0.107 Angle : 0.581 11.094 11722 Z= 0.294 Chirality : 0.043 0.374 1356 Planarity : 0.004 0.065 1503 Dihedral : 3.846 18.297 1238 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.51 % Allowed : 22.86 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.25), residues: 1135 helix: 2.16 (0.27), residues: 380 sheet: -0.50 (0.32), residues: 266 loop : -0.84 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 42 HIS 0.003 0.001 HIS S 35 PHE 0.011 0.001 PHE B 151 TYR 0.012 0.001 TYR R 242 ARG 0.005 0.000 ARG S 18 Details of bonding type rmsd hydrogen bonds : bond 0.03259 ( 421) hydrogen bonds : angle 4.28052 ( 1203) SS BOND : bond 0.00192 ( 2) SS BOND : angle 0.84353 ( 4) covalent geometry : bond 0.00240 ( 8584) covalent geometry : angle 0.58052 (11718) *********************** 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 142 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.893 Fit side-chains REVERT: R 50 GLN cc_start: 0.8840 (mm-40) cc_final: 0.8488 (mm-40) REVERT: R 63 ILE cc_start: 0.8003 (OUTLIER) cc_final: 0.7571 (mp) REVERT: R 215 SER cc_start: 0.8536 (OUTLIER) cc_final: 0.8311 (t) REVERT: B 96 ARG cc_start: 0.8459 (mtt180) cc_final: 0.7958 (mmp80) REVERT: B 217 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8302 (pmt) REVERT: B 239 ASN cc_start: 0.6839 (OUTLIER) cc_final: 0.6146 (p0) REVERT: B 264 TYR cc_start: 0.6740 (m-80) cc_final: 0.6169 (m-80) REVERT: B 298 ASP cc_start: 0.7405 (t70) cc_final: 0.7111 (t70) REVERT: G 28 ILE cc_start: 0.7070 (OUTLIER) cc_final: 0.6562 (tp) REVERT: S 18 ARG cc_start: 0.6656 (ttt90) cc_final: 0.6319 (ttt90) REVERT: S 223 ASP cc_start: 0.7565 (m-30) cc_final: 0.7063 (t0) REVERT: S 234 GLU cc_start: 0.8808 (pt0) cc_final: 0.8556 (pt0) outliers start: 20 outliers final: 14 residues processed: 135 average time/residue: 0.9195 time to fit residues: 135.2014 Evaluate side-chains 135 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 61 MET Chi-restraints excluded: chain B residue 76 ASP 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 239 ASN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain S residue 63 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 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 111 optimal weight: 0.5980 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 167 HIS R 184 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4074 r_free = 0.4074 target = 0.135702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.112750 restraints weight = 15933.323| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.91 r_work: 0.3640 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 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 0.037 8586 Z= 0.139 Angle : 0.611 12.771 11722 Z= 0.310 Chirality : 0.044 0.369 1356 Planarity : 0.004 0.066 1503 Dihedral : 3.917 18.020 1238 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.76 % Allowed : 23.37 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.25), residues: 1135 helix: 2.10 (0.27), residues: 376 sheet: -0.52 (0.32), residues: 261 loop : -0.87 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 42 HIS 0.003 0.001 HIS S 35 PHE 0.050 0.001 PHE R 109 TYR 0.022 0.002 TYR B 59 ARG 0.005 0.000 ARG S 18 Details of bonding type rmsd hydrogen bonds : bond 0.03489 ( 421) hydrogen bonds : angle 4.32203 ( 1203) SS BOND : bond 0.00201 ( 2) SS BOND : angle 0.87235 ( 4) covalent geometry : bond 0.00324 ( 8584) covalent geometry : angle 0.61125 (11718) ********************** 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 138 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.908 Fit side-chains REVERT: R 59 MET cc_start: 0.7909 (mmm) cc_final: 0.7311 (mtp) REVERT: R 63 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7635 (mp) REVERT: R 215 SER cc_start: 0.8563 (OUTLIER) cc_final: 0.8340 (t) REVERT: B 96 ARG cc_start: 0.8496 (mtt180) cc_final: 0.7954 (mmp80) REVERT: B 217 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8311 (pmt) REVERT: B 264 TYR cc_start: 0.6803 (m-80) cc_final: 0.6173 (m-80) REVERT: B 298 ASP cc_start: 0.7485 (t70) cc_final: 0.7190 (t70) REVERT: G 28 ILE cc_start: 0.7073 (OUTLIER) cc_final: 0.6579 (tp) REVERT: G 38 MET cc_start: 0.6650 (tmm) cc_final: 0.5727 (tpt) REVERT: G 42 GLU cc_start: 0.6472 (pp20) cc_final: 0.5992 (pm20) REVERT: S 18 ARG cc_start: 0.6724 (ttt90) cc_final: 0.6377 (ttt90) REVERT: S 223 ASP cc_start: 0.7570 (m-30) cc_final: 0.7059 (t0) REVERT: S 234 GLU cc_start: 0.8852 (pt0) cc_final: 0.8630 (pt0) outliers start: 22 outliers final: 16 residues processed: 131 average time/residue: 0.8746 time to fit residues: 124.5799 Evaluate side-chains 134 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 61 MET 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 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 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 0.0060 chunk 110 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 184 ASN R 211 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 194 ASN ** 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 = 0.4075 r_free = 0.4075 target = 0.135714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.112518 restraints weight = 16053.812| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.94 r_work: 0.3625 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3716 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= 0.133 Angle : 0.613 12.873 11722 Z= 0.310 Chirality : 0.044 0.426 1356 Planarity : 0.004 0.067 1503 Dihedral : 3.944 18.319 1238 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.64 % Allowed : 23.62 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.25), residues: 1135 helix: 2.00 (0.27), residues: 382 sheet: -0.55 (0.32), residues: 260 loop : -0.90 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 42 HIS 0.003 0.001 HIS S 35 PHE 0.038 0.001 PHE R 109 TYR 0.021 0.001 TYR B 59 ARG 0.005 0.000 ARG S 18 Details of bonding type rmsd hydrogen bonds : bond 0.03540 ( 421) hydrogen bonds : angle 4.34796 ( 1203) SS BOND : bond 0.00185 ( 2) SS BOND : angle 0.90574 ( 4) covalent geometry : bond 0.00307 ( 8584) covalent geometry : angle 0.61287 (11718) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6962.82 seconds wall clock time: 120 minutes 13.09 seconds (7213.09 seconds total)