Starting phenix.real_space_refine on Wed Mar 12 23:24:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jvg_61838/03_2025/9jvg_61838.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jvg_61838/03_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_61838/03_2025/9jvg_61838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jvg_61838/03_2025/9jvg_61838.map" model { file = "/net/cci-nas-00/data/ceres_data/9jvg_61838/03_2025/9jvg_61838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jvg_61838/03_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-5624/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: 6.89, per 1000 atoms: 0.82 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: 2.98 Conformation dependent library (CDL) restraints added in 1.5 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: 1.07 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: 2.53 Time building geometry restraints manager: 3.41 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: 1.600 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 26.080 Find NCS groups from input model: 0.100 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:13.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.820 ------------------------------------------------------------------------------- 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 8584 Z= 0.517 Angle : 0.794 10.537 11718 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 *********************** 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 : 0.890 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: 1.0041 time to fit residues: 226.8218 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 : 0.871 ------------------------------------------------------------------------------- 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 = 0.113456 restraints weight = 15945.934| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.89 r_work: 0.3640 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- 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 8584 Z= 0.223 Angle : 0.607 10.275 11718 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 *********************** 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 : 0.944 Fit side-chains revert: symmetry clash REVERT: A 347 ARG cc_start: 0.8633 (mtm-85) cc_final: 0.8432 (mtm-85) REVERT: R 116 ASP cc_start: 0.8653 (t0) cc_final: 0.8381 (t0) REVERT: R 125 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8388 (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: 0.6936 (mtt180) REVERT: R 215 SER cc_start: 0.8644 (OUTLIER) cc_final: 0.8372 (t) REVERT: B 264 TYR cc_start: 0.6584 (m-80) cc_final: 0.5870 (m-80) REVERT: G 38 MET cc_start: 0.6626 (tmm) cc_final: 0.6259 (tpt) REVERT: S 93 MET cc_start: 0.8286 (ttp) cc_final: 0.7964 (ttp) REVERT: S 223 ASP cc_start: 0.7513 (m-30) cc_final: 0.6856 (t0) REVERT: S 245 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7843 (mm) outliers start: 33 outliers final: 10 residues processed: 156 average time/residue: 1.0006 time to fit residues: 168.2800 Evaluate side-chains 125 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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: 0.9990 chunk 13 optimal weight: 0.0770 chunk 91 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 90 optimal weight: 0.6980 chunk 100 optimal weight: 0.0270 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 = 0.4092 r_free = 0.4092 target = 0.136804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.114030 restraints weight = 15977.778| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.89 r_work: 0.3651 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8584 Z= 0.183 Angle : 0.567 11.421 11718 Z= 0.297 Chirality : 0.042 0.136 1356 Planarity : 0.004 0.047 1503 Dihedral : 4.202 18.816 1238 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.39 % Allowed : 15.08 % Favored : 81.53 % 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: 0.08 (0.25), residues: 1135 helix: 1.87 (0.27), residues: 368 sheet: -0.39 (0.30), residues: 271 loop : -1.07 (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 0.014 0.001 PHE R 276 TYR 0.026 0.001 TYR A 391 ARG 0.005 0.000 ARG S 18 *********************** 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 160 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 1.059 Fit side-chains REVERT: A 347 ARG cc_start: 0.8577 (mtm-85) cc_final: 0.8371 (mtm-85) REVERT: A 392 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8655 (mp0) REVERT: R 59 MET cc_start: 0.8419 (mmm) cc_final: 0.8170 (mmm) REVERT: R 63 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7491 (mp) REVERT: R 132 ARG cc_start: 0.7313 (mtp-110) cc_final: 0.6972 (mtt180) REVERT: R 183 MET cc_start: 0.8099 (tpp) cc_final: 0.7778 (tpp) REVERT: R 215 SER cc_start: 0.8599 (OUTLIER) cc_final: 0.8361 (t) REVERT: R 280 ASN cc_start: 0.7776 (t0) cc_final: 0.7371 (t0) REVERT: B 217 MET cc_start: 0.8505 (pmm) cc_final: 0.8217 (pmt) REVERT: B 221 THR cc_start: 0.8002 (t) cc_final: 0.7682 (m) REVERT: B 264 TYR cc_start: 0.6433 (m-80) cc_final: 0.6060 (m-80) REVERT: S 93 MET cc_start: 0.8244 (ttp) cc_final: 0.7996 (ttp) REVERT: S 223 ASP cc_start: 0.7485 (m-30) cc_final: 0.6876 (t0) REVERT: S 234 GLU cc_start: 0.8725 (pt0) cc_final: 0.8343 (pt0) outliers start: 27 outliers final: 12 residues processed: 150 average time/residue: 0.9448 time to fit residues: 154.0196 Evaluate side-chains 124 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 R residue 216 THR Chi-restraints excluded: chain B residue 18 ILE 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 21 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 86 LEU 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: 2.9990 chunk 100 optimal weight: 0.0020 chunk 111 optimal weight: 1.9990 chunk 15 optimal weight: 0.0570 chunk 56 optimal weight: 1.9990 chunk 89 optimal weight: 0.0470 chunk 68 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 90 optimal weight: 0.4980 chunk 59 optimal weight: 0.9980 overall best weight: 0.3204 ------------------------------------------------------------------------------- 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 = 0.4110 r_free = 0.4110 target = 0.138232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.115492 restraints weight = 15842.779| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.91 r_work: 0.3672 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8584 Z= 0.160 Angle : 0.548 10.636 11718 Z= 0.282 Chirality : 0.042 0.269 1356 Planarity : 0.004 0.052 1503 Dihedral : 3.962 17.892 1238 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.64 % Allowed : 17.09 % Favored : 79.27 % 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: 0.15 (0.25), residues: 1135 helix: 2.01 (0.27), residues: 377 sheet: -0.52 (0.31), residues: 272 loop : -1.05 (0.28), residues: 486 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 0.018 0.001 TYR A 391 ARG 0.005 0.000 ARG S 18 *********************** 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 160 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.848 Fit side-chains REVERT: R 59 MET cc_start: 0.8560 (mmm) cc_final: 0.8268 (mmm) REVERT: R 63 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7485 (mp) REVERT: R 132 ARG cc_start: 0.7364 (mtp-110) cc_final: 0.6975 (mtt180) REVERT: R 215 SER cc_start: 0.8528 (OUTLIER) cc_final: 0.8297 (t) REVERT: R 280 ASN cc_start: 0.7690 (t0) cc_final: 0.7408 (t0) REVERT: B 217 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8218 (pmt) REVERT: B 221 THR cc_start: 0.7963 (t) cc_final: 0.7646 (m) REVERT: B 264 TYR cc_start: 0.6635 (m-80) cc_final: 0.6134 (m-80) REVERT: G 28 ILE cc_start: 0.7170 (OUTLIER) cc_final: 0.6588 (tp) REVERT: S 158 SER cc_start: 0.8464 (p) cc_final: 0.8252 (t) REVERT: S 223 ASP cc_start: 0.7480 (m-30) cc_final: 0.6928 (t0) outliers start: 29 outliers final: 8 residues processed: 147 average time/residue: 0.9175 time to fit residues: 146.1151 Evaluate side-chains 125 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 217 MET 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 117 LEU Chi-restraints excluded: chain S residue 135 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 6 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 0.2980 chunk 106 optimal weight: 0.7980 chunk 32 optimal weight: 0.0970 chunk 46 optimal weight: 0.9990 chunk 95 optimal weight: 0.0570 chunk 20 optimal weight: 1.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- 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 220 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.137580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.114815 restraints weight = 15927.391| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.92 r_work: 0.3665 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8584 Z= 0.165 Angle : 0.536 10.133 11718 Z= 0.279 Chirality : 0.042 0.289 1356 Planarity : 0.004 0.053 1503 Dihedral : 3.871 18.007 1238 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.27 % Allowed : 19.60 % Favored : 77.14 % 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: 0.28 (0.25), residues: 1135 helix: 2.10 (0.27), residues: 378 sheet: -0.48 (0.31), residues: 266 loop : -0.94 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 42 HIS 0.004 0.001 HIS S 35 PHE 0.010 0.001 PHE R 99 TYR 0.016 0.001 TYR A 391 ARG 0.005 0.000 ARG S 18 *********************** 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 146 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.835 Fit side-chains REVERT: R 59 MET cc_start: 0.8632 (mmm) cc_final: 0.8303 (mmm) REVERT: R 63 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7491 (mp) REVERT: R 132 ARG cc_start: 0.7352 (mtp-110) cc_final: 0.6984 (mtt180) REVERT: R 215 SER cc_start: 0.8529 (OUTLIER) cc_final: 0.8305 (t) REVERT: B 96 ARG cc_start: 0.8426 (mtt180) cc_final: 0.8200 (mtt180) REVERT: B 217 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8204 (pmt) REVERT: B 221 THR cc_start: 0.7989 (t) cc_final: 0.7664 (m) REVERT: B 264 TYR cc_start: 0.6716 (m-80) cc_final: 0.6141 (m-80) REVERT: G 28 ILE cc_start: 0.7156 (OUTLIER) cc_final: 0.6625 (tp) REVERT: S 38 ARG cc_start: 0.7607 (ptp90) cc_final: 0.7300 (ptp-170) REVERT: S 93 MET cc_start: 0.8127 (ttp) cc_final: 0.7815 (ttp) REVERT: S 223 ASP cc_start: 0.7471 (m-30) cc_final: 0.6847 (t0) outliers start: 26 outliers final: 10 residues processed: 137 average time/residue: 0.9701 time to fit residues: 143.1464 Evaluate side-chains 126 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 215 SER Chi-restraints excluded: chain R residue 216 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 217 MET 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 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: 1.9990 chunk 107 optimal weight: 0.0970 chunk 13 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 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 = 0.4074 r_free = 0.4074 target = 0.135767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.112920 restraints weight = 15860.919| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.88 r_work: 0.3632 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8584 Z= 0.205 Angle : 0.556 10.035 11718 Z= 0.290 Chirality : 0.043 0.327 1356 Planarity : 0.004 0.054 1503 Dihedral : 3.915 17.875 1238 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % 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 (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: 0.29 (0.25), residues: 1135 helix: 2.11 (0.27), residues: 377 sheet: -0.47 (0.31), residues: 272 loop : -0.93 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 42 HIS 0.004 0.001 HIS S 35 PHE 0.012 0.001 PHE S 80 TYR 0.016 0.002 TYR A 391 ARG 0.006 0.000 ARG S 18 *********************** 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 154 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 0.989 Fit side-chains REVERT: R 59 MET cc_start: 0.8667 (mmm) cc_final: 0.8337 (mmm) REVERT: R 63 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.7617 (mp) REVERT: R 132 ARG cc_start: 0.7399 (mtp-110) cc_final: 0.7069 (mtt180) REVERT: R 215 SER cc_start: 0.8565 (OUTLIER) cc_final: 0.8345 (t) REVERT: R 280 ASN cc_start: 0.7883 (t0) cc_final: 0.7611 (t0) REVERT: B 96 ARG cc_start: 0.8522 (mtt180) cc_final: 0.8278 (mtt180) REVERT: B 217 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8262 (pmt) REVERT: B 264 TYR cc_start: 0.6698 (m-80) cc_final: 0.6127 (m-80) REVERT: G 28 ILE cc_start: 0.7117 (OUTLIER) cc_final: 0.6612 (tp) REVERT: S 18 ARG cc_start: 0.6656 (ttt90) cc_final: 0.6423 (ttt90) REVERT: S 38 ARG cc_start: 0.7685 (ptp90) cc_final: 0.7410 (ptp-170) REVERT: S 93 MET cc_start: 0.8063 (ttp) cc_final: 0.7702 (ttp) REVERT: S 113 GLN cc_start: 0.7711 (mm110) cc_final: 0.7503 (mm-40) REVERT: S 223 ASP cc_start: 0.7490 (m-30) cc_final: 0.6825 (t0) outliers start: 35 outliers final: 16 residues processed: 143 average time/residue: 1.0052 time to fit residues: 155.0065 Evaluate side-chains 129 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 76 ASP 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 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 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: 2.9990 chunk 51 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 65 optimal weight: 0.0980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.135038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.112156 restraints weight = 16030.452| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.93 r_work: 0.3621 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8584 Z= 0.216 Angle : 0.573 10.138 11718 Z= 0.297 Chirality : 0.043 0.351 1356 Planarity : 0.004 0.057 1503 Dihedral : 3.985 17.708 1238 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.77 % Allowed : 20.73 % 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 (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: 0.28 (0.25), residues: 1135 helix: 2.05 (0.27), residues: 378 sheet: -0.50 (0.32), residues: 262 loop : -0.88 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 42 HIS 0.004 0.001 HIS S 35 PHE 0.014 0.001 PHE S 80 TYR 0.016 0.001 TYR A 391 ARG 0.006 0.000 ARG S 18 *********************** 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 145 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.939 Fit side-chains REVERT: R 59 MET cc_start: 0.8662 (mmm) cc_final: 0.8330 (mmm) REVERT: R 63 ILE cc_start: 0.8019 (OUTLIER) cc_final: 0.7583 (mp) REVERT: R 215 SER cc_start: 0.8621 (OUTLIER) cc_final: 0.8398 (t) REVERT: B 96 ARG cc_start: 0.8467 (mtt180) cc_final: 0.7917 (mmp80) REVERT: B 217 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8259 (pmt) REVERT: B 264 TYR cc_start: 0.6787 (m-80) cc_final: 0.6151 (m-80) REVERT: G 28 ILE cc_start: 0.7082 (OUTLIER) cc_final: 0.6600 (tp) REVERT: S 93 MET cc_start: 0.8211 (ttp) cc_final: 0.7857 (ttp) REVERT: S 113 GLN cc_start: 0.7767 (mm110) cc_final: 0.7523 (mm-40) REVERT: S 223 ASP cc_start: 0.7545 (m-30) cc_final: 0.6887 (t0) outliers start: 30 outliers final: 19 residues processed: 136 average time/residue: 0.9352 time to fit residues: 137.9617 Evaluate side-chains 132 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 61 MET Chi-restraints excluded: chain B residue 76 ASP 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 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 46 GLU 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: 5.9990 chunk 80 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.130811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.107477 restraints weight = 16228.611| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.91 r_work: 0.3550 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8584 Z= 0.344 Angle : 0.643 11.742 11718 Z= 0.338 Chirality : 0.046 0.385 1356 Planarity : 0.004 0.062 1503 Dihedral : 4.412 18.699 1238 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.15 % Allowed : 20.60 % 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: 0.07 (0.25), residues: 1135 helix: 1.87 (0.27), residues: 379 sheet: -0.57 (0.32), residues: 266 loop : -1.03 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 42 HIS 0.005 0.001 HIS S 35 PHE 0.019 0.002 PHE S 80 TYR 0.025 0.002 TYR A 391 ARG 0.008 0.000 ARG S 18 *********************** 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 147 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 0.888 Fit side-chains REVERT: R 50 GLN cc_start: 0.8934 (mm-40) cc_final: 0.8583 (mm-40) REVERT: R 59 MET cc_start: 0.8615 (mmm) cc_final: 0.8326 (mmm) REVERT: R 63 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7693 (mp) REVERT: R 215 SER cc_start: 0.8659 (OUTLIER) cc_final: 0.8416 (t) REVERT: B 96 ARG cc_start: 0.8483 (mtt180) cc_final: 0.7950 (mmp80) REVERT: B 217 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8409 (pmt) REVERT: B 264 TYR cc_start: 0.6784 (m-80) cc_final: 0.6070 (m-80) REVERT: B 298 ASP cc_start: 0.7568 (t70) cc_final: 0.7232 (t70) REVERT: G 28 ILE cc_start: 0.7511 (OUTLIER) cc_final: 0.6994 (tp) REVERT: G 42 GLU cc_start: 0.6126 (mt-10) cc_final: 0.5834 (mp0) REVERT: S 113 GLN cc_start: 0.7746 (mm110) cc_final: 0.7528 (mm110) REVERT: S 223 ASP cc_start: 0.7603 (m-30) cc_final: 0.6861 (t0) outliers start: 33 outliers final: 21 residues processed: 137 average time/residue: 0.9324 time to fit residues: 138.4442 Evaluate side-chains 131 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 61 MET Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 177 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 21 SER 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 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: 0.9980 chunk 39 optimal weight: 0.0970 chunk 104 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 29 optimal weight: 0.3980 chunk 68 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 48 optimal weight: 0.4980 chunk 45 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4073 r_free = 0.4073 target = 0.135512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.112542 restraints weight = 16050.715| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.92 r_work: 0.3633 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8584 Z= 0.181 Angle : 0.590 15.142 11718 Z= 0.302 Chirality : 0.044 0.440 1356 Planarity : 0.004 0.062 1503 Dihedral : 4.089 18.590 1238 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.39 % Allowed : 23.37 % Favored : 74.25 % 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: 0.26 (0.25), residues: 1135 helix: 2.13 (0.27), residues: 377 sheet: -0.55 (0.32), residues: 268 loop : -0.94 (0.27), residues: 490 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 0.012 0.001 PHE S 80 TYR 0.016 0.001 TYR R 270 ARG 0.007 0.000 ARG S 18 *********************** 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 146 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.869 Fit side-chains REVERT: R 50 GLN cc_start: 0.8897 (mm-40) cc_final: 0.8514 (mm-40) REVERT: R 63 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7675 (mt) REVERT: R 215 SER cc_start: 0.8623 (OUTLIER) cc_final: 0.8405 (t) REVERT: B 96 ARG cc_start: 0.8451 (mtt180) cc_final: 0.7926 (mmp80) REVERT: B 217 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8277 (pmt) REVERT: B 264 TYR cc_start: 0.6902 (m-80) cc_final: 0.6272 (m-80) REVERT: B 298 ASP cc_start: 0.7440 (t70) cc_final: 0.7118 (t70) REVERT: G 28 ILE cc_start: 0.7262 (OUTLIER) cc_final: 0.6744 (tp) REVERT: S 38 ARG cc_start: 0.7691 (ptp-170) cc_final: 0.7416 (ptp-170) REVERT: S 113 GLN cc_start: 0.7783 (mm110) cc_final: 0.7546 (mm-40) REVERT: S 223 ASP cc_start: 0.7577 (m-30) cc_final: 0.7024 (t0) REVERT: S 230 MET cc_start: 0.7731 (ttp) cc_final: 0.7323 (tmm) outliers start: 19 outliers final: 16 residues processed: 139 average time/residue: 0.9163 time to fit residues: 138.2000 Evaluate side-chains 132 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 371 ASN 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 76 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 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: 2.9990 chunk 23 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 105 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN R 184 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4067 r_free = 0.4067 target = 0.134994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.112050 restraints weight = 15927.878| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.91 r_work: 0.3627 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.289 8584 Z= 0.437 Angle : 1.087 59.098 11718 Z= 0.601 Chirality : 0.045 0.437 1356 Planarity : 0.006 0.153 1503 Dihedral : 4.196 27.064 1238 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.17 % Favored : 96.74 % Rotamer: Outliers : 2.64 % Allowed : 24.25 % Favored : 73.12 % Cbeta Deviations : 0.09 % 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: 0.26 (0.25), residues: 1135 helix: 2.11 (0.27), residues: 377 sheet: -0.55 (0.32), residues: 268 loop : -0.92 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 42 HIS 0.004 0.001 HIS R 271 PHE 0.010 0.001 PHE B 151 TYR 0.029 0.002 TYR R 270 ARG 0.032 0.001 ARG R 249 ********************** 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 135 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 1.061 Fit side-chains REVERT: R 50 GLN cc_start: 0.8895 (mm-40) cc_final: 0.8552 (mm-40) REVERT: R 63 ILE cc_start: 0.7902 (OUTLIER) cc_final: 0.7685 (mt) REVERT: R 215 SER cc_start: 0.8627 (OUTLIER) cc_final: 0.8408 (t) REVERT: B 96 ARG cc_start: 0.8441 (mtt180) cc_final: 0.7928 (mmp80) REVERT: B 217 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8263 (pmt) REVERT: B 264 TYR cc_start: 0.6904 (m-80) cc_final: 0.6247 (m-80) REVERT: B 298 ASP cc_start: 0.7447 (t70) cc_final: 0.7117 (t70) REVERT: G 28 ILE cc_start: 0.7262 (OUTLIER) cc_final: 0.6747 (tp) REVERT: S 38 ARG cc_start: 0.7696 (ptp-170) cc_final: 0.7450 (ptp-170) REVERT: S 113 GLN cc_start: 0.7789 (mm110) cc_final: 0.7559 (mm-40) REVERT: S 223 ASP cc_start: 0.7576 (m-30) cc_final: 0.7035 (t0) REVERT: S 230 MET cc_start: 0.7740 (ttp) cc_final: 0.7314 (tmm) outliers start: 21 outliers final: 16 residues processed: 126 average time/residue: 0.9774 time to fit residues: 133.2385 Evaluate side-chains 131 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 61 MET 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 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: 2.9990 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 37 optimal weight: 0.0270 chunk 74 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 65 optimal weight: 0.2980 chunk 2 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN R 184 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4066 r_free = 0.4066 target = 0.134999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.111988 restraints weight = 16097.045| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.93 r_work: 0.3619 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8584 Z= 0.208 Angle : 0.609 12.653 11718 Z= 0.312 Chirality : 0.044 0.399 1356 Planarity : 0.005 0.065 1503 Dihedral : 4.095 21.547 1238 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.64 % Allowed : 24.12 % Favored : 73.24 % 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: 0.28 (0.25), residues: 1135 helix: 2.10 (0.27), residues: 377 sheet: -0.53 (0.32), residues: 267 loop : -0.90 (0.28), residues: 491 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 0.018 0.001 PHE S 80 TYR 0.020 0.002 TYR R 270 ARG 0.007 0.000 ARG S 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7130.54 seconds wall clock time: 123 minutes 1.51 seconds (7381.51 seconds total)