Starting phenix.real_space_refine on Wed Sep 17 12:05:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j0b_61052/09_2025/9j0b_61052.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j0b_61052/09_2025/9j0b_61052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j0b_61052/09_2025/9j0b_61052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j0b_61052/09_2025/9j0b_61052.map" model { file = "/net/cci-nas-00/data/ceres_data/9j0b_61052/09_2025/9j0b_61052.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j0b_61052/09_2025/9j0b_61052.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.071 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 57 5.16 5 C 5533 2.51 5 N 1446 2.21 5 O 1561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8599 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1620 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 9, 'GLU:plan': 12, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 89 Chain: "B" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2484 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 5, 'GLN:plan1': 3, 'ARG:plan': 6, 'GLU:plan': 5, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 83 Chain: "G" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 373 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "R" Number of atoms: 2313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2313 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 10, 'TRANS': 284} Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 4, 'ARG:plan': 3, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 67 Chain: "S" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1773 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "R" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'UPG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.30, per 1000 atoms: 0.27 Number of scatterers: 8599 At special positions: 0 Unit cell: (85.696, 120.64, 120.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 P 2 15.00 O 1561 8.00 N 1446 7.00 C 5533 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 94 " - pdb=" SG CYS R 172 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 542.0 milliseconds Enol-peptide restraints added in 1.4 microseconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2142 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 40.0% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.808A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.339A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 3.877A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.522A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.219A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 329 through 351 removed outlier: 4.160A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.532A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.547A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'R' and resid 23 through 48 removed outlier: 3.772A pdb=" N VAL R 27 " --> pdb=" O GLN R 23 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU R 38 " --> pdb=" O ILE R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 54 through 82 removed outlier: 3.506A pdb=" N ILE R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) Proline residue: R 75 - end of helix Processing helix chain 'R' and resid 89 through 96 Processing helix chain 'R' and resid 96 through 125 Processing helix chain 'R' and resid 134 through 154 removed outlier: 4.464A pdb=" N LYS R 139 " --> pdb=" O VAL R 135 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU R 140 " --> pdb=" O SER R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 159 Processing helix chain 'R' and resid 171 through 176 removed outlier: 3.770A pdb=" N LYS R 176 " --> pdb=" O ILE R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 215 Processing helix chain 'R' and resid 222 through 262 Proline residue: R 248 - end of helix removed outlier: 4.998A pdb=" N ILE R 254 " --> pdb=" O HIS R 250 " (cutoff:3.500A) Proline residue: R 255 - end of helix Processing helix chain 'R' and resid 266 through 291 removed outlier: 3.885A pdb=" N VAL R 288 " --> pdb=" O SER R 284 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N CYS R 289 " --> pdb=" O ALA R 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 292 through 294 No H-bonds generated for 'chain 'R' and resid 292 through 294' Processing helix chain 'R' and resid 299 through 308 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.100A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.563A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.683A pdb=" N ASP S 223 " --> pdb=" O GLU S 220 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 220 through 224' Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.269A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 3.505A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.654A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.269A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.801A 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 152 removed outlier: 3.849A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.014A 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: 6.982A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.345A 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: 3.843A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.569A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.126A 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 10 through 12 removed outlier: 5.910A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.513A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1302 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.50 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2710 1.34 - 1.46: 1930 1.46 - 1.58: 4064 1.58 - 1.69: 4 1.69 - 1.81: 82 Bond restraints: 8790 Sorted by residual: bond pdb=" C4 UPG R 401 " pdb=" C5 UPG R 401 " ideal model delta sigma weight residual 1.441 1.389 0.052 2.00e-02 2.50e+03 6.79e+00 bond pdb=" C4 UPG R 401 " pdb=" N3 UPG R 401 " ideal model delta sigma weight residual 1.388 1.337 0.051 2.00e-02 2.50e+03 6.45e+00 bond pdb=" C5 UPG R 401 " pdb=" C6 UPG R 401 " ideal model delta sigma weight residual 1.342 1.388 -0.046 2.00e-02 2.50e+03 5.33e+00 bond pdb=" O3B UPG R 401 " pdb=" PB UPG R 401 " ideal model delta sigma weight residual 1.652 1.611 0.041 2.00e-02 2.50e+03 4.18e+00 bond pdb=" O3A UPG R 401 " pdb=" PB UPG R 401 " ideal model delta sigma weight residual 1.648 1.608 0.040 2.00e-02 2.50e+03 4.06e+00 ... (remaining 8785 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 11724 1.52 - 3.05: 186 3.05 - 4.57: 27 4.57 - 6.10: 11 6.10 - 7.62: 5 Bond angle restraints: 11953 Sorted by residual: angle pdb=" N ILE R 132 " pdb=" CA ILE R 132 " pdb=" C ILE R 132 " ideal model delta sigma weight residual 110.21 103.46 6.75 1.13e+00 7.83e-01 3.57e+01 angle pdb=" N SER R 134 " pdb=" CA SER R 134 " pdb=" C SER R 134 " ideal model delta sigma weight residual 110.50 105.24 5.26 1.41e+00 5.03e-01 1.39e+01 angle pdb=" CA ILE R 132 " pdb=" C ILE R 132 " pdb=" N GLN R 133 " ideal model delta sigma weight residual 115.26 118.87 -3.61 1.11e+00 8.12e-01 1.06e+01 angle pdb=" C ILE R 132 " pdb=" N GLN R 133 " pdb=" CA GLN R 133 " ideal model delta sigma weight residual 122.19 117.90 4.29 1.41e+00 5.03e-01 9.27e+00 angle pdb=" N THR R 129 " pdb=" CA THR R 129 " pdb=" C THR R 129 " ideal model delta sigma weight residual 111.28 114.45 -3.17 1.09e+00 8.42e-01 8.45e+00 ... (remaining 11948 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 4693 16.73 - 33.46: 386 33.46 - 50.19: 83 50.19 - 66.91: 12 66.91 - 83.64: 6 Dihedral angle restraints: 5180 sinusoidal: 1861 harmonic: 3319 Sorted by residual: dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 160.29 19.71 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA HIS R 250 " pdb=" C HIS R 250 " pdb=" N ILE R 251 " pdb=" CA ILE R 251 " ideal model delta harmonic sigma weight residual 180.00 162.90 17.10 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA ARG S 191 " pdb=" C ARG S 191 " pdb=" N MET S 192 " pdb=" CA MET S 192 " ideal model delta harmonic sigma weight residual 180.00 163.49 16.51 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 5177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1061 0.044 - 0.087: 249 0.087 - 0.131: 77 0.131 - 0.175: 2 0.175 - 0.218: 3 Chirality restraints: 1392 Sorted by residual: chirality pdb=" C1' UPG R 401 " pdb=" C2' UPG R 401 " pdb=" O3B UPG R 401 " pdb=" O5' UPG R 401 " both_signs ideal model delta sigma weight residual False -2.23 -2.45 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ILE R 132 " pdb=" N ILE R 132 " pdb=" C ILE R 132 " pdb=" CB ILE R 132 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.65e-01 chirality pdb=" CB ILE A 265 " pdb=" CA ILE A 265 " pdb=" CG1 ILE A 265 " pdb=" CG2 ILE A 265 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.70e-01 ... (remaining 1389 not shown) Planarity restraints: 1490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 132 " 0.012 2.00e-02 2.50e+03 2.45e-02 6.01e+00 pdb=" C ILE R 132 " -0.042 2.00e-02 2.50e+03 pdb=" O ILE R 132 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN R 133 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 191 " -0.011 2.00e-02 2.50e+03 1.25e-02 2.73e+00 pdb=" CG PHE R 191 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE R 191 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE R 191 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE R 191 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 191 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE R 191 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO B 236 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.019 5.00e-02 4.00e+02 ... (remaining 1487 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 292 2.72 - 3.26: 8547 3.26 - 3.81: 15013 3.81 - 4.35: 18611 4.35 - 4.90: 31793 Nonbonded interactions: 74256 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 175 " model vdw 2.171 3.040 nonbonded pdb=" OD1 ASN R 188 " pdb=" OG1 THR R 257 " model vdw 2.184 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.248 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.254 3.040 nonbonded pdb=" OH TYR A 230 " pdb=" O SER A 281 " model vdw 2.266 3.040 ... (remaining 74251 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: 3.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.220 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8792 Z= 0.141 Angle : 0.516 7.619 11957 Z= 0.281 Chirality : 0.041 0.218 1392 Planarity : 0.003 0.034 1490 Dihedral : 13.126 83.644 3032 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.12 % Allowed : 0.58 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.26), residues: 1125 helix: 2.15 (0.26), residues: 410 sheet: 0.34 (0.29), residues: 299 loop : 0.07 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 98 TYR 0.010 0.001 TYR S 190 PHE 0.029 0.001 PHE R 191 TRP 0.021 0.001 TRP B 82 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8790) covalent geometry : angle 0.51625 (11953) SS BOND : bond 0.00295 ( 2) SS BOND : angle 0.87800 ( 4) hydrogen bonds : bond 0.12644 ( 469) hydrogen bonds : angle 5.42834 ( 1302) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 203 time to evaluate : 0.353 Fit side-chains REVERT: R 210 THR cc_start: 0.8345 (m) cc_final: 0.8139 (m) REVERT: S 204 SER cc_start: 0.8184 (p) cc_final: 0.7950 (t) outliers start: 1 outliers final: 0 residues processed: 204 average time/residue: 0.4864 time to fit residues: 106.9581 Evaluate side-chains 137 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN B 125 ASN B 293 ASN S 82 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 = 0.4311 r_free = 0.4311 target = 0.187574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.152181 restraints weight = 10073.387| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 1.96 r_work: 0.3619 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 8792 Z= 0.223 Angle : 0.623 16.020 11957 Z= 0.320 Chirality : 0.045 0.173 1392 Planarity : 0.004 0.031 1490 Dihedral : 6.360 70.378 1273 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.34 % Allowed : 12.69 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.25), residues: 1125 helix: 1.91 (0.26), residues: 404 sheet: 0.09 (0.28), residues: 298 loop : -0.02 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 98 TYR 0.016 0.002 TYR S 190 PHE 0.028 0.002 PHE R 191 TRP 0.013 0.002 TRP B 211 HIS 0.003 0.001 HIS R 250 Details of bonding type rmsd covalent geometry : bond 0.00525 ( 8790) covalent geometry : angle 0.62265 (11953) SS BOND : bond 0.00766 ( 2) SS BOND : angle 1.14478 ( 4) hydrogen bonds : bond 0.04192 ( 469) hydrogen bonds : angle 4.88645 ( 1302) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: R 46 ILE cc_start: 0.8612 (mm) cc_final: 0.8294 (mp) REVERT: S 204 SER cc_start: 0.8255 (p) cc_final: 0.7973 (t) outliers start: 29 outliers final: 13 residues processed: 163 average time/residue: 0.5185 time to fit residues: 90.8090 Evaluate side-chains 141 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 116 SER Chi-restraints excluded: chain R residue 224 SER Chi-restraints excluded: chain R residue 270 LYS Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 138 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 64 optimal weight: 0.0870 chunk 66 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 15 optimal weight: 0.0980 chunk 94 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 overall best weight: 0.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN B 293 ASN S 194 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.189442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.154588 restraints weight = 10025.088| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.95 r_work: 0.3648 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8792 Z= 0.130 Angle : 0.519 11.165 11957 Z= 0.273 Chirality : 0.042 0.197 1392 Planarity : 0.003 0.031 1490 Dihedral : 6.069 66.159 1273 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.11 % Favored : 96.80 % Rotamer: Outliers : 2.65 % Allowed : 16.96 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.25), residues: 1125 helix: 2.04 (0.26), residues: 404 sheet: 0.01 (0.28), residues: 292 loop : -0.01 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 180 TYR 0.016 0.001 TYR S 190 PHE 0.018 0.001 PHE R 195 TRP 0.016 0.001 TRP B 211 HIS 0.002 0.001 HIS R 250 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8790) covalent geometry : angle 0.51864 (11953) SS BOND : bond 0.00455 ( 2) SS BOND : angle 0.83425 ( 4) hydrogen bonds : bond 0.03652 ( 469) hydrogen bonds : angle 4.63847 ( 1302) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 318 GLU cc_start: 0.8315 (tp30) cc_final: 0.8034 (tt0) REVERT: R 46 ILE cc_start: 0.8631 (mm) cc_final: 0.8333 (mp) REVERT: R 79 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8196 (tm) REVERT: R 93 VAL cc_start: 0.7876 (OUTLIER) cc_final: 0.7660 (p) REVERT: R 185 LYS cc_start: 0.7633 (ttpt) cc_final: 0.7297 (ttpt) REVERT: S 204 SER cc_start: 0.8237 (p) cc_final: 0.7953 (t) outliers start: 23 outliers final: 10 residues processed: 154 average time/residue: 0.4962 time to fit residues: 82.2300 Evaluate side-chains 142 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 116 SER Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 138 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 13 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 107 optimal weight: 0.2980 chunk 82 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 0.0050 chunk 45 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN B 125 ASN B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.190536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.155876 restraints weight = 10214.737| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 1.97 r_work: 0.3665 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8792 Z= 0.111 Angle : 0.494 12.927 11957 Z= 0.260 Chirality : 0.041 0.217 1392 Planarity : 0.003 0.030 1490 Dihedral : 5.829 65.310 1273 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.11 % Favored : 96.80 % Rotamer: Outliers : 3.11 % Allowed : 17.30 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.25), residues: 1125 helix: 2.07 (0.26), residues: 410 sheet: -0.02 (0.28), residues: 291 loop : -0.11 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 24 TYR 0.015 0.001 TYR S 190 PHE 0.017 0.001 PHE R 195 TRP 0.015 0.001 TRP B 211 HIS 0.003 0.001 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8790) covalent geometry : angle 0.49435 (11953) SS BOND : bond 0.00350 ( 2) SS BOND : angle 0.76524 ( 4) hydrogen bonds : bond 0.03370 ( 469) hydrogen bonds : angle 4.47678 ( 1302) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 318 GLU cc_start: 0.8265 (tp30) cc_final: 0.7977 (tt0) REVERT: B 134 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7233 (ppt170) REVERT: B 189 SER cc_start: 0.9140 (p) cc_final: 0.8933 (t) REVERT: B 337 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8110 (mttm) REVERT: R 46 ILE cc_start: 0.8643 (mm) cc_final: 0.8356 (mp) REVERT: R 185 LYS cc_start: 0.7657 (ttpt) cc_final: 0.7324 (ttpt) REVERT: R 214 PHE cc_start: 0.7682 (m-10) cc_final: 0.7416 (m-10) REVERT: S 204 SER cc_start: 0.8293 (p) cc_final: 0.8003 (t) outliers start: 27 outliers final: 12 residues processed: 165 average time/residue: 0.4618 time to fit residues: 82.4320 Evaluate side-chains 146 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain R residue 116 SER Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 138 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 54 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN B 293 ASN R 260 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.188025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.152787 restraints weight = 10167.185| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.97 r_work: 0.3618 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8792 Z= 0.147 Angle : 0.525 12.511 11957 Z= 0.275 Chirality : 0.043 0.219 1392 Planarity : 0.003 0.028 1490 Dihedral : 5.802 68.287 1273 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.29 % Favored : 96.62 % Rotamer: Outliers : 3.00 % Allowed : 18.69 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.25), residues: 1125 helix: 1.94 (0.26), residues: 416 sheet: -0.14 (0.29), residues: 289 loop : -0.12 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 24 TYR 0.016 0.001 TYR R 121 PHE 0.016 0.001 PHE R 195 TRP 0.011 0.001 TRP B 211 HIS 0.003 0.001 HIS R 250 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8790) covalent geometry : angle 0.52526 (11953) SS BOND : bond 0.00337 ( 2) SS BOND : angle 0.89983 ( 4) hydrogen bonds : bond 0.03592 ( 469) hydrogen bonds : angle 4.55338 ( 1302) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 318 GLU cc_start: 0.8208 (tp30) cc_final: 0.7917 (tt0) REVERT: B 134 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7274 (ppt170) REVERT: B 337 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8218 (mttm) REVERT: R 214 PHE cc_start: 0.7752 (m-10) cc_final: 0.7465 (m-10) REVERT: S 204 SER cc_start: 0.8385 (p) cc_final: 0.8047 (t) outliers start: 26 outliers final: 15 residues processed: 156 average time/residue: 0.4857 time to fit residues: 81.8297 Evaluate side-chains 142 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain R residue 116 SER Chi-restraints excluded: chain R residue 241 VAL Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 138 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 44 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 101 optimal weight: 0.0570 chunk 81 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.188494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.153657 restraints weight = 10150.341| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.97 r_work: 0.3629 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8792 Z= 0.128 Angle : 0.512 11.144 11957 Z= 0.268 Chirality : 0.042 0.234 1392 Planarity : 0.003 0.037 1490 Dihedral : 5.698 70.915 1273 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.29 % Favored : 96.62 % Rotamer: Outliers : 3.34 % Allowed : 19.61 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.26), residues: 1125 helix: 2.06 (0.26), residues: 410 sheet: -0.18 (0.29), residues: 289 loop : -0.16 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 208 TYR 0.018 0.001 TYR R 121 PHE 0.017 0.001 PHE R 195 TRP 0.013 0.001 TRP B 211 HIS 0.002 0.001 HIS R 250 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8790) covalent geometry : angle 0.51228 (11953) SS BOND : bond 0.00385 ( 2) SS BOND : angle 0.82798 ( 4) hydrogen bonds : bond 0.03480 ( 469) hydrogen bonds : angle 4.50276 ( 1302) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 318 GLU cc_start: 0.8180 (tp30) cc_final: 0.7895 (tt0) REVERT: B 16 ASN cc_start: 0.7490 (m-40) cc_final: 0.7255 (m-40) REVERT: B 134 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7322 (ppt170) REVERT: B 189 SER cc_start: 0.9107 (p) cc_final: 0.8902 (t) REVERT: B 337 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8191 (mttm) REVERT: R 46 ILE cc_start: 0.8642 (mm) cc_final: 0.8349 (mp) REVERT: R 100 LEU cc_start: 0.8598 (tp) cc_final: 0.8224 (tt) REVERT: R 214 PHE cc_start: 0.7763 (m-10) cc_final: 0.7495 (m-10) REVERT: S 204 SER cc_start: 0.8362 (p) cc_final: 0.8025 (t) outliers start: 29 outliers final: 19 residues processed: 156 average time/residue: 0.4672 time to fit residues: 78.8504 Evaluate side-chains 150 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain R residue 116 SER Chi-restraints excluded: chain R residue 241 VAL Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 270 LYS Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 162 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 46 optimal weight: 0.0980 chunk 78 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 5 optimal weight: 0.0980 chunk 26 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.189797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.155197 restraints weight = 10220.927| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 1.97 r_work: 0.3661 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8792 Z= 0.111 Angle : 0.499 9.709 11957 Z= 0.261 Chirality : 0.041 0.245 1392 Planarity : 0.003 0.036 1490 Dihedral : 5.477 73.980 1273 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.56 % Favored : 96.36 % Rotamer: Outliers : 3.34 % Allowed : 19.95 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.26), residues: 1125 helix: 2.16 (0.26), residues: 411 sheet: -0.15 (0.29), residues: 294 loop : -0.10 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 208 TYR 0.017 0.001 TYR R 121 PHE 0.016 0.001 PHE R 195 TRP 0.014 0.001 TRP B 211 HIS 0.002 0.000 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8790) covalent geometry : angle 0.49884 (11953) SS BOND : bond 0.00279 ( 2) SS BOND : angle 0.73643 ( 4) hydrogen bonds : bond 0.03271 ( 469) hydrogen bonds : angle 4.41369 ( 1302) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 209 LYS cc_start: 0.8301 (pttm) cc_final: 0.8081 (tmmt) REVERT: A 271 LYS cc_start: 0.7705 (ptmt) cc_final: 0.7476 (ptmm) REVERT: A 318 GLU cc_start: 0.8059 (tp30) cc_final: 0.7780 (tt0) REVERT: B 16 ASN cc_start: 0.7525 (m-40) cc_final: 0.7309 (m-40) REVERT: B 134 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7286 (ppt170) REVERT: R 46 ILE cc_start: 0.8653 (mm) cc_final: 0.8366 (mp) REVERT: R 100 LEU cc_start: 0.8564 (tp) cc_final: 0.8197 (tt) REVERT: R 214 PHE cc_start: 0.7737 (m-10) cc_final: 0.7477 (m-10) REVERT: R 236 PHE cc_start: 0.7407 (m-10) cc_final: 0.7141 (m-10) REVERT: S 19 LYS cc_start: 0.7925 (tttm) cc_final: 0.7684 (tttp) REVERT: S 204 SER cc_start: 0.8346 (p) cc_final: 0.8016 (t) outliers start: 29 outliers final: 20 residues processed: 158 average time/residue: 0.4817 time to fit residues: 81.9122 Evaluate side-chains 155 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 116 SER Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 162 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 96 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.188871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.153993 restraints weight = 10074.434| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 1.95 r_work: 0.3629 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8792 Z= 0.136 Angle : 0.527 13.031 11957 Z= 0.273 Chirality : 0.043 0.252 1392 Planarity : 0.003 0.032 1490 Dihedral : 5.538 74.530 1273 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.47 % Favored : 96.44 % Rotamer: Outliers : 3.11 % Allowed : 20.88 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.26), residues: 1125 helix: 2.15 (0.26), residues: 411 sheet: -0.20 (0.29), residues: 289 loop : -0.14 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 24 TYR 0.017 0.001 TYR R 121 PHE 0.016 0.001 PHE R 195 TRP 0.011 0.001 TRP B 211 HIS 0.003 0.001 HIS R 250 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8790) covalent geometry : angle 0.52649 (11953) SS BOND : bond 0.00378 ( 2) SS BOND : angle 0.81302 ( 4) hydrogen bonds : bond 0.03440 ( 469) hydrogen bonds : angle 4.43216 ( 1302) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 209 LYS cc_start: 0.8312 (pttm) cc_final: 0.8080 (tmmt) REVERT: A 271 LYS cc_start: 0.7705 (ptmt) cc_final: 0.7500 (ptmm) REVERT: A 318 GLU cc_start: 0.8069 (tp30) cc_final: 0.7780 (tt0) REVERT: B 16 ASN cc_start: 0.7485 (m-40) cc_final: 0.7283 (m-40) REVERT: B 134 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7328 (ppt170) REVERT: R 29 TYR cc_start: 0.7921 (OUTLIER) cc_final: 0.7418 (m-80) REVERT: R 46 ILE cc_start: 0.8648 (mm) cc_final: 0.8354 (mp) REVERT: R 100 LEU cc_start: 0.8564 (tp) cc_final: 0.8197 (tt) REVERT: R 214 PHE cc_start: 0.7728 (m-10) cc_final: 0.7446 (m-10) REVERT: S 19 LYS cc_start: 0.7929 (tttm) cc_final: 0.7722 (tttp) REVERT: S 204 SER cc_start: 0.8357 (p) cc_final: 0.8018 (t) outliers start: 27 outliers final: 20 residues processed: 157 average time/residue: 0.4846 time to fit residues: 82.1572 Evaluate side-chains 157 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 29 TYR Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 116 SER Chi-restraints excluded: chain R residue 241 VAL Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 162 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 26 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 107 optimal weight: 0.0060 chunk 82 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 79 optimal weight: 8.9990 chunk 36 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.188816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.154157 restraints weight = 10113.524| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.94 r_work: 0.3650 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8792 Z= 0.124 Angle : 0.522 11.904 11957 Z= 0.269 Chirality : 0.042 0.258 1392 Planarity : 0.003 0.031 1490 Dihedral : 5.460 76.140 1273 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.38 % Favored : 96.53 % Rotamer: Outliers : 3.23 % Allowed : 21.11 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.26), residues: 1125 helix: 2.15 (0.26), residues: 412 sheet: -0.22 (0.29), residues: 301 loop : -0.12 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 24 TYR 0.018 0.001 TYR A 302 PHE 0.016 0.001 PHE R 195 TRP 0.012 0.001 TRP B 211 HIS 0.002 0.001 HIS R 250 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8790) covalent geometry : angle 0.52192 (11953) SS BOND : bond 0.00345 ( 2) SS BOND : angle 0.73259 ( 4) hydrogen bonds : bond 0.03368 ( 469) hydrogen bonds : angle 4.42319 ( 1302) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 209 LYS cc_start: 0.8323 (pttm) cc_final: 0.8077 (tmmt) REVERT: A 243 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8638 (mmm) REVERT: A 271 LYS cc_start: 0.7670 (ptmt) cc_final: 0.7445 (ptmm) REVERT: A 318 GLU cc_start: 0.8017 (tp30) cc_final: 0.7713 (tt0) REVERT: B 16 ASN cc_start: 0.7492 (m-40) cc_final: 0.7269 (m-40) REVERT: B 134 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7246 (ppt170) REVERT: B 234 PHE cc_start: 0.9303 (OUTLIER) cc_final: 0.9060 (m-80) REVERT: R 29 TYR cc_start: 0.7880 (OUTLIER) cc_final: 0.7400 (m-80) REVERT: R 46 ILE cc_start: 0.8610 (mm) cc_final: 0.8307 (mp) REVERT: R 100 LEU cc_start: 0.8490 (tp) cc_final: 0.8101 (tt) REVERT: R 140 LEU cc_start: 0.8061 (tp) cc_final: 0.7807 (tm) REVERT: R 214 PHE cc_start: 0.7727 (m-10) cc_final: 0.7467 (m-10) REVERT: R 236 PHE cc_start: 0.7418 (m-10) cc_final: 0.7166 (m-10) REVERT: S 19 LYS cc_start: 0.7901 (tttm) cc_final: 0.7625 (tttp) REVERT: S 204 SER cc_start: 0.8317 (p) cc_final: 0.7978 (t) outliers start: 28 outliers final: 23 residues processed: 156 average time/residue: 0.4585 time to fit residues: 77.5360 Evaluate side-chains 162 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 29 TYR Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 116 SER Chi-restraints excluded: chain R residue 241 VAL Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 162 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 22 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 94 optimal weight: 0.0980 chunk 74 optimal weight: 0.0040 chunk 44 optimal weight: 0.0980 chunk 109 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 overall best weight: 0.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.189859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.155335 restraints weight = 10102.237| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 1.95 r_work: 0.3661 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8792 Z= 0.105 Angle : 0.520 11.327 11957 Z= 0.267 Chirality : 0.042 0.260 1392 Planarity : 0.004 0.066 1490 Dihedral : 5.412 76.641 1273 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.20 % Favored : 96.71 % Rotamer: Outliers : 3.00 % Allowed : 21.45 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.26), residues: 1125 helix: 2.21 (0.26), residues: 412 sheet: -0.21 (0.29), residues: 301 loop : -0.10 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 24 TYR 0.015 0.001 TYR R 121 PHE 0.016 0.001 PHE R 195 TRP 0.014 0.001 TRP B 211 HIS 0.002 0.000 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 8790) covalent geometry : angle 0.51982 (11953) SS BOND : bond 0.00298 ( 2) SS BOND : angle 0.74452 ( 4) hydrogen bonds : bond 0.03292 ( 469) hydrogen bonds : angle 4.39122 ( 1302) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 209 LYS cc_start: 0.8343 (pttm) cc_final: 0.8125 (tmmt) REVERT: A 243 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8692 (mmm) REVERT: A 271 LYS cc_start: 0.7695 (ptmt) cc_final: 0.7493 (ptmm) REVERT: A 318 GLU cc_start: 0.8023 (tp30) cc_final: 0.7751 (tt0) REVERT: B 134 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7269 (ppt170) REVERT: B 234 PHE cc_start: 0.9288 (OUTLIER) cc_final: 0.9050 (m-80) REVERT: R 29 TYR cc_start: 0.7917 (OUTLIER) cc_final: 0.7431 (m-80) REVERT: R 46 ILE cc_start: 0.8645 (mm) cc_final: 0.8361 (mp) REVERT: R 100 LEU cc_start: 0.8511 (tp) cc_final: 0.8139 (tt) REVERT: R 140 LEU cc_start: 0.8101 (tp) cc_final: 0.7860 (tm) REVERT: R 214 PHE cc_start: 0.7720 (m-10) cc_final: 0.7465 (m-10) REVERT: R 236 PHE cc_start: 0.7442 (m-10) cc_final: 0.7168 (m-10) REVERT: S 19 LYS cc_start: 0.7940 (tttm) cc_final: 0.7700 (tttp) REVERT: S 204 SER cc_start: 0.8344 (p) cc_final: 0.8015 (t) outliers start: 26 outliers final: 20 residues processed: 152 average time/residue: 0.4889 time to fit residues: 80.1928 Evaluate side-chains 156 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 29 TYR Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 116 SER Chi-restraints excluded: chain R residue 241 VAL Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 162 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 84 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 106 optimal weight: 0.0030 chunk 100 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.189594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.155274 restraints weight = 10119.913| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 1.94 r_work: 0.3656 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8792 Z= 0.115 Angle : 0.522 10.648 11957 Z= 0.267 Chirality : 0.042 0.266 1392 Planarity : 0.003 0.053 1490 Dihedral : 5.385 77.196 1273 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.47 % Favored : 96.44 % Rotamer: Outliers : 2.88 % Allowed : 21.57 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.26), residues: 1125 helix: 2.20 (0.27), residues: 413 sheet: -0.19 (0.29), residues: 301 loop : -0.09 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 24 TYR 0.015 0.001 TYR R 121 PHE 0.015 0.001 PHE R 195 TRP 0.013 0.001 TRP B 211 HIS 0.002 0.001 HIS R 250 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8790) covalent geometry : angle 0.52196 (11953) SS BOND : bond 0.00329 ( 2) SS BOND : angle 0.77974 ( 4) hydrogen bonds : bond 0.03286 ( 469) hydrogen bonds : angle 4.39542 ( 1302) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3495.11 seconds wall clock time: 60 minutes 30.55 seconds (3630.55 seconds total)