Starting phenix.real_space_refine on Wed Feb 4 06:28:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yda_72798/02_2026/9yda_72798.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yda_72798/02_2026/9yda_72798.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yda_72798/02_2026/9yda_72798.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yda_72798/02_2026/9yda_72798.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yda_72798/02_2026/9yda_72798.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yda_72798/02_2026/9yda_72798.map" } resolution = 2.9 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= 0.022 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 62 5.16 5 C 5769 2.51 5 N 1542 2.21 5 O 1663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9036 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2377 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 18, 'TRANS': 281} Chain: "B" Number of atoms: 2558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2558 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "H" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1785 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "A" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1867 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.14, per 1000 atoms: 0.24 Number of scatterers: 9036 At special positions: 0 Unit cell: (118.422, 111.996, 134.946, 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 62 16.00 O 1663 8.00 N 1542 7.00 C 5769 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 126 " - pdb=" SG CYS R 203 " distance=2.01 Simple disulfide: pdb=" SG CYS H 39 " - pdb=" SG CYS H 113 " distance=2.04 Simple disulfide: pdb=" SG CYS H 176 " - pdb=" SG CYS H 246 " distance=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 345.5 milliseconds 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: 2144 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 37.4% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'R' and resid 50 through 81 removed outlier: 3.755A pdb=" N HIS R 54 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL R 74 " --> pdb=" O THR R 70 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR R 78 " --> pdb=" O VAL R 74 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET R 79 " --> pdb=" O LEU R 75 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS R 80 " --> pdb=" O ALA R 76 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE R 81 " --> pdb=" O ALA R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 85 removed outlier: 3.724A pdb=" N ARG R 85 " --> pdb=" O LYS R 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 82 through 85' Processing helix chain 'R' and resid 86 through 88 No H-bonds generated for 'chain 'R' and resid 86 through 88' Processing helix chain 'R' and resid 89 through 115 removed outlier: 3.789A pdb=" N VAL R 115 " --> pdb=" O VAL R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 122 through 157 removed outlier: 3.739A pdb=" N CYS R 136 " --> pdb=" O THR R 132 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA R 145 " --> pdb=" O LEU R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 165 through 184 removed outlier: 3.563A pdb=" N ALA R 169 " --> pdb=" O ASP R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 189 Processing helix chain 'R' and resid 215 through 228 Processing helix chain 'R' and resid 228 through 251 removed outlier: 3.718A pdb=" N LEU R 232 " --> pdb=" O CYS R 228 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL R 249 " --> pdb=" O ALA R 245 " (cutoff:3.500A) Processing helix chain 'R' and resid 256 through 294 removed outlier: 3.751A pdb=" N LYS R 264 " --> pdb=" O GLN R 260 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 302 through 304 No H-bonds generated for 'chain 'R' and resid 302 through 304' Processing helix chain 'R' and resid 305 through 312 Processing helix chain 'R' and resid 313 through 323 removed outlier: 3.788A pdb=" N TYR R 317 " --> pdb=" O SER R 313 " (cutoff:3.500A) Proline residue: R 319 - end of helix Processing helix chain 'R' and resid 326 through 334 Processing helix chain 'B' and resid 10 through 25 removed outlier: 3.835A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.558A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.755A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'H' and resid 91 through 93 No H-bonds generated for 'chain 'H' and resid 91 through 93' Processing helix chain 'H' and resid 104 through 108 removed outlier: 3.754A pdb=" N THR H 108 " --> pdb=" O SER H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 237 through 241 removed outlier: 4.027A pdb=" N VAL H 241 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.612A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.794A pdb=" N ILE A 49 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.508A pdb=" N GLN A 202 " --> pdb=" O LYS A 199 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN A 205 " --> pdb=" O GLN A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 234 Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.534A pdb=" N LEU A 238 " --> pdb=" O ASN A 235 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG A 239 " --> pdb=" O ARG A 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 235 through 239' Processing helix chain 'A' and resid 249 through 260 removed outlier: 3.513A pdb=" N LEU A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 267 Processing helix chain 'A' and resid 268 through 274 Processing helix chain 'A' and resid 287 through 307 removed outlier: 3.501A pdb=" N THR A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA A 307 " --> pdb=" O ARG A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 347 removed outlier: 3.761A pdb=" N ARG A 330 " --> pdb=" O GLU A 326 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE A 331 " --> pdb=" O ASN A 327 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 194 through 196 Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.686A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.700A 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: 7.045A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.018A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.844A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.087A 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: 6.986A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.722A 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: 6.958A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.727A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 20 through 24 removed outlier: 3.538A pdb=" N SER H 88 " --> pdb=" O PHE H 97 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 27 through 29 removed outlier: 6.040A pdb=" N GLY H 27 " --> pdb=" O THR H 135 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N MET H 51 " --> pdb=" O TYR H 67 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N TYR H 67 " --> pdb=" O MET H 51 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TRP H 53 " --> pdb=" O VAL H 65 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 157 through 159 Processing sheet with id=AB3, first strand: chain 'H' and resid 163 through 165 removed outlier: 6.792A pdb=" N TRP H 193 " --> pdb=" O LEU H 205 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 163 through 165 removed outlier: 4.111A pdb=" N THR H 255 " --> pdb=" O GLN H 248 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 175 through 180 removed outlier: 6.436A pdb=" N HIS A 34 " --> pdb=" O HIS A 186 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N PHE A 188 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU A 36 " --> pdb=" O PHE A 188 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA A 209 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE A 210 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N PHE A 246 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE A 212 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ASN A 248 " --> pdb=" O PHE A 212 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL A 214 " --> pdb=" O ASN A 248 " (cutoff:3.500A) 418 hydrogen bonds defined for protein. 1155 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: 1.17 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1820 1.33 - 1.45: 2333 1.45 - 1.57: 5009 1.57 - 1.69: 0 1.69 - 1.82: 89 Bond restraints: 9251 Sorted by residual: bond pdb=" CA ARG B 22 " pdb=" C ARG B 22 " ideal model delta sigma weight residual 1.524 1.473 0.051 1.29e-02 6.01e+03 1.55e+01 bond pdb=" N ILE R 246 " pdb=" CA ILE R 246 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.21e-02 6.83e+03 1.01e+01 bond pdb=" N PRO R 186 " pdb=" CD PRO R 186 " ideal model delta sigma weight residual 1.473 1.517 -0.044 1.40e-02 5.10e+03 9.69e+00 bond pdb=" N VAL R 120 " pdb=" CA VAL R 120 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.37e-02 5.33e+03 9.39e+00 bond pdb=" N LYS R 157 " pdb=" CA LYS R 157 " ideal model delta sigma weight residual 1.457 1.498 -0.042 1.41e-02 5.03e+03 8.67e+00 ... (remaining 9246 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 12135 1.66 - 3.32: 359 3.32 - 4.99: 49 4.99 - 6.65: 8 6.65 - 8.31: 6 Bond angle restraints: 12557 Sorted by residual: angle pdb=" CA TRP R 179 " pdb=" CB TRP R 179 " pdb=" CG TRP R 179 " ideal model delta sigma weight residual 113.60 121.12 -7.52 1.90e+00 2.77e-01 1.57e+01 angle pdb=" C LYS R 157 " pdb=" N PRO R 158 " pdb=" CA PRO R 158 " ideal model delta sigma weight residual 119.28 123.49 -4.21 1.10e+00 8.26e-01 1.46e+01 angle pdb=" N LEU B 55 " pdb=" CA LEU B 55 " pdb=" CB LEU B 55 " ideal model delta sigma weight residual 110.53 104.96 5.57 1.49e+00 4.50e-01 1.40e+01 angle pdb=" C MET H 209 " pdb=" N SER H 210 " pdb=" CA SER H 210 " ideal model delta sigma weight residual 123.05 128.81 -5.76 1.57e+00 4.06e-01 1.35e+01 angle pdb=" CA TRP R 243 " pdb=" CB TRP R 243 " pdb=" CG TRP R 243 " ideal model delta sigma weight residual 113.60 120.35 -6.75 1.90e+00 2.77e-01 1.26e+01 ... (remaining 12552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 5062 17.97 - 35.93: 276 35.93 - 53.90: 92 53.90 - 71.86: 15 71.86 - 89.83: 9 Dihedral angle restraints: 5454 sinusoidal: 2125 harmonic: 3329 Sorted by residual: dihedral pdb=" C ARG B 256 " pdb=" N ARG B 256 " pdb=" CA ARG B 256 " pdb=" CB ARG B 256 " ideal model delta harmonic sigma weight residual -122.60 -132.25 9.65 0 2.50e+00 1.60e-01 1.49e+01 dihedral pdb=" CB CYS R 126 " pdb=" SG CYS R 126 " pdb=" SG CYS R 203 " pdb=" CB CYS R 203 " ideal model delta sinusoidal sigma weight residual -86.00 -117.60 31.60 1 1.00e+01 1.00e-02 1.42e+01 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 180.00 162.34 17.66 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 5451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1237 0.082 - 0.165: 149 0.165 - 0.247: 6 0.247 - 0.330: 0 0.330 - 0.412: 1 Chirality restraints: 1393 Sorted by residual: chirality pdb=" CA ARG B 256 " pdb=" N ARG B 256 " pdb=" C ARG B 256 " pdb=" CB ARG B 256 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" CA ARG B 48 " pdb=" N ARG B 48 " pdb=" C ARG B 48 " pdb=" CB ARG B 48 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA LEU B 55 " pdb=" N LEU B 55 " pdb=" C LEU B 55 " pdb=" CB LEU B 55 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1390 not shown) Planarity restraints: 1596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE R 164 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.85e+00 pdb=" C PHE R 164 " 0.045 2.00e-02 2.50e+03 pdb=" O PHE R 164 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP R 165 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 RET R 401 " 0.025 2.00e-02 2.50e+03 1.88e-02 4.43e+00 pdb=" C11 RET R 401 " -0.022 2.00e-02 2.50e+03 pdb=" C19 RET R 401 " 0.002 2.00e-02 2.50e+03 pdb=" C8 RET R 401 " -0.020 2.00e-02 2.50e+03 pdb=" C9 RET R 401 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 155 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.83e+00 pdb=" C VAL R 155 " -0.029 2.00e-02 2.50e+03 pdb=" O VAL R 155 " 0.011 2.00e-02 2.50e+03 pdb=" N CYS R 156 " 0.010 2.00e-02 2.50e+03 ... (remaining 1593 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 3637 2.91 - 3.41: 7733 3.41 - 3.90: 13987 3.90 - 4.40: 15750 4.40 - 4.90: 27879 Nonbonded interactions: 68986 Sorted by model distance: nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.410 3.040 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.417 3.040 nonbonded pdb=" OD1 ASP B 228 " pdb=" NH2 ARG A 198 " model vdw 2.418 3.120 nonbonded pdb=" NZ LYS B 57 " pdb=" OD1 ASN A 205 " model vdw 2.431 3.120 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.432 3.040 ... (remaining 68981 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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.540 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 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 : 0.006 0.161 9255 Z= 0.341 Angle : 0.687 8.311 12563 Z= 0.416 Chirality : 0.049 0.412 1393 Planarity : 0.004 0.054 1596 Dihedral : 13.356 89.831 3301 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.62 % Allowed : 8.82 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.24), residues: 1135 helix: 0.82 (0.25), residues: 374 sheet: 1.02 (0.31), residues: 280 loop : -0.35 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 163 TYR 0.020 0.001 TYR H 207 PHE 0.018 0.001 PHE R 159 TRP 0.016 0.001 TRP R 195 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00527 ( 9251) covalent geometry : angle 0.68622 (12557) SS BOND : bond 0.01078 ( 3) SS BOND : angle 2.02541 ( 6) hydrogen bonds : bond 0.21661 ( 414) hydrogen bonds : angle 6.37507 ( 1155) Misc. bond : bond 0.16091 ( 1) *********************** 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 208 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 202 time to evaluate : 0.389 Fit side-chains REVERT: R 71 ASN cc_start: 0.7197 (m-40) cc_final: 0.6949 (m110) REVERT: R 81 PHE cc_start: 0.6931 (m-80) cc_final: 0.6574 (m-10) REVERT: R 110 SER cc_start: 0.7824 (m) cc_final: 0.7440 (p) REVERT: R 332 CYS cc_start: 0.7302 (m) cc_final: 0.6964 (m) REVERT: B 111 TYR cc_start: 0.8695 (m-80) cc_final: 0.8189 (m-80) REVERT: B 234 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.8471 (m-80) REVERT: H 157 MET cc_start: 0.7412 (mmm) cc_final: 0.7151 (mmt) REVERT: A 176 THR cc_start: 0.8307 (m) cc_final: 0.8019 (t) outliers start: 6 outliers final: 3 residues processed: 205 average time/residue: 0.6009 time to fit residues: 131.0017 Evaluate side-chains 190 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 186 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain A residue 308 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.0670 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 253 GLN B 62 HIS H 56 GLN H 203 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.121218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.104280 restraints weight = 12868.216| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.98 r_work: 0.3196 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9255 Z= 0.164 Angle : 0.583 7.344 12563 Z= 0.316 Chirality : 0.044 0.161 1393 Planarity : 0.005 0.047 1596 Dihedral : 5.107 58.753 1266 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.28 % Allowed : 11.90 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.25), residues: 1135 helix: 2.10 (0.26), residues: 375 sheet: 1.29 (0.31), residues: 272 loop : -0.29 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 303 TYR 0.025 0.002 TYR H 207 PHE 0.013 0.002 PHE B 199 TRP 0.016 0.002 TRP H 64 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 9251) covalent geometry : angle 0.58154 (12557) SS BOND : bond 0.01116 ( 3) SS BOND : angle 1.78695 ( 6) hydrogen bonds : bond 0.07472 ( 414) hydrogen bonds : angle 4.60246 ( 1155) Misc. bond : bond 0.00018 ( 1) *********************** 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 215 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 0.338 Fit side-chains REVERT: R 71 ASN cc_start: 0.7642 (m-40) cc_final: 0.7136 (m110) REVERT: R 81 PHE cc_start: 0.7399 (m-80) cc_final: 0.7157 (m-10) REVERT: R 110 SER cc_start: 0.7959 (m) cc_final: 0.7739 (m) REVERT: R 309 PHE cc_start: 0.7003 (t80) cc_final: 0.6633 (t80) REVERT: B 22 ARG cc_start: 0.7899 (mtm-85) cc_final: 0.7257 (mtm-85) REVERT: B 46 ARG cc_start: 0.8264 (mtt180) cc_final: 0.8016 (mtt-85) REVERT: B 111 TYR cc_start: 0.8739 (m-80) cc_final: 0.8245 (m-80) REVERT: B 155 ASN cc_start: 0.8262 (t0) cc_final: 0.8013 (t0) REVERT: B 234 PHE cc_start: 0.8806 (OUTLIER) cc_final: 0.8420 (m-80) REVERT: B 258 ASP cc_start: 0.7766 (t0) cc_final: 0.7253 (t70) REVERT: A 188 PHE cc_start: 0.8470 (m-80) cc_final: 0.8168 (m-80) REVERT: A 292 ARG cc_start: 0.7875 (ttp80) cc_final: 0.7593 (ttp80) outliers start: 32 outliers final: 12 residues processed: 195 average time/residue: 0.5653 time to fit residues: 117.1096 Evaluate side-chains 192 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 179 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain H residue 113 CYS Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 290 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 59 optimal weight: 3.9990 chunk 107 optimal weight: 0.0050 chunk 82 optimal weight: 0.0370 chunk 2 optimal weight: 0.6980 chunk 69 optimal weight: 0.0050 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 98 optimal weight: 0.0670 chunk 101 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 GLN A 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.127261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.110333 restraints weight = 12878.738| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.98 r_work: 0.3297 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9255 Z= 0.097 Angle : 0.458 7.089 12563 Z= 0.249 Chirality : 0.040 0.138 1393 Planarity : 0.004 0.041 1596 Dihedral : 4.717 59.819 1264 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.95 % Allowed : 15.08 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.25), residues: 1135 helix: 2.39 (0.27), residues: 382 sheet: 1.34 (0.32), residues: 259 loop : -0.32 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 214 TYR 0.013 0.001 TYR H 207 PHE 0.011 0.001 PHE B 199 TRP 0.014 0.001 TRP R 243 HIS 0.002 0.000 HIS R 123 Details of bonding type rmsd covalent geometry : bond 0.00185 ( 9251) covalent geometry : angle 0.45820 (12557) SS BOND : bond 0.00487 ( 3) SS BOND : angle 0.68028 ( 6) hydrogen bonds : bond 0.04489 ( 414) hydrogen bonds : angle 4.05748 ( 1155) Misc. bond : bond 0.00030 ( 1) *********************** 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 207 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 0.254 Fit side-chains REVERT: R 110 SER cc_start: 0.7690 (m) cc_final: 0.7490 (m) REVERT: R 208 PHE cc_start: 0.8486 (m-80) cc_final: 0.7822 (m-80) REVERT: R 309 PHE cc_start: 0.6971 (t80) cc_final: 0.6593 (t80) REVERT: B 22 ARG cc_start: 0.7862 (mtm-85) cc_final: 0.7291 (mtm-85) REVERT: B 46 ARG cc_start: 0.8218 (mtt180) cc_final: 0.7958 (mtt-85) REVERT: B 111 TYR cc_start: 0.8653 (m-80) cc_final: 0.8261 (m-80) REVERT: B 195 ASP cc_start: 0.8138 (p0) cc_final: 0.7938 (p0) REVERT: B 258 ASP cc_start: 0.7683 (t0) cc_final: 0.7149 (t70) REVERT: G 51 LEU cc_start: 0.7698 (tp) cc_final: 0.7425 (tp) REVERT: A 190 VAL cc_start: 0.8388 (t) cc_final: 0.8155 (p) REVERT: A 292 ARG cc_start: 0.7793 (ttp80) cc_final: 0.7465 (ttp80) REVERT: A 334 ASP cc_start: 0.7935 (m-30) cc_final: 0.7700 (m-30) REVERT: A 337 ASP cc_start: 0.8139 (t70) cc_final: 0.7931 (t0) outliers start: 19 outliers final: 10 residues processed: 196 average time/residue: 0.5818 time to fit residues: 120.9169 Evaluate side-chains 195 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 185 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 251 GLU Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 342 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 71 ASN B 175 GLN H 56 GLN A 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.120346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.103471 restraints weight = 13015.584| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.01 r_work: 0.3181 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9255 Z= 0.173 Angle : 0.571 6.234 12563 Z= 0.309 Chirality : 0.044 0.167 1393 Planarity : 0.005 0.051 1596 Dihedral : 4.883 59.038 1264 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.15 % Allowed : 16.31 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.25), residues: 1135 helix: 2.21 (0.26), residues: 376 sheet: 1.29 (0.31), residues: 272 loop : -0.43 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.031 0.002 TYR H 207 PHE 0.016 0.002 PHE R 277 TRP 0.014 0.002 TRP B 82 HIS 0.005 0.001 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 9251) covalent geometry : angle 0.56949 (12557) SS BOND : bond 0.01185 ( 3) SS BOND : angle 1.82156 ( 6) hydrogen bonds : bond 0.07258 ( 414) hydrogen bonds : angle 4.41504 ( 1155) Misc. bond : bond 0.00045 ( 1) *********************** 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 207 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 186 time to evaluate : 0.265 Fit side-chains REVERT: R 110 SER cc_start: 0.7918 (m) cc_final: 0.7674 (m) REVERT: R 309 PHE cc_start: 0.7010 (t80) cc_final: 0.6633 (t80) REVERT: B 22 ARG cc_start: 0.7907 (mtm-85) cc_final: 0.7547 (mtt180) REVERT: B 46 ARG cc_start: 0.8310 (mtt180) cc_final: 0.8057 (mtt-85) REVERT: B 111 TYR cc_start: 0.8756 (m-80) cc_final: 0.8255 (m-80) REVERT: B 155 ASN cc_start: 0.8263 (t0) cc_final: 0.8024 (t0) REVERT: B 195 ASP cc_start: 0.8149 (p0) cc_final: 0.7917 (p0) REVERT: B 258 ASP cc_start: 0.7716 (t0) cc_final: 0.7240 (t0) REVERT: G 51 LEU cc_start: 0.7975 (tp) cc_final: 0.7658 (tp) REVERT: H 195 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8250 (tp) REVERT: A 292 ARG cc_start: 0.8099 (ttp80) cc_final: 0.7759 (ttp80) outliers start: 21 outliers final: 16 residues processed: 191 average time/residue: 0.5232 time to fit residues: 106.1920 Evaluate side-chains 200 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 247 ARG Chi-restraints excluded: chain R residue 252 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain H residue 113 CYS Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 342 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 46 optimal weight: 0.0980 chunk 92 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 54 HIS R 71 ASN B 88 ASN B 175 GLN B 237 ASN H 56 GLN A 179 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.121124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.104407 restraints weight = 12887.966| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.99 r_work: 0.3201 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9255 Z= 0.148 Angle : 0.536 6.205 12563 Z= 0.290 Chirality : 0.043 0.159 1393 Planarity : 0.004 0.053 1596 Dihedral : 4.610 59.554 1261 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.87 % Allowed : 15.79 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.25), residues: 1135 helix: 2.26 (0.27), residues: 375 sheet: 1.29 (0.31), residues: 272 loop : -0.51 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.022 0.002 TYR H 207 PHE 0.014 0.002 PHE B 199 TRP 0.014 0.001 TRP H 64 HIS 0.004 0.001 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 9251) covalent geometry : angle 0.53503 (12557) SS BOND : bond 0.00984 ( 3) SS BOND : angle 1.53417 ( 6) hydrogen bonds : bond 0.06433 ( 414) hydrogen bonds : angle 4.25988 ( 1155) Misc. bond : bond 0.00044 ( 1) *********************** 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 215 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 187 time to evaluate : 0.308 Fit side-chains REVERT: R 226 THR cc_start: 0.8116 (p) cc_final: 0.7883 (t) REVERT: R 309 PHE cc_start: 0.7004 (t80) cc_final: 0.6607 (t80) REVERT: B 22 ARG cc_start: 0.7907 (mtm-85) cc_final: 0.7641 (mtt180) REVERT: B 46 ARG cc_start: 0.8288 (mtt180) cc_final: 0.8042 (mtt-85) REVERT: B 111 TYR cc_start: 0.8734 (m-80) cc_final: 0.8170 (m-80) REVERT: B 155 ASN cc_start: 0.8284 (t0) cc_final: 0.7974 (t0) REVERT: B 195 ASP cc_start: 0.8143 (p0) cc_final: 0.7901 (p0) REVERT: B 254 ASP cc_start: 0.7701 (p0) cc_final: 0.7382 (p0) REVERT: B 258 ASP cc_start: 0.7758 (t0) cc_final: 0.7511 (t70) REVERT: B 335 PHE cc_start: 0.8665 (m-10) cc_final: 0.8156 (m-80) REVERT: G 51 LEU cc_start: 0.7966 (tp) cc_final: 0.7680 (tp) REVERT: A 42 ASP cc_start: 0.7770 (m-30) cc_final: 0.7517 (m-30) REVERT: A 292 ARG cc_start: 0.8105 (ttp80) cc_final: 0.7659 (ttp80) REVERT: A 334 ASP cc_start: 0.7980 (m-30) cc_final: 0.7710 (m-30) outliers start: 28 outliers final: 21 residues processed: 197 average time/residue: 0.4964 time to fit residues: 104.1138 Evaluate side-chains 209 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 252 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE 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 G residue 21 MET Chi-restraints excluded: chain H residue 113 CYS Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 342 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 chunk 66 optimal weight: 0.0000 chunk 67 optimal weight: 0.0060 chunk 100 optimal weight: 0.1980 chunk 94 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 8 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.2400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 71 ASN B 175 GLN H 56 GLN A 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.124846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.108161 restraints weight = 12893.188| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.99 r_work: 0.3258 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9255 Z= 0.100 Angle : 0.463 5.975 12563 Z= 0.250 Chirality : 0.040 0.148 1393 Planarity : 0.004 0.048 1596 Dihedral : 4.360 59.384 1261 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.26 % Allowed : 16.82 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.25), residues: 1135 helix: 2.54 (0.27), residues: 376 sheet: 1.33 (0.31), residues: 270 loop : -0.45 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.020 0.001 TYR R 116 PHE 0.013 0.001 PHE R 81 TRP 0.012 0.001 TRP B 297 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00198 ( 9251) covalent geometry : angle 0.46225 (12557) SS BOND : bond 0.00607 ( 3) SS BOND : angle 0.86195 ( 6) hydrogen bonds : bond 0.04637 ( 414) hydrogen bonds : angle 3.98425 ( 1155) Misc. bond : bond 0.00024 ( 1) *********************** 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 215 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 193 time to evaluate : 0.252 Fit side-chains REVERT: R 158 PRO cc_start: 0.7405 (Cg_exo) cc_final: 0.7178 (Cg_endo) REVERT: R 226 THR cc_start: 0.8037 (p) cc_final: 0.7816 (t) REVERT: R 255 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7353 (mm-30) REVERT: R 309 PHE cc_start: 0.6968 (t80) cc_final: 0.6569 (t80) REVERT: B 22 ARG cc_start: 0.7854 (mtm-85) cc_final: 0.7301 (mtm-85) REVERT: B 46 ARG cc_start: 0.8233 (mtt180) cc_final: 0.7983 (mtt-85) REVERT: B 111 TYR cc_start: 0.8671 (m-80) cc_final: 0.8256 (m-80) REVERT: B 155 ASN cc_start: 0.8304 (t0) cc_final: 0.8054 (t0) REVERT: B 254 ASP cc_start: 0.7793 (p0) cc_final: 0.7499 (p0) REVERT: B 258 ASP cc_start: 0.7681 (t0) cc_final: 0.7088 (t70) REVERT: B 335 PHE cc_start: 0.8619 (m-10) cc_final: 0.8285 (m-80) REVERT: G 51 LEU cc_start: 0.7855 (tp) cc_final: 0.7626 (tp) REVERT: H 195 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8241 (tp) REVERT: A 292 ARG cc_start: 0.7976 (ttp80) cc_final: 0.7729 (ttp80) REVERT: A 334 ASP cc_start: 0.7942 (m-30) cc_final: 0.7640 (m-30) REVERT: A 337 ASP cc_start: 0.8059 (t70) cc_final: 0.7848 (t0) outliers start: 22 outliers final: 17 residues processed: 202 average time/residue: 0.4879 time to fit residues: 104.8404 Evaluate side-chains 210 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 247 ARG Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 251 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 342 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 16 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 7 optimal weight: 0.0870 chunk 14 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 71 ASN B 175 GLN H 56 GLN A 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.121093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.104411 restraints weight = 12937.721| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.00 r_work: 0.3203 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9255 Z= 0.147 Angle : 0.538 6.031 12563 Z= 0.289 Chirality : 0.042 0.163 1393 Planarity : 0.004 0.051 1596 Dihedral : 4.548 59.662 1261 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.97 % Allowed : 16.51 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.25), residues: 1135 helix: 2.33 (0.27), residues: 376 sheet: 1.11 (0.32), residues: 269 loop : -0.50 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 214 TYR 0.026 0.001 TYR H 207 PHE 0.014 0.001 PHE B 199 TRP 0.016 0.002 TRP R 183 HIS 0.004 0.001 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9251) covalent geometry : angle 0.53707 (12557) SS BOND : bond 0.00962 ( 3) SS BOND : angle 1.45052 ( 6) hydrogen bonds : bond 0.06491 ( 414) hydrogen bonds : angle 4.24436 ( 1155) Misc. bond : bond 0.00043 ( 1) *********************** 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 223 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 194 time to evaluate : 0.357 Fit side-chains REVERT: R 226 THR cc_start: 0.8049 (p) cc_final: 0.7840 (t) REVERT: R 309 PHE cc_start: 0.6948 (t80) cc_final: 0.6569 (t80) REVERT: B 22 ARG cc_start: 0.7886 (mtm-85) cc_final: 0.7215 (mtt-85) REVERT: B 46 ARG cc_start: 0.8255 (mtt180) cc_final: 0.8012 (mtt-85) REVERT: B 111 TYR cc_start: 0.8734 (m-80) cc_final: 0.8161 (m-80) REVERT: B 155 ASN cc_start: 0.8288 (t0) cc_final: 0.8033 (t0) REVERT: B 247 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7233 (p0) REVERT: B 258 ASP cc_start: 0.7732 (t0) cc_final: 0.7080 (t70) REVERT: G 51 LEU cc_start: 0.7966 (tp) cc_final: 0.7687 (tp) REVERT: H 195 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8232 (tp) REVERT: A 42 ASP cc_start: 0.7764 (m-30) cc_final: 0.7523 (m-30) REVERT: A 292 ARG cc_start: 0.8067 (ttp80) cc_final: 0.7787 (ttp80) outliers start: 29 outliers final: 19 residues processed: 206 average time/residue: 0.5369 time to fit residues: 117.7564 Evaluate side-chains 210 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 284 TYR Chi-restraints excluded: chain R residue 303 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain H residue 113 CYS Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 342 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 89 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 61 optimal weight: 0.0270 chunk 63 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 104 optimal weight: 0.4980 chunk 88 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 71 ASN B 175 GLN H 56 GLN A 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.121706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.105078 restraints weight = 12808.954| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.98 r_work: 0.3207 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9255 Z= 0.135 Angle : 0.526 6.299 12563 Z= 0.283 Chirality : 0.042 0.158 1393 Planarity : 0.004 0.052 1596 Dihedral : 4.549 59.980 1261 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.56 % Allowed : 17.44 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.25), residues: 1135 helix: 2.33 (0.27), residues: 376 sheet: 1.07 (0.32), residues: 269 loop : -0.52 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 214 TYR 0.021 0.001 TYR H 207 PHE 0.013 0.001 PHE B 199 TRP 0.013 0.001 TRP H 64 HIS 0.004 0.001 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9251) covalent geometry : angle 0.52513 (12557) SS BOND : bond 0.00863 ( 3) SS BOND : angle 1.27690 ( 6) hydrogen bonds : bond 0.06040 ( 414) hydrogen bonds : angle 4.17511 ( 1155) Misc. bond : bond 0.00042 ( 1) *********************** 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 216 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 0.407 Fit side-chains REVERT: R 158 PRO cc_start: 0.7477 (Cg_exo) cc_final: 0.7256 (Cg_endo) REVERT: R 309 PHE cc_start: 0.6952 (t80) cc_final: 0.6574 (t80) REVERT: B 22 ARG cc_start: 0.7871 (mtm-85) cc_final: 0.7206 (mtt-85) REVERT: B 46 ARG cc_start: 0.8251 (mtt180) cc_final: 0.8011 (mtt-85) REVERT: B 111 TYR cc_start: 0.8715 (m-80) cc_final: 0.8135 (m-80) REVERT: B 155 ASN cc_start: 0.8281 (t0) cc_final: 0.8021 (t0) REVERT: B 247 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7226 (p0) REVERT: B 254 ASP cc_start: 0.7827 (p0) cc_final: 0.7425 (p0) REVERT: B 258 ASP cc_start: 0.7761 (t0) cc_final: 0.7075 (t70) REVERT: B 335 PHE cc_start: 0.8610 (m-10) cc_final: 0.8279 (m-80) REVERT: G 51 LEU cc_start: 0.7954 (tp) cc_final: 0.7697 (tp) REVERT: H 195 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8233 (tp) REVERT: A 42 ASP cc_start: 0.7747 (m-30) cc_final: 0.7523 (m-30) REVERT: A 292 ARG cc_start: 0.8061 (ttp80) cc_final: 0.7774 (ttp80) REVERT: A 334 ASP cc_start: 0.7921 (m-30) cc_final: 0.7686 (m-30) outliers start: 25 outliers final: 20 residues processed: 203 average time/residue: 0.5753 time to fit residues: 124.0667 Evaluate side-chains 210 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 252 GLN Chi-restraints excluded: chain R residue 284 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain H residue 113 CYS Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 342 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 45 optimal weight: 0.3980 chunk 36 optimal weight: 0.0370 chunk 79 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 44 optimal weight: 0.0770 chunk 78 optimal weight: 0.0970 chunk 21 optimal weight: 0.7980 overall best weight: 0.2414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 71 ASN B 175 GLN H 56 GLN A 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.125069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.108408 restraints weight = 12895.206| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.99 r_work: 0.3269 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9255 Z= 0.100 Angle : 0.474 5.800 12563 Z= 0.256 Chirality : 0.040 0.148 1393 Planarity : 0.004 0.050 1596 Dihedral : 4.341 59.256 1261 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.15 % Allowed : 17.85 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.25), residues: 1135 helix: 2.53 (0.27), residues: 377 sheet: 1.18 (0.32), residues: 271 loop : -0.33 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 214 TYR 0.016 0.001 TYR R 116 PHE 0.012 0.001 PHE B 199 TRP 0.012 0.001 TRP H 64 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 9251) covalent geometry : angle 0.47336 (12557) SS BOND : bond 0.00638 ( 3) SS BOND : angle 1.03406 ( 6) hydrogen bonds : bond 0.04543 ( 414) hydrogen bonds : angle 3.97266 ( 1155) Misc. bond : bond 0.00029 ( 1) *********************** 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 213 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 0.234 Fit side-chains REVERT: R 60 MET cc_start: 0.7738 (mtp) cc_final: 0.7422 (mtp) REVERT: R 158 PRO cc_start: 0.7342 (Cg_exo) cc_final: 0.7106 (Cg_endo) REVERT: R 255 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7350 (mm-30) REVERT: R 309 PHE cc_start: 0.6933 (t80) cc_final: 0.6556 (t80) REVERT: B 22 ARG cc_start: 0.7835 (mtm-85) cc_final: 0.7274 (mtt-85) REVERT: B 46 ARG cc_start: 0.8209 (mtt180) cc_final: 0.7966 (mtt-85) REVERT: B 111 TYR cc_start: 0.8664 (m-80) cc_final: 0.8289 (m-80) REVERT: B 155 ASN cc_start: 0.8307 (t0) cc_final: 0.7994 (t0) REVERT: B 254 ASP cc_start: 0.7817 (p0) cc_final: 0.7603 (p0) REVERT: B 335 PHE cc_start: 0.8576 (m-10) cc_final: 0.8216 (m-80) REVERT: G 51 LEU cc_start: 0.7892 (tp) cc_final: 0.7662 (tp) REVERT: H 195 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8234 (tp) REVERT: A 292 ARG cc_start: 0.7979 (ttp80) cc_final: 0.7466 (ttp80) REVERT: A 334 ASP cc_start: 0.7933 (m-30) cc_final: 0.7656 (m-30) outliers start: 21 outliers final: 15 residues processed: 204 average time/residue: 0.5433 time to fit residues: 118.2197 Evaluate side-chains 206 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 190 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 284 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 342 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 36 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 93 optimal weight: 0.3980 chunk 3 optimal weight: 0.6980 chunk 55 optimal weight: 0.0980 chunk 49 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 69 optimal weight: 0.0570 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 71 ASN B 175 GLN H 56 GLN A 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.123600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.106942 restraints weight = 12805.661| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.98 r_work: 0.3245 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9255 Z= 0.116 Angle : 0.505 7.410 12563 Z= 0.270 Chirality : 0.041 0.153 1393 Planarity : 0.004 0.053 1596 Dihedral : 4.377 59.353 1261 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.85 % Allowed : 18.67 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.25), residues: 1135 helix: 2.51 (0.27), residues: 377 sheet: 1.15 (0.32), residues: 268 loop : -0.33 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 214 TYR 0.020 0.001 TYR H 207 PHE 0.018 0.001 PHE R 69 TRP 0.022 0.001 TRP R 183 HIS 0.003 0.001 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9251) covalent geometry : angle 0.50390 (12557) SS BOND : bond 0.00807 ( 3) SS BOND : angle 1.28343 ( 6) hydrogen bonds : bond 0.05221 ( 414) hydrogen bonds : angle 4.03391 ( 1155) Misc. bond : bond 0.00034 ( 1) ********************** 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 205 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 187 time to evaluate : 0.338 Fit side-chains REVERT: R 60 MET cc_start: 0.7763 (mtp) cc_final: 0.7451 (mtp) REVERT: R 158 PRO cc_start: 0.7377 (Cg_exo) cc_final: 0.7147 (Cg_endo) REVERT: R 309 PHE cc_start: 0.6916 (t80) cc_final: 0.6550 (t80) REVERT: B 22 ARG cc_start: 0.7852 (mtm-85) cc_final: 0.7122 (mtt-85) REVERT: B 46 ARG cc_start: 0.8232 (mtt180) cc_final: 0.7991 (mtt-85) REVERT: B 111 TYR cc_start: 0.8697 (m-80) cc_final: 0.8187 (m-80) REVERT: B 155 ASN cc_start: 0.8289 (t0) cc_final: 0.8071 (t0) REVERT: B 254 ASP cc_start: 0.7826 (p0) cc_final: 0.7454 (p0) REVERT: B 258 ASP cc_start: 0.7707 (t0) cc_final: 0.6804 (t70) REVERT: B 277 SER cc_start: 0.8807 (t) cc_final: 0.8572 (m) REVERT: B 318 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8327 (tt) REVERT: B 335 PHE cc_start: 0.8585 (m-10) cc_final: 0.8308 (m-80) REVERT: G 51 LEU cc_start: 0.7927 (tp) cc_final: 0.7683 (tp) REVERT: H 195 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8216 (tp) REVERT: A 292 ARG cc_start: 0.8010 (ttp80) cc_final: 0.7723 (ttp80) REVERT: A 334 ASP cc_start: 0.7937 (m-30) cc_final: 0.7679 (m-30) outliers start: 18 outliers final: 16 residues processed: 199 average time/residue: 0.6091 time to fit residues: 128.6698 Evaluate side-chains 205 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 187 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 284 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 342 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 83 optimal weight: 1.9990 chunk 69 optimal weight: 0.0980 chunk 75 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 26 optimal weight: 0.0030 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 71 ASN B 175 GLN H 56 GLN A 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.122649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.105976 restraints weight = 12741.837| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.98 r_work: 0.3231 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9255 Z= 0.125 Angle : 0.521 7.539 12563 Z= 0.279 Chirality : 0.041 0.156 1393 Planarity : 0.004 0.057 1596 Dihedral : 4.426 59.608 1261 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.85 % Allowed : 18.36 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.25), residues: 1135 helix: 2.50 (0.27), residues: 376 sheet: 1.14 (0.32), residues: 268 loop : -0.33 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 214 TYR 0.021 0.001 TYR H 207 PHE 0.016 0.001 PHE R 69 TRP 0.026 0.001 TRP R 183 HIS 0.003 0.001 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9251) covalent geometry : angle 0.52057 (12557) SS BOND : bond 0.00874 ( 3) SS BOND : angle 1.40768 ( 6) hydrogen bonds : bond 0.05611 ( 414) hydrogen bonds : angle 4.08729 ( 1155) Misc. bond : bond 0.00039 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3369.44 seconds wall clock time: 57 minutes 53.20 seconds (3473.20 seconds total)