Starting phenix.real_space_refine on Wed Mar 4 10:10:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7znq_14813/03_2026/7znq_14813.cif Found real_map, /net/cci-nas-00/data/ceres_data/7znq_14813/03_2026/7znq_14813.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7znq_14813/03_2026/7znq_14813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7znq_14813/03_2026/7znq_14813.map" model { file = "/net/cci-nas-00/data/ceres_data/7znq_14813/03_2026/7znq_14813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7znq_14813/03_2026/7znq_14813.cif" } resolution = 3.04 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= 0.018 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 Cu 1 5.60 5 Mg 1 5.21 5 S 44 5.16 5 C 8224 2.51 5 N 2255 2.21 5 O 2336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12862 Number of models: 1 Model: "" Number of chains: 8 Chain: "f" Number of atoms: 2367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2367 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 12, 'TRANS': 294} Chain: "F" Number of atoms: 2367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2367 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 12, 'TRANS': 294} Chain: "Y" Number of atoms: 2030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2030 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 8, 'TRANS': 260} Chain breaks: 1 Chain: "y" Number of atoms: 1910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1910 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 8, 'TRANS': 241} Chain breaks: 2 Chain: "D" Number of atoms: 3077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3077 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 16, 'TRANS': 375} Chain breaks: 1 Chain: "L" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1108 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11876 SG CYS L 45 34.329 40.988 141.651 1.00 79.98 S ATOM 11899 SG CYS L 48 36.435 41.705 143.966 1.00 89.23 S ATOM 12080 SG CYS L 72 32.929 42.618 145.143 1.00 99.19 S Time building chain proxies: 3.40, per 1000 atoms: 0.26 Number of scatterers: 12862 At special positions: 0 Unit cell: (86.1, 88.56, 193.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Cu 1 28.99 S 44 16.00 Mg 1 11.99 O 2336 8.00 N 2255 7.00 C 8224 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.99 Conformation dependent library (CDL) restraints added in 564.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 45 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 72 " 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3006 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 14 sheets defined 47.1% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'f' and resid 40 through 50 Processing helix chain 'f' and resid 72 through 74 No H-bonds generated for 'chain 'f' and resid 72 through 74' Processing helix chain 'f' and resid 90 through 103 removed outlier: 3.502A pdb=" N THR f 94 " --> pdb=" O SER f 90 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU f 95 " --> pdb=" O GLY f 91 " (cutoff:3.500A) Processing helix chain 'f' and resid 105 through 107 No H-bonds generated for 'chain 'f' and resid 105 through 107' Processing helix chain 'f' and resid 108 through 116 Processing helix chain 'f' and resid 125 through 129 Processing helix chain 'f' and resid 130 through 143 Processing helix chain 'f' and resid 160 through 178 removed outlier: 3.572A pdb=" N ARG f 177 " --> pdb=" O ARG f 173 " (cutoff:3.500A) Processing helix chain 'f' and resid 211 through 219 Processing helix chain 'f' and resid 232 through 238 removed outlier: 4.071A pdb=" N GLN f 238 " --> pdb=" O ASP f 234 " (cutoff:3.500A) Processing helix chain 'f' and resid 238 through 243 removed outlier: 3.946A pdb=" N ASP f 242 " --> pdb=" O GLN f 238 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA f 243 " --> pdb=" O ARG f 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 238 through 243' Processing helix chain 'f' and resid 263 through 275 removed outlier: 3.502A pdb=" N LEU f 267 " --> pdb=" O HIS f 263 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ARG f 269 " --> pdb=" O LEU f 265 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN f 270 " --> pdb=" O VAL f 266 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU f 271 " --> pdb=" O LEU f 267 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY f 275 " --> pdb=" O LEU f 271 " (cutoff:3.500A) Processing helix chain 'f' and resid 286 through 297 Processing helix chain 'F' and resid 40 through 50 Processing helix chain 'F' and resid 69 through 74 Processing helix chain 'F' and resid 90 through 103 removed outlier: 3.559A pdb=" N LEU F 95 " --> pdb=" O GLY F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 116 removed outlier: 3.847A pdb=" N ASP F 110 " --> pdb=" O LEU F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 129 Processing helix chain 'F' and resid 130 through 143 Processing helix chain 'F' and resid 160 through 176 removed outlier: 3.956A pdb=" N GLN F 165 " --> pdb=" O PRO F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 219 removed outlier: 3.591A pdb=" N ARG F 216 " --> pdb=" O LEU F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 244 removed outlier: 3.837A pdb=" N ALA F 243 " --> pdb=" O TRP F 240 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY F 244 " --> pdb=" O THR F 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 240 through 244' Processing helix chain 'F' and resid 263 through 274 removed outlier: 3.764A pdb=" N GLU F 274 " --> pdb=" O GLN F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 298 Processing helix chain 'Y' and resid 3 through 16 removed outlier: 3.573A pdb=" N SER Y 13 " --> pdb=" O ARG Y 9 " (cutoff:3.500A) Processing helix chain 'Y' and resid 18 through 43 removed outlier: 3.673A pdb=" N LEU Y 22 " --> pdb=" O ASN Y 18 " (cutoff:3.500A) Processing helix chain 'Y' and resid 50 through 74 Proline residue: Y 67 - end of helix Processing helix chain 'Y' and resid 78 through 84 removed outlier: 3.509A pdb=" N GLU Y 83 " --> pdb=" O VAL Y 79 " (cutoff:3.500A) Processing helix chain 'Y' and resid 85 through 93 removed outlier: 4.130A pdb=" N LEU Y 89 " --> pdb=" O GLY Y 85 " (cutoff:3.500A) Processing helix chain 'Y' and resid 97 through 131 removed outlier: 3.677A pdb=" N ALA Y 124 " --> pdb=" O PHE Y 120 " (cutoff:3.500A) Processing helix chain 'Y' and resid 135 through 168 removed outlier: 3.695A pdb=" N LEU Y 139 " --> pdb=" O GLU Y 135 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TRP Y 141 " --> pdb=" O GLY Y 137 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS Y 167 " --> pdb=" O VAL Y 163 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL Y 168 " --> pdb=" O LEU Y 164 " (cutoff:3.500A) Processing helix chain 'Y' and resid 170 through 187 removed outlier: 3.541A pdb=" N VAL Y 186 " --> pdb=" O TRP Y 182 " (cutoff:3.500A) Processing helix chain 'Y' and resid 187 through 201 removed outlier: 3.647A pdb=" N SER Y 200 " --> pdb=" O LEU Y 196 " (cutoff:3.500A) Processing helix chain 'Y' and resid 208 through 215 removed outlier: 3.509A pdb=" N LEU Y 213 " --> pdb=" O PRO Y 210 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU Y 214 " --> pdb=" O TRP Y 211 " (cutoff:3.500A) Processing helix chain 'Y' and resid 216 through 226 removed outlier: 3.781A pdb=" N ARG Y 222 " --> pdb=" O THR Y 218 " (cutoff:3.500A) Processing helix chain 'Y' and resid 232 through 245 removed outlier: 3.911A pdb=" N MET Y 236 " --> pdb=" O GLY Y 233 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY Y 237 " --> pdb=" O SER Y 234 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL Y 238 " --> pdb=" O ALA Y 235 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU Y 239 " --> pdb=" O MET Y 236 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA Y 243 " --> pdb=" O SER Y 240 " (cutoff:3.500A) Processing helix chain 'Y' and resid 248 through 274 removed outlier: 4.271A pdb=" N LEU Y 252 " --> pdb=" O PRO Y 248 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TRP Y 253 " --> pdb=" O ALA Y 249 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER Y 263 " --> pdb=" O TRP Y 259 " (cutoff:3.500A) Processing helix chain 'y' and resid 3 through 17 removed outlier: 3.890A pdb=" N LYS y 10 " --> pdb=" O ASN y 6 " (cutoff:3.500A) Processing helix chain 'y' and resid 18 through 42 Processing helix chain 'y' and resid 51 through 75 Proline residue: y 67 - end of helix removed outlier: 3.561A pdb=" N ALA y 74 " --> pdb=" O ALA y 70 " (cutoff:3.500A) Processing helix chain 'y' and resid 78 through 84 Processing helix chain 'y' and resid 85 through 93 removed outlier: 3.817A pdb=" N LEU y 89 " --> pdb=" O GLY y 85 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR y 92 " --> pdb=" O MET y 88 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR y 93 " --> pdb=" O LEU y 89 " (cutoff:3.500A) Processing helix chain 'y' and resid 96 through 131 removed outlier: 4.197A pdb=" N ALA y 123 " --> pdb=" O GLY y 119 " (cutoff:3.500A) Processing helix chain 'y' and resid 136 through 168 removed outlier: 3.538A pdb=" N TRP y 141 " --> pdb=" O GLY y 137 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY y 166 " --> pdb=" O TYR y 162 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS y 167 " --> pdb=" O VAL y 163 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL y 168 " --> pdb=" O LEU y 164 " (cutoff:3.500A) Processing helix chain 'y' and resid 170 through 187 removed outlier: 3.521A pdb=" N ALA y 174 " --> pdb=" O GLU y 170 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL y 186 " --> pdb=" O TRP y 182 " (cutoff:3.500A) Processing helix chain 'y' and resid 187 through 200 Processing helix chain 'y' and resid 208 through 213 Processing helix chain 'y' and resid 216 through 226 removed outlier: 3.520A pdb=" N ILE y 220 " --> pdb=" O ASN y 216 " (cutoff:3.500A) Processing helix chain 'y' and resid 250 through 272 removed outlier: 3.740A pdb=" N SER y 263 " --> pdb=" O TRP y 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 34 removed outlier: 3.813A pdb=" N THR D 34 " --> pdb=" O SER D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 383 removed outlier: 3.665A pdb=" N ARG D 378 " --> pdb=" O ASP D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 388 Processing helix chain 'D' and resid 392 through 405 removed outlier: 3.711A pdb=" N GLU D 396 " --> pdb=" O SER D 392 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 34 removed outlier: 3.624A pdb=" N SER L 33 " --> pdb=" O VAL L 30 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU L 34 " --> pdb=" O GLN L 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 30 through 34' Processing helix chain 'L' and resid 73 through 82 removed outlier: 3.670A pdb=" N GLY L 79 " --> pdb=" O ALA L 75 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 88 removed outlier: 4.541A pdb=" N LEU L 88 " --> pdb=" O PRO L 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 148 removed outlier: 3.842A pdb=" N ALA L 142 " --> pdb=" O GLU L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 173 Processing sheet with id=AA1, first strand: chain 'f' and resid 76 through 79 removed outlier: 3.928A pdb=" N ALA f 208 " --> pdb=" O ILE f 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'f' and resid 246 through 248 removed outlier: 4.225A pdb=" N GLU f 256 " --> pdb=" O ARG f 248 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 4 through 9 removed outlier: 3.599A pdb=" N VAL F 4 " --> pdb=" O LEU F 26 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LEU F 22 " --> pdb=" O GLY F 8 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 76 through 79 removed outlier: 3.876A pdb=" N LEU F 79 " --> pdb=" O LEU F 151 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA F 208 " --> pdb=" O ILE F 200 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA F 202 " --> pdb=" O LEU F 206 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU F 206 " --> pdb=" O ALA F 202 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 246 through 248 removed outlier: 3.818A pdb=" N ARG F 248 " --> pdb=" O GLU F 256 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER F 228 " --> pdb=" O ASP F 279 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP F 279 " --> pdb=" O SER F 228 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 50 through 51 removed outlier: 6.285A pdb=" N GLY D 50 " --> pdb=" O VAL D 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 56 through 58 removed outlier: 6.748A pdb=" N PHE D 56 " --> pdb=" O LEU D 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 94 through 96 removed outlier: 6.955A pdb=" N LEU D 95 " --> pdb=" O ARG D 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 133 through 134 removed outlier: 6.307A pdb=" N VAL D 134 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE D 184 " --> pdb=" O HIS D 207 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N MET D 209 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE D 186 " --> pdb=" O MET D 209 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA D 229 " --> pdb=" O GLY D 205 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N HIS D 207 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N MET D 231 " --> pdb=" O HIS D 207 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N MET D 209 " --> pdb=" O MET D 231 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TYR D 228 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ASN D 254 " --> pdb=" O TYR D 228 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU D 230 " --> pdb=" O ASN D 254 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA D 287 " --> pdb=" O TYR D 249 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE D 310 " --> pdb=" O ALA D 287 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N PHE D 289 " --> pdb=" O ILE D 310 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU D 312 " --> pdb=" O PHE D 289 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N TYR D 291 " --> pdb=" O LEU D 312 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU D 308 " --> pdb=" O GLN D 332 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LYS D 334 " --> pdb=" O LEU D 308 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE D 310 " --> pdb=" O LYS D 334 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 146 through 148 removed outlier: 3.837A pdb=" N ARG D 178 " --> pdb=" O ILE D 147 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL D 177 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE D 199 " --> pdb=" O ARG D 222 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 170 through 173 removed outlier: 6.013A pdb=" N ASN D 192 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE D 217 " --> pdb=" O ASN D 192 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU D 194 " --> pdb=" O ILE D 217 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 242 through 244 removed outlier: 6.278A pdb=" N SER D 243 " --> pdb=" O SER D 267 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 69 through 71 Processing sheet with id=AB5, first strand: chain 'L' and resid 134 through 136 597 hydrogen bonds defined for protein. 1704 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.08 Time building geometry restraints manager: 1.36 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: 3290 1.33 - 1.45: 2380 1.45 - 1.57: 7358 1.57 - 1.69: 1 1.69 - 1.81: 75 Bond restraints: 13104 Sorted by residual: bond pdb=" C ILE y 51 " pdb=" N PRO y 52 " ideal model delta sigma weight residual 1.337 1.377 -0.040 1.24e-02 6.50e+03 1.03e+01 bond pdb=" N ASN D 361 " pdb=" CA ASN D 361 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.31e-02 5.83e+03 6.69e+00 bond pdb=" N CYS L 48 " pdb=" CA CYS L 48 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.28e-02 6.10e+03 5.95e+00 bond pdb=" N MET L 129 " pdb=" CA MET L 129 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.68e+00 bond pdb=" N MET L 50 " pdb=" CA MET L 50 " ideal model delta sigma weight residual 1.453 1.484 -0.031 1.31e-02 5.83e+03 5.45e+00 ... (remaining 13099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.94: 17617 3.94 - 7.88: 140 7.88 - 11.82: 18 11.82 - 15.75: 2 15.75 - 19.69: 1 Bond angle restraints: 17778 Sorted by residual: angle pdb=" C ASP D 359 " pdb=" CA ASP D 359 " pdb=" CB ASP D 359 " ideal model delta sigma weight residual 112.09 102.56 9.53 1.43e+00 4.89e-01 4.45e+01 angle pdb=" CA GLU y 201 " pdb=" CB GLU y 201 " pdb=" CG GLU y 201 " ideal model delta sigma weight residual 114.10 125.95 -11.85 2.00e+00 2.50e-01 3.51e+01 angle pdb=" N GLU L 76 " pdb=" CA GLU L 76 " pdb=" C GLU L 76 " ideal model delta sigma weight residual 113.23 106.20 7.03 1.24e+00 6.50e-01 3.21e+01 angle pdb=" CA LEU D 89 " pdb=" CB LEU D 89 " pdb=" CG LEU D 89 " ideal model delta sigma weight residual 116.30 135.99 -19.69 3.50e+00 8.16e-02 3.17e+01 angle pdb=" CA ARG L 66 " pdb=" CB ARG L 66 " pdb=" CG ARG L 66 " ideal model delta sigma weight residual 114.10 123.31 -9.21 2.00e+00 2.50e-01 2.12e+01 ... (remaining 17773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.56: 6661 16.56 - 33.11: 814 33.11 - 49.67: 228 49.67 - 66.22: 46 66.22 - 82.78: 9 Dihedral angle restraints: 7758 sinusoidal: 3048 harmonic: 4710 Sorted by residual: dihedral pdb=" CA ASP D 182 " pdb=" C ASP D 182 " pdb=" N GLY D 183 " pdb=" CA GLY D 183 " ideal model delta harmonic sigma weight residual 180.00 -154.24 -25.76 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA GLN f 108 " pdb=" C GLN f 108 " pdb=" N VAL f 109 " pdb=" CA VAL f 109 " ideal model delta harmonic sigma weight residual -180.00 -158.71 -21.29 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" C ASP D 182 " pdb=" N ASP D 182 " pdb=" CA ASP D 182 " pdb=" CB ASP D 182 " ideal model delta harmonic sigma weight residual -122.60 -133.00 10.40 0 2.50e+00 1.60e-01 1.73e+01 ... (remaining 7755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1826 0.084 - 0.168: 199 0.168 - 0.251: 10 0.251 - 0.335: 3 0.335 - 0.419: 1 Chirality restraints: 2039 Sorted by residual: chirality pdb=" CB ILE D 72 " pdb=" CA ILE D 72 " pdb=" CG1 ILE D 72 " pdb=" CG2 ILE D 72 " both_signs ideal model delta sigma weight residual False 2.64 3.06 -0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" CA GLU y 201 " pdb=" N GLU y 201 " pdb=" C GLU y 201 " pdb=" CB GLU y 201 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CB ILE D 147 " pdb=" CA ILE D 147 " pdb=" CG1 ILE D 147 " pdb=" CG2 ILE D 147 " both_signs ideal model delta sigma weight residual False 2.64 2.92 -0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 2036 not shown) Planarity restraints: 2282 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 109 " -0.019 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" C VAL D 109 " 0.066 2.00e-02 2.50e+03 pdb=" O VAL D 109 " -0.025 2.00e-02 2.50e+03 pdb=" N PHE D 110 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 226 " -0.016 2.00e-02 2.50e+03 3.13e-02 9.78e+00 pdb=" C THR D 226 " 0.054 2.00e-02 2.50e+03 pdb=" O THR D 226 " -0.021 2.00e-02 2.50e+03 pdb=" N GLY D 227 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET y 66 " -0.047 5.00e-02 4.00e+02 7.09e-02 8.05e+00 pdb=" N PRO y 67 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO y 67 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO y 67 " -0.040 5.00e-02 4.00e+02 ... (remaining 2279 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 42 2.45 - 3.06: 7383 3.06 - 3.68: 19170 3.68 - 4.29: 27835 4.29 - 4.90: 47590 Nonbonded interactions: 102020 Sorted by model distance: nonbonded pdb=" OE1 GLU L 76 " pdb="ZN ZN L 201 " model vdw 1.840 2.230 nonbonded pdb=" OD1 ASP D 359 " pdb="MG MG D 501 " model vdw 1.887 2.170 nonbonded pdb=" OE2 GLU L 76 " pdb="ZN ZN L 201 " model vdw 2.010 2.230 nonbonded pdb=" OD1 ASN D 361 " pdb="MG MG D 501 " model vdw 2.015 2.170 nonbonded pdb=" SD MET D 231 " pdb="CU CU D 502 " model vdw 2.038 2.600 ... (remaining 102015 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 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'f' } ncs_group { reference = (chain 'Y' and (resid 2 through 43 or resid 51 through 227 or resid 245 through \ 275)) selection = chain 'y' } 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: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.430 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 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 : 0.004 0.053 13107 Z= 0.220 Angle : 0.903 19.693 17778 Z= 0.485 Chirality : 0.051 0.419 2039 Planarity : 0.006 0.071 2282 Dihedral : 15.839 82.777 4752 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.00 % Favored : 93.70 % Rotamer: Outliers : 0.22 % Allowed : 20.62 % Favored : 79.15 % Cbeta Deviations : 0.07 % 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 are not related in a simple way. whole: -2.57 (0.18), residues: 1650 helix: -0.97 (0.16), residues: 703 sheet: -1.80 (0.34), residues: 207 loop : -2.35 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG L 87 TYR 0.012 0.001 TYR D 204 PHE 0.021 0.001 PHE y 146 TRP 0.014 0.001 TRP y 211 HIS 0.006 0.001 HIS F 37 Details of bonding type rmsd covalent geometry : bond 0.00429 (13104) covalent geometry : angle 0.90345 (17778) hydrogen bonds : bond 0.15885 ( 597) hydrogen bonds : angle 6.03290 ( 1704) metal coordination : bond 0.03290 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 134 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: F 16 MET cc_start: 0.8610 (pmm) cc_final: 0.8207 (pmm) REVERT: D 89 LEU cc_start: 0.8828 (tt) cc_final: 0.8448 (mt) REVERT: D 390 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7750 (mmm) REVERT: L 171 GLN cc_start: 0.8464 (tm-30) cc_final: 0.7832 (tm-30) outliers start: 3 outliers final: 2 residues processed: 135 average time/residue: 0.1141 time to fit residues: 21.7935 Evaluate side-chains 129 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 126 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain L residue 63 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 0.3980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 11 GLN f 261 ASN D 75 GLN D 160 ASN D 163 HIS L 96 HIS L 172 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.096715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.063817 restraints weight = 26852.710| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.11 r_work: 0.2837 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13107 Z= 0.122 Angle : 0.522 9.603 17778 Z= 0.268 Chirality : 0.041 0.200 2039 Planarity : 0.004 0.055 2282 Dihedral : 4.614 44.014 1815 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.18 % Favored : 95.52 % Rotamer: Outliers : 1.26 % Allowed : 19.81 % Favored : 78.93 % 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 are not related in a simple way. whole: -0.99 (0.20), residues: 1650 helix: 0.94 (0.19), residues: 702 sheet: -1.71 (0.35), residues: 211 loop : -1.95 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG f 224 TYR 0.012 0.001 TYR L 118 PHE 0.018 0.001 PHE y 120 TRP 0.009 0.001 TRP y 211 HIS 0.006 0.001 HIS L 110 Details of bonding type rmsd covalent geometry : bond 0.00278 (13104) covalent geometry : angle 0.52236 (17778) hydrogen bonds : bond 0.03729 ( 597) hydrogen bonds : angle 4.03817 ( 1704) metal coordination : bond 0.00199 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: f 224 ARG cc_start: 0.8686 (ttp-110) cc_final: 0.8462 (ttp80) REVERT: Y 82 ASP cc_start: 0.8868 (t70) cc_final: 0.8520 (t0) REVERT: y 201 GLU cc_start: 0.8606 (pm20) cc_final: 0.8314 (pm20) REVERT: D 426 LYS cc_start: 0.9122 (mtmm) cc_final: 0.8710 (mmtm) REVERT: L 43 ASP cc_start: 0.8187 (m-30) cc_final: 0.7500 (m-30) REVERT: L 52 ILE cc_start: 0.9042 (mt) cc_final: 0.8818 (mm) REVERT: L 100 ARG cc_start: 0.9004 (mtm110) cc_final: 0.8799 (mtm110) REVERT: L 171 GLN cc_start: 0.8108 (tm-30) cc_final: 0.7560 (tm-30) outliers start: 17 outliers final: 11 residues processed: 142 average time/residue: 0.1166 time to fit residues: 23.5067 Evaluate side-chains 131 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain Y residue 146 PHE Chi-restraints excluded: chain Y residue 229 PHE Chi-restraints excluded: chain y residue 129 LEU Chi-restraints excluded: chain y residue 164 LEU Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 120 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 48 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 53 optimal weight: 20.0000 chunk 57 optimal weight: 7.9990 chunk 128 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 157 optimal weight: 20.0000 chunk 77 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.095274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.061024 restraints weight = 27876.847| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 3.13 r_work: 0.2734 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13107 Z= 0.226 Angle : 0.594 8.978 17778 Z= 0.302 Chirality : 0.043 0.185 2039 Planarity : 0.004 0.048 2282 Dihedral : 4.522 28.381 1809 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.97 % Favored : 94.73 % Rotamer: Outliers : 3.04 % Allowed : 19.58 % Favored : 77.37 % 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 are not related in a simple way. whole: -0.63 (0.21), residues: 1650 helix: 1.39 (0.20), residues: 715 sheet: -2.04 (0.35), residues: 208 loop : -1.79 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 66 TYR 0.016 0.002 TYR D 204 PHE 0.028 0.002 PHE y 120 TRP 0.008 0.001 TRP D 352 HIS 0.005 0.001 HIS f 37 Details of bonding type rmsd covalent geometry : bond 0.00533 (13104) covalent geometry : angle 0.59398 (17778) hydrogen bonds : bond 0.04821 ( 597) hydrogen bonds : angle 4.18347 ( 1704) metal coordination : bond 0.00529 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 119 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: f 16 MET cc_start: 0.8771 (pmm) cc_final: 0.8507 (pmm) REVERT: f 224 ARG cc_start: 0.8728 (ttp-110) cc_final: 0.8414 (ttp80) REVERT: F 57 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7336 (mp0) REVERT: Y 138 MET cc_start: 0.7376 (tmm) cc_final: 0.7172 (tmm) REVERT: Y 207 GLU cc_start: 0.6026 (tp30) cc_final: 0.5745 (tp30) REVERT: D 426 LYS cc_start: 0.9120 (mtmm) cc_final: 0.8692 (mmtm) REVERT: L 43 ASP cc_start: 0.8024 (m-30) cc_final: 0.7409 (m-30) REVERT: L 100 ARG cc_start: 0.8875 (mtm180) cc_final: 0.8567 (mtm110) REVERT: L 171 GLN cc_start: 0.8216 (tm-30) cc_final: 0.7256 (tm-30) outliers start: 41 outliers final: 25 residues processed: 152 average time/residue: 0.1290 time to fit residues: 27.9270 Evaluate side-chains 145 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 126 VAL Chi-restraints excluded: chain f residue 128 THR Chi-restraints excluded: chain f residue 160 ASP Chi-restraints excluded: chain f residue 187 VAL Chi-restraints excluded: chain f residue 221 LEU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain Y residue 112 LEU Chi-restraints excluded: chain Y residue 229 PHE Chi-restraints excluded: chain y residue 138 MET Chi-restraints excluded: chain y residue 164 LEU Chi-restraints excluded: chain y residue 274 ARG Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 170 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 144 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 128 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 20 optimal weight: 0.0470 chunk 28 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.096621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.063843 restraints weight = 27010.838| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.11 r_work: 0.2835 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13107 Z= 0.092 Angle : 0.492 10.689 17778 Z= 0.250 Chirality : 0.040 0.133 2039 Planarity : 0.003 0.044 2282 Dihedral : 4.126 26.228 1809 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.24 % Favored : 95.45 % Rotamer: Outliers : 2.37 % Allowed : 20.40 % Favored : 77.23 % 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 are not related in a simple way. whole: -0.06 (0.21), residues: 1650 helix: 1.98 (0.20), residues: 704 sheet: -1.61 (0.35), residues: 221 loop : -1.62 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 66 TYR 0.010 0.001 TYR f 291 PHE 0.015 0.001 PHE y 120 TRP 0.006 0.001 TRP Y 253 HIS 0.002 0.000 HIS D 163 Details of bonding type rmsd covalent geometry : bond 0.00204 (13104) covalent geometry : angle 0.49153 (17778) hydrogen bonds : bond 0.03133 ( 597) hydrogen bonds : angle 3.77319 ( 1704) metal coordination : bond 0.00125 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.544 Fit side-chains REVERT: f 16 MET cc_start: 0.8768 (pmm) cc_final: 0.8474 (pmm) REVERT: f 224 ARG cc_start: 0.8690 (ttp-110) cc_final: 0.8385 (ttp80) REVERT: Y 82 ASP cc_start: 0.8960 (t0) cc_final: 0.8743 (t0) REVERT: Y 207 GLU cc_start: 0.5887 (tp30) cc_final: 0.5547 (tp30) REVERT: y 216 ASN cc_start: 0.8882 (t0) cc_final: 0.8461 (t0) REVERT: D 426 LYS cc_start: 0.9095 (mtmm) cc_final: 0.8688 (mmtm) REVERT: L 43 ASP cc_start: 0.7074 (m-30) cc_final: 0.6765 (m-30) REVERT: L 65 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.8883 (ptmm) REVERT: L 100 ARG cc_start: 0.8938 (mtm180) cc_final: 0.8706 (mtm110) REVERT: L 171 GLN cc_start: 0.8216 (tm-30) cc_final: 0.7314 (tm-30) outliers start: 32 outliers final: 21 residues processed: 152 average time/residue: 0.1235 time to fit residues: 27.2612 Evaluate side-chains 143 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 184 CYS Chi-restraints excluded: chain f residue 187 VAL Chi-restraints excluded: chain f residue 221 LEU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain Y residue 38 LEU Chi-restraints excluded: chain Y residue 146 PHE Chi-restraints excluded: chain Y residue 229 PHE Chi-restraints excluded: chain y residue 138 MET Chi-restraints excluded: chain y residue 164 LEU Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 153 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 40 optimal weight: 7.9990 chunk 104 optimal weight: 0.7980 chunk 116 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 137 optimal weight: 0.6980 chunk 27 optimal weight: 30.0000 chunk 68 optimal weight: 0.8980 chunk 159 optimal weight: 9.9990 overall best weight: 1.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.094919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.061751 restraints weight = 27332.255| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.14 r_work: 0.2791 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13107 Z= 0.139 Angle : 0.526 10.010 17778 Z= 0.266 Chirality : 0.041 0.195 2039 Planarity : 0.003 0.043 2282 Dihedral : 4.135 26.351 1809 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.79 % Favored : 94.91 % Rotamer: Outliers : 3.34 % Allowed : 20.18 % Favored : 76.48 % 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 are not related in a simple way. whole: 0.09 (0.21), residues: 1650 helix: 2.13 (0.20), residues: 706 sheet: -1.61 (0.34), residues: 226 loop : -1.55 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 66 TYR 0.010 0.001 TYR f 86 PHE 0.013 0.001 PHE Y 157 TRP 0.006 0.001 TRP y 211 HIS 0.002 0.001 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00327 (13104) covalent geometry : angle 0.52576 (17778) hydrogen bonds : bond 0.03724 ( 597) hydrogen bonds : angle 3.83437 ( 1704) metal coordination : bond 0.00390 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 119 time to evaluate : 0.494 Fit side-chains REVERT: f 16 MET cc_start: 0.8745 (pmm) cc_final: 0.8494 (pmm) REVERT: f 224 ARG cc_start: 0.8723 (ttp-110) cc_final: 0.8383 (ttp80) REVERT: f 288 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8255 (mp0) REVERT: F 57 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: F 224 ARG cc_start: 0.9006 (ttp-170) cc_final: 0.8368 (ttp-170) REVERT: Y 82 ASP cc_start: 0.8929 (t0) cc_final: 0.8679 (t0) REVERT: Y 207 GLU cc_start: 0.5909 (tp30) cc_final: 0.5586 (tp30) REVERT: L 65 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.8894 (ptmm) REVERT: L 171 GLN cc_start: 0.8269 (tm-30) cc_final: 0.7339 (tm-30) outliers start: 45 outliers final: 31 residues processed: 155 average time/residue: 0.1128 time to fit residues: 25.7704 Evaluate side-chains 152 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 118 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 84 THR Chi-restraints excluded: chain f residue 107 THR Chi-restraints excluded: chain f residue 126 VAL Chi-restraints excluded: chain f residue 128 THR Chi-restraints excluded: chain f residue 184 CYS Chi-restraints excluded: chain f residue 187 VAL Chi-restraints excluded: chain f residue 221 LEU Chi-restraints excluded: chain f residue 288 GLU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain Y residue 38 LEU Chi-restraints excluded: chain Y residue 146 PHE Chi-restraints excluded: chain Y residue 229 PHE Chi-restraints excluded: chain y residue 129 LEU Chi-restraints excluded: chain y residue 138 MET Chi-restraints excluded: chain y residue 164 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 170 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 163 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 23 optimal weight: 40.0000 chunk 147 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 196 ASN ** F 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.092286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.059138 restraints weight = 27436.864| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 3.11 r_work: 0.2753 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 13107 Z= 0.234 Angle : 0.594 10.566 17778 Z= 0.301 Chirality : 0.043 0.208 2039 Planarity : 0.004 0.043 2282 Dihedral : 4.413 26.974 1809 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.33 % Favored : 94.36 % Rotamer: Outliers : 3.71 % Allowed : 20.40 % Favored : 75.89 % 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 are not related in a simple way. whole: -0.03 (0.21), residues: 1650 helix: 2.04 (0.20), residues: 703 sheet: -1.92 (0.36), residues: 208 loop : -1.54 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 66 TYR 0.016 0.002 TYR D 204 PHE 0.016 0.001 PHE Y 143 TRP 0.008 0.001 TRP y 211 HIS 0.004 0.001 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00558 (13104) covalent geometry : angle 0.59417 (17778) hydrogen bonds : bond 0.04615 ( 597) hydrogen bonds : angle 4.08716 ( 1704) metal coordination : bond 0.00618 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 116 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: f 224 ARG cc_start: 0.8763 (ttp-110) cc_final: 0.8364 (ttp80) REVERT: f 288 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8247 (mp0) REVERT: F 57 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: Y 82 ASP cc_start: 0.8915 (t0) cc_final: 0.8661 (t0) REVERT: Y 207 GLU cc_start: 0.6096 (tp30) cc_final: 0.5770 (tp30) REVERT: L 65 LYS cc_start: 0.9362 (OUTLIER) cc_final: 0.8941 (ptmm) REVERT: L 161 GLN cc_start: 0.8609 (mm-40) cc_final: 0.8074 (mm-40) REVERT: L 171 GLN cc_start: 0.8255 (tm-30) cc_final: 0.7300 (tm-30) outliers start: 50 outliers final: 40 residues processed: 157 average time/residue: 0.1140 time to fit residues: 26.2158 Evaluate side-chains 157 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 114 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 84 THR Chi-restraints excluded: chain f residue 107 THR Chi-restraints excluded: chain f residue 126 VAL Chi-restraints excluded: chain f residue 128 THR Chi-restraints excluded: chain f residue 184 CYS Chi-restraints excluded: chain f residue 187 VAL Chi-restraints excluded: chain f residue 191 VAL Chi-restraints excluded: chain f residue 221 LEU Chi-restraints excluded: chain f residue 288 GLU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain Y residue 38 LEU Chi-restraints excluded: chain Y residue 112 LEU Chi-restraints excluded: chain Y residue 146 PHE Chi-restraints excluded: chain Y residue 229 PHE Chi-restraints excluded: chain y residue 129 LEU Chi-restraints excluded: chain y residue 138 MET Chi-restraints excluded: chain y residue 164 LEU Chi-restraints excluded: chain y residue 173 SER Chi-restraints excluded: chain y residue 226 LEU Chi-restraints excluded: chain y residue 274 ARG Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 170 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 150 optimal weight: 0.4980 chunk 122 optimal weight: 7.9990 chunk 23 optimal weight: 30.0000 chunk 147 optimal weight: 0.4980 chunk 131 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 153 optimal weight: 7.9990 chunk 140 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 196 ASN ** D 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.094961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.062183 restraints weight = 27022.445| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.10 r_work: 0.2800 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13107 Z= 0.109 Angle : 0.515 11.035 17778 Z= 0.261 Chirality : 0.040 0.170 2039 Planarity : 0.003 0.044 2282 Dihedral : 4.128 25.136 1809 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.42 % Favored : 95.27 % Rotamer: Outliers : 2.97 % Allowed : 20.77 % Favored : 76.26 % 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 are not related in a simple way. whole: 0.25 (0.21), residues: 1650 helix: 2.31 (0.20), residues: 705 sheet: -1.59 (0.35), residues: 226 loop : -1.50 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 66 TYR 0.009 0.001 TYR f 291 PHE 0.011 0.001 PHE Y 157 TRP 0.006 0.001 TRP y 211 HIS 0.003 0.001 HIS f 37 Details of bonding type rmsd covalent geometry : bond 0.00251 (13104) covalent geometry : angle 0.51486 (17778) hydrogen bonds : bond 0.03400 ( 597) hydrogen bonds : angle 3.80782 ( 1704) metal coordination : bond 0.00341 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 117 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: f 224 ARG cc_start: 0.8735 (ttp-110) cc_final: 0.8353 (ttp80) REVERT: f 288 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8263 (mp0) REVERT: F 57 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7283 (mp0) REVERT: Y 82 ASP cc_start: 0.8912 (t0) cc_final: 0.8678 (t0) REVERT: Y 207 GLU cc_start: 0.5954 (tp30) cc_final: 0.5602 (tp30) REVERT: L 155 ARG cc_start: 0.9049 (mmt90) cc_final: 0.8776 (mmm-85) REVERT: L 171 GLN cc_start: 0.8235 (tm-30) cc_final: 0.7352 (tm-30) outliers start: 40 outliers final: 30 residues processed: 149 average time/residue: 0.1023 time to fit residues: 22.6172 Evaluate side-chains 147 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 84 THR Chi-restraints excluded: chain f residue 107 THR Chi-restraints excluded: chain f residue 126 VAL Chi-restraints excluded: chain f residue 187 VAL Chi-restraints excluded: chain f residue 191 VAL Chi-restraints excluded: chain f residue 221 LEU Chi-restraints excluded: chain f residue 288 GLU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain Y residue 38 LEU Chi-restraints excluded: chain Y residue 146 PHE Chi-restraints excluded: chain Y residue 229 PHE Chi-restraints excluded: chain y residue 129 LEU Chi-restraints excluded: chain y residue 138 MET Chi-restraints excluded: chain y residue 164 LEU Chi-restraints excluded: chain y residue 213 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 170 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 27 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 157 optimal weight: 20.0000 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 196 ASN ** F 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.092329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.058500 restraints weight = 27438.354| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.19 r_work: 0.2750 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 13107 Z= 0.291 Angle : 0.651 13.355 17778 Z= 0.325 Chirality : 0.045 0.242 2039 Planarity : 0.004 0.050 2282 Dihedral : 4.491 27.545 1809 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.06 % Favored : 93.64 % Rotamer: Outliers : 3.26 % Allowed : 20.92 % Favored : 75.82 % 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 are not related in a simple way. whole: -0.04 (0.21), residues: 1650 helix: 2.03 (0.20), residues: 704 sheet: -1.92 (0.36), residues: 208 loop : -1.55 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG L 66 TYR 0.017 0.002 TYR D 204 PHE 0.017 0.002 PHE Y 143 TRP 0.009 0.001 TRP D 352 HIS 0.005 0.001 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00696 (13104) covalent geometry : angle 0.65074 (17778) hydrogen bonds : bond 0.04978 ( 597) hydrogen bonds : angle 4.17306 ( 1704) metal coordination : bond 0.00728 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 111 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: f 288 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8292 (mp0) REVERT: F 57 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7447 (mp0) REVERT: Y 82 ASP cc_start: 0.8928 (t0) cc_final: 0.8689 (t0) REVERT: Y 207 GLU cc_start: 0.6146 (tp30) cc_final: 0.5835 (tp30) REVERT: L 65 LYS cc_start: 0.9328 (ttmm) cc_final: 0.9002 (tmtt) REVERT: L 171 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7374 (tm-30) outliers start: 44 outliers final: 34 residues processed: 148 average time/residue: 0.0989 time to fit residues: 22.1719 Evaluate side-chains 145 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 84 THR Chi-restraints excluded: chain f residue 107 THR Chi-restraints excluded: chain f residue 126 VAL Chi-restraints excluded: chain f residue 128 THR Chi-restraints excluded: chain f residue 184 CYS Chi-restraints excluded: chain f residue 187 VAL Chi-restraints excluded: chain f residue 191 VAL Chi-restraints excluded: chain f residue 221 LEU Chi-restraints excluded: chain f residue 288 GLU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain Y residue 38 LEU Chi-restraints excluded: chain Y residue 229 PHE Chi-restraints excluded: chain y residue 21 LEU Chi-restraints excluded: chain y residue 129 LEU Chi-restraints excluded: chain y residue 138 MET Chi-restraints excluded: chain y residue 164 LEU Chi-restraints excluded: chain y residue 173 SER Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 170 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 162 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 27 optimal weight: 0.0060 chunk 54 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 196 ASN ** D 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 110 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.095512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.062574 restraints weight = 27021.444| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 3.13 r_work: 0.2812 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 13107 Z= 0.100 Angle : 0.525 11.530 17778 Z= 0.264 Chirality : 0.040 0.194 2039 Planarity : 0.003 0.050 2282 Dihedral : 4.133 25.889 1809 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.36 % Favored : 95.33 % Rotamer: Outliers : 2.60 % Allowed : 21.74 % Favored : 75.67 % 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 are not related in a simple way. whole: 0.36 (0.22), residues: 1650 helix: 2.45 (0.20), residues: 703 sheet: -1.59 (0.35), residues: 226 loop : -1.45 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG L 66 TYR 0.007 0.001 TYR f 291 PHE 0.011 0.001 PHE y 120 TRP 0.006 0.001 TRP Y 141 HIS 0.003 0.001 HIS D 163 Details of bonding type rmsd covalent geometry : bond 0.00225 (13104) covalent geometry : angle 0.52484 (17778) hydrogen bonds : bond 0.03245 ( 597) hydrogen bonds : angle 3.79112 ( 1704) metal coordination : bond 0.00185 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 288 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8276 (mp0) REVERT: F 57 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7275 (mp0) REVERT: Y 82 ASP cc_start: 0.8930 (t0) cc_final: 0.8698 (t0) REVERT: Y 207 GLU cc_start: 0.5974 (tp30) cc_final: 0.5666 (tp30) REVERT: L 155 ARG cc_start: 0.9076 (mmt90) cc_final: 0.8867 (mmm-85) REVERT: L 171 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7332 (tm-30) outliers start: 35 outliers final: 28 residues processed: 145 average time/residue: 0.1111 time to fit residues: 23.8697 Evaluate side-chains 144 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 84 THR Chi-restraints excluded: chain f residue 107 THR Chi-restraints excluded: chain f residue 126 VAL Chi-restraints excluded: chain f residue 187 VAL Chi-restraints excluded: chain f residue 221 LEU Chi-restraints excluded: chain f residue 288 GLU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain Y residue 38 LEU Chi-restraints excluded: chain Y residue 229 PHE Chi-restraints excluded: chain y residue 129 LEU Chi-restraints excluded: chain y residue 138 MET Chi-restraints excluded: chain y residue 164 LEU Chi-restraints excluded: chain y residue 173 SER Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 153 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 41 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 chunk 151 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 196 ASN ** F 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.091733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.057776 restraints weight = 27628.570| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 3.22 r_work: 0.2730 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 13107 Z= 0.335 Angle : 0.693 11.195 17778 Z= 0.347 Chirality : 0.047 0.222 2039 Planarity : 0.004 0.062 2282 Dihedral : 4.586 27.757 1809 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.24 % Favored : 93.45 % Rotamer: Outliers : 2.67 % Allowed : 21.44 % Favored : 75.89 % 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 are not related in a simple way. whole: -0.03 (0.21), residues: 1650 helix: 2.04 (0.20), residues: 702 sheet: -1.93 (0.36), residues: 208 loop : -1.52 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG L 66 TYR 0.019 0.002 TYR D 204 PHE 0.018 0.002 PHE Y 157 TRP 0.011 0.001 TRP D 352 HIS 0.005 0.001 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00797 (13104) covalent geometry : angle 0.69303 (17778) hydrogen bonds : bond 0.05322 ( 597) hydrogen bonds : angle 4.26795 ( 1704) metal coordination : bond 0.00860 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 288 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8280 (mp0) REVERT: F 57 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7502 (mp0) REVERT: Y 82 ASP cc_start: 0.8934 (t0) cc_final: 0.8689 (t0) REVERT: Y 207 GLU cc_start: 0.6163 (tp30) cc_final: 0.5859 (tp30) REVERT: L 65 LYS cc_start: 0.9334 (ttmm) cc_final: 0.8976 (tmtt) outliers start: 36 outliers final: 32 residues processed: 139 average time/residue: 0.1186 time to fit residues: 24.2371 Evaluate side-chains 141 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 84 THR Chi-restraints excluded: chain f residue 107 THR Chi-restraints excluded: chain f residue 126 VAL Chi-restraints excluded: chain f residue 160 ASP Chi-restraints excluded: chain f residue 184 CYS Chi-restraints excluded: chain f residue 187 VAL Chi-restraints excluded: chain f residue 191 VAL Chi-restraints excluded: chain f residue 288 GLU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain Y residue 38 LEU Chi-restraints excluded: chain Y residue 229 PHE Chi-restraints excluded: chain y residue 129 LEU Chi-restraints excluded: chain y residue 138 MET Chi-restraints excluded: chain y residue 164 LEU Chi-restraints excluded: chain y residue 173 SER Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 154 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 15 optimal weight: 0.0000 chunk 13 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 120 optimal weight: 7.9990 chunk 124 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 196 ASN ** D 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 110 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.095482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.062452 restraints weight = 26956.151| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.14 r_work: 0.2809 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 13107 Z= 0.100 Angle : 0.535 11.766 17778 Z= 0.270 Chirality : 0.040 0.188 2039 Planarity : 0.004 0.055 2282 Dihedral : 4.177 25.649 1809 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.42 % Favored : 95.27 % Rotamer: Outliers : 2.30 % Allowed : 22.18 % Favored : 75.52 % 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 are not related in a simple way. whole: 0.35 (0.22), residues: 1650 helix: 2.44 (0.20), residues: 703 sheet: -1.67 (0.34), residues: 232 loop : -1.42 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG L 66 TYR 0.007 0.001 TYR f 291 PHE 0.011 0.001 PHE y 120 TRP 0.006 0.001 TRP Y 5 HIS 0.004 0.001 HIS D 163 Details of bonding type rmsd covalent geometry : bond 0.00226 (13104) covalent geometry : angle 0.53518 (17778) hydrogen bonds : bond 0.03217 ( 597) hydrogen bonds : angle 3.78391 ( 1704) metal coordination : bond 0.00159 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2931.21 seconds wall clock time: 50 minutes 54.85 seconds (3054.85 seconds total)