Starting phenix.real_space_refine on Wed Jul 30 21:21:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7znq_14813/07_2025/7znq_14813.cif Found real_map, /net/cci-nas-00/data/ceres_data/7znq_14813/07_2025/7znq_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_14813/07_2025/7znq_14813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7znq_14813/07_2025/7znq_14813.map" model { file = "/net/cci-nas-00/data/ceres_data/7znq_14813/07_2025/7znq_14813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7znq_14813/07_2025/7znq_14813.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 9.30, per 1000 atoms: 0.72 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: 3.15 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.54 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: 3.98 Time building geometry restraints manager: 3.77 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: 1.200 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: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 38.230 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 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:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.760 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.014 0.001 TRP y 211 HIS 0.006 0.001 HIS F 37 PHE 0.021 0.001 PHE y 146 TYR 0.012 0.001 TYR D 204 ARG 0.014 0.000 ARG L 87 Details of bonding type rmsd hydrogen bonds : bond 0.15885 ( 597) hydrogen bonds : angle 6.03290 ( 1704) metal coordination : bond 0.03290 ( 3) covalent geometry : bond 0.00429 (13104) covalent geometry : angle 0.90345 (17778) *********************** 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 : 1.577 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: 0.3052 time to fit residues: 59.3937 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 : 2.178 ------------------------------------------------------------------------------- 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 138 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 68 optimal weight: 0.0570 chunk 42 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 overall best weight: 3.1704 ------------------------------------------------------------------------------- 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 77 GLN D 160 ASN D 163 HIS L 96 HIS L 172 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.093739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.060538 restraints weight = 27003.663| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.09 r_work: 0.2784 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13107 Z= 0.215 Angle : 0.594 9.575 17778 Z= 0.304 Chirality : 0.043 0.190 2039 Planarity : 0.004 0.056 2282 Dihedral : 4.862 48.326 1815 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.91 % Favored : 94.79 % Rotamer: Outliers : 2.45 % Allowed : 19.36 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.20), residues: 1650 helix: 0.84 (0.19), residues: 709 sheet: -1.73 (0.37), residues: 194 loop : -2.06 (0.20), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP y 211 HIS 0.008 0.001 HIS L 110 PHE 0.021 0.002 PHE y 120 TYR 0.015 0.002 TYR D 204 ARG 0.005 0.000 ARG L 155 Details of bonding type rmsd hydrogen bonds : bond 0.04697 ( 597) hydrogen bonds : angle 4.19363 ( 1704) metal coordination : bond 0.00265 ( 3) covalent geometry : bond 0.00505 (13104) covalent geometry : angle 0.59380 (17778) *********************** 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 155 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 1.617 Fit side-chains revert: symmetry clash REVERT: Y 82 ASP cc_start: 0.8904 (t70) cc_final: 0.8565 (t0) REVERT: Y 138 MET cc_start: 0.7436 (tmm) cc_final: 0.7137 (tmm) REVERT: Y 207 GLU cc_start: 0.5980 (tp30) cc_final: 0.5685 (tp30) REVERT: y 201 GLU cc_start: 0.8635 (pm20) cc_final: 0.8318 (pm20) REVERT: D 426 LYS cc_start: 0.9127 (mtmm) cc_final: 0.8707 (mmtm) REVERT: L 43 ASP cc_start: 0.8273 (m-30) cc_final: 0.7953 (m-30) outliers start: 33 outliers final: 22 residues processed: 149 average time/residue: 0.3221 time to fit residues: 67.4471 Evaluate side-chains 139 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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 32 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain Y residue 88 MET 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 D residue 120 ILE Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 141 ASP Chi-restraints excluded: chain L residue 153 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 61 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 30 optimal weight: 8.9990 chunk 161 optimal weight: 7.9990 chunk 143 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.095907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.061907 restraints weight = 27547.435| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.10 r_work: 0.2773 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13107 Z= 0.161 Angle : 0.539 8.956 17778 Z= 0.276 Chirality : 0.042 0.161 2039 Planarity : 0.004 0.047 2282 Dihedral : 4.405 27.402 1809 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.48 % Favored : 95.21 % Rotamer: Outliers : 2.74 % Allowed : 20.18 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.21), residues: 1650 helix: 1.46 (0.20), residues: 716 sheet: -1.98 (0.36), residues: 208 loop : -1.81 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP y 211 HIS 0.004 0.001 HIS f 37 PHE 0.024 0.001 PHE y 120 TYR 0.010 0.001 TYR D 204 ARG 0.008 0.000 ARG L 66 Details of bonding type rmsd hydrogen bonds : bond 0.04105 ( 597) hydrogen bonds : angle 4.02703 ( 1704) metal coordination : bond 0.00380 ( 3) covalent geometry : bond 0.00379 (13104) covalent geometry : angle 0.53871 (17778) *********************** 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 156 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 119 time to evaluate : 2.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: f 16 MET cc_start: 0.8789 (pmm) cc_final: 0.8471 (pmm) REVERT: f 224 ARG cc_start: 0.8914 (ttp80) cc_final: 0.8525 (ttp80) REVERT: F 57 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7303 (mp0) REVERT: Y 82 ASP cc_start: 0.8885 (t70) cc_final: 0.8576 (t0) REVERT: Y 138 MET cc_start: 0.7348 (tmm) cc_final: 0.7074 (tmm) REVERT: Y 207 GLU cc_start: 0.5957 (tp30) cc_final: 0.5660 (tp30) REVERT: Y 236 MET cc_start: 0.8129 (mpp) cc_final: 0.7772 (mpp) REVERT: D 426 LYS cc_start: 0.9107 (mtmm) cc_final: 0.8706 (mmtm) REVERT: L 70 LYS cc_start: 0.8043 (mtmt) cc_final: 0.7783 (mtmt) REVERT: L 110 HIS cc_start: 0.8296 (OUTLIER) cc_final: 0.8086 (m-70) REVERT: L 171 GLN cc_start: 0.8210 (tm-30) cc_final: 0.7258 (tm-30) outliers start: 37 outliers final: 24 residues processed: 147 average time/residue: 0.3971 time to fit residues: 86.0565 Evaluate side-chains 143 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 107 THR 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 38 LEU Chi-restraints excluded: chain Y residue 112 LEU Chi-restraints excluded: chain Y residue 229 PHE Chi-restraints excluded: chain y residue 21 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 295 PHE 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 110 HIS Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 169 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 5.9990 chunk 161 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 162 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 0.6980 chunk 23 optimal weight: 30.0000 chunk 73 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 overall best weight: 3.8986 ------------------------------------------------------------------------------- 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 = 0.3570 r_free = 0.3570 target = 0.094250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.060093 restraints weight = 27510.184| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 3.10 r_work: 0.2767 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 13107 Z= 0.251 Angle : 0.603 10.830 17778 Z= 0.306 Chirality : 0.044 0.222 2039 Planarity : 0.004 0.044 2282 Dihedral : 4.557 27.885 1809 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.45 % Favored : 94.24 % Rotamer: Outliers : 4.23 % Allowed : 19.21 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.21), residues: 1650 helix: 1.70 (0.20), residues: 705 sheet: -2.01 (0.36), residues: 208 loop : -1.69 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 352 HIS 0.004 0.001 HIS F 97 PHE 0.016 0.002 PHE Y 157 TYR 0.015 0.002 TYR D 204 ARG 0.008 0.000 ARG L 66 Details of bonding type rmsd hydrogen bonds : bond 0.04839 ( 597) hydrogen bonds : angle 4.15711 ( 1704) metal coordination : bond 0.00688 ( 3) covalent geometry : bond 0.00598 (13104) covalent geometry : angle 0.60317 (17778) *********************** 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 174 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 117 time to evaluate : 2.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: f 16 MET cc_start: 0.8747 (pmm) cc_final: 0.8530 (pmm) REVERT: f 224 ARG cc_start: 0.8907 (ttp80) cc_final: 0.8394 (ttp80) REVERT: F 57 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: Y 82 ASP cc_start: 0.8962 (t70) cc_final: 0.8678 (t0) REVERT: Y 138 MET cc_start: 0.7472 (tmm) cc_final: 0.7228 (tmm) REVERT: Y 207 GLU cc_start: 0.6078 (tp30) cc_final: 0.5758 (tp30) REVERT: D 218 ASP cc_start: 0.8570 (t0) cc_final: 0.8340 (t0) REVERT: D 426 LYS cc_start: 0.9131 (mtmm) cc_final: 0.8724 (mmtm) REVERT: L 70 LYS cc_start: 0.8166 (mtmt) cc_final: 0.7957 (mtmt) REVERT: L 161 GLN cc_start: 0.8609 (mm-40) cc_final: 0.8081 (mm-40) outliers start: 57 outliers final: 41 residues processed: 164 average time/residue: 0.3197 time to fit residues: 77.7374 Evaluate side-chains 157 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 115 time to evaluate : 2.441 ------------------------------------------------------------------------------- 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 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 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 130 SER 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 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 158 LEU Chi-restraints excluded: chain y residue 164 LEU 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 160 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 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 169 SER Chi-restraints excluded: chain L residue 170 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 71 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 155 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 144 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.092911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.059168 restraints weight = 27478.836| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 3.17 r_work: 0.2762 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13107 Z= 0.230 Angle : 0.584 9.800 17778 Z= 0.298 Chirality : 0.043 0.204 2039 Planarity : 0.004 0.043 2282 Dihedral : 4.526 26.847 1809 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.27 % Favored : 94.42 % Rotamer: Outliers : 4.15 % Allowed : 19.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.21), residues: 1650 helix: 1.83 (0.20), residues: 703 sheet: -1.99 (0.36), residues: 208 loop : -1.68 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 352 HIS 0.004 0.001 HIS F 97 PHE 0.015 0.001 PHE Y 143 TYR 0.013 0.001 TYR D 204 ARG 0.008 0.000 ARG L 66 Details of bonding type rmsd hydrogen bonds : bond 0.04587 ( 597) hydrogen bonds : angle 4.13228 ( 1704) metal coordination : bond 0.00707 ( 3) covalent geometry : bond 0.00549 (13104) covalent geometry : angle 0.58439 (17778) *********************** 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 172 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 116 time to evaluate : 1.954 Fit side-chains revert: symmetry clash REVERT: f 224 ARG cc_start: 0.8911 (ttp80) cc_final: 0.8403 (ttp80) REVERT: f 288 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8267 (mp0) REVERT: F 57 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8042 (mp0) REVERT: Y 82 ASP cc_start: 0.8937 (t70) cc_final: 0.8648 (t0) REVERT: Y 207 GLU cc_start: 0.6110 (tp30) cc_final: 0.5803 (tp30) REVERT: D 218 ASP cc_start: 0.8663 (t0) cc_final: 0.8432 (t0) REVERT: L 70 LYS cc_start: 0.8206 (mtmt) cc_final: 0.7980 (mtmt) REVERT: L 100 ARG cc_start: 0.8873 (mtm110) cc_final: 0.8630 (mtm110) outliers start: 56 outliers final: 43 residues processed: 164 average time/residue: 0.3082 time to fit residues: 75.0822 Evaluate side-chains 159 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 114 time to evaluate : 2.405 ------------------------------------------------------------------------------- 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 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 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 26 LEU Chi-restraints excluded: chain Y residue 38 LEU Chi-restraints excluded: chain Y residue 86 THR 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 158 LEU Chi-restraints excluded: chain y residue 164 LEU Chi-restraints excluded: chain y residue 173 SER 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 160 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 389 LEU 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 169 SER 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 105 optimal weight: 10.0000 chunk 157 optimal weight: 20.0000 chunk 31 optimal weight: 0.0470 chunk 162 optimal weight: 8.9990 chunk 64 optimal weight: 0.0670 chunk 141 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 0.0970 chunk 91 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.095066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.062334 restraints weight = 27234.787| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 3.12 r_work: 0.2803 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 13107 Z= 0.095 Angle : 0.503 10.680 17778 Z= 0.256 Chirality : 0.040 0.162 2039 Planarity : 0.003 0.041 2282 Dihedral : 4.185 25.037 1809 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.73 % Favored : 94.97 % Rotamer: Outliers : 3.19 % Allowed : 21.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.21), residues: 1650 helix: 2.26 (0.20), residues: 703 sheet: -1.62 (0.34), residues: 226 loop : -1.59 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Y 253 HIS 0.003 0.000 HIS D 163 PHE 0.012 0.001 PHE Y 157 TYR 0.008 0.001 TYR L 118 ARG 0.010 0.000 ARG L 66 Details of bonding type rmsd hydrogen bonds : bond 0.03273 ( 597) hydrogen bonds : angle 3.79164 ( 1704) metal coordination : bond 0.00256 ( 3) covalent geometry : bond 0.00211 (13104) covalent geometry : angle 0.50321 (17778) *********************** 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 161 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 118 time to evaluate : 1.446 Fit side-chains revert: symmetry clash REVERT: f 38 ASN cc_start: 0.8647 (m-40) cc_final: 0.8422 (m110) REVERT: f 288 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8244 (mp0) REVERT: F 57 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: F 160 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7669 (t0) REVERT: Y 82 ASP cc_start: 0.8883 (t70) cc_final: 0.8616 (t0) REVERT: Y 207 GLU cc_start: 0.5940 (tp30) cc_final: 0.5614 (tp30) REVERT: L 43 ASP cc_start: 0.7930 (m-30) cc_final: 0.7623 (m-30) REVERT: L 65 LYS cc_start: 0.9367 (OUTLIER) cc_final: 0.8991 (tmtt) REVERT: L 70 LYS cc_start: 0.8027 (mtmt) cc_final: 0.7805 (mtmt) REVERT: L 100 ARG cc_start: 0.8934 (mtm110) cc_final: 0.8698 (mtm110) outliers start: 43 outliers final: 25 residues processed: 152 average time/residue: 0.2576 time to fit residues: 57.0681 Evaluate side-chains 142 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 84 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 57 GLU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain Y residue 38 LEU Chi-restraints excluded: chain Y residue 86 THR 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 173 SER 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 350 ASN 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 145 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 153 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 141 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.093533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.060589 restraints weight = 27057.150| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 3.11 r_work: 0.2764 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13107 Z= 0.155 Angle : 0.537 11.030 17778 Z= 0.272 Chirality : 0.042 0.231 2039 Planarity : 0.003 0.042 2282 Dihedral : 4.196 25.844 1809 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.27 % Favored : 94.42 % Rotamer: Outliers : 3.64 % Allowed : 20.92 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.21), residues: 1650 helix: 2.27 (0.20), residues: 706 sheet: -1.58 (0.38), residues: 194 loop : -1.55 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP y 211 HIS 0.003 0.001 HIS F 97 PHE 0.013 0.001 PHE Y 157 TYR 0.011 0.001 TYR D 204 ARG 0.011 0.000 ARG L 66 Details of bonding type rmsd hydrogen bonds : bond 0.03875 ( 597) hydrogen bonds : angle 3.87139 ( 1704) metal coordination : bond 0.00476 ( 3) covalent geometry : bond 0.00368 (13104) covalent geometry : angle 0.53732 (17778) *********************** 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 161 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 112 time to evaluate : 1.371 Fit side-chains revert: symmetry clash REVERT: f 288 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8240 (mp0) REVERT: F 57 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: Y 82 ASP cc_start: 0.8887 (t70) cc_final: 0.8626 (t0) REVERT: Y 207 GLU cc_start: 0.5964 (tp30) cc_final: 0.5645 (tp30) REVERT: L 65 LYS cc_start: 0.9393 (OUTLIER) cc_final: 0.9033 (tmtt) REVERT: L 70 LYS cc_start: 0.8064 (mtmt) cc_final: 0.7821 (mtmt) REVERT: L 100 ARG cc_start: 0.8906 (mtm110) cc_final: 0.8669 (mtm110) REVERT: L 148 MET cc_start: 0.9372 (pmm) cc_final: 0.9100 (pmm) REVERT: L 155 ARG cc_start: 0.8857 (mmm-85) cc_final: 0.8629 (mmm-85) outliers start: 49 outliers final: 37 residues processed: 154 average time/residue: 0.2413 time to fit residues: 55.3413 Evaluate side-chains 151 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 111 time to evaluate : 1.409 ------------------------------------------------------------------------------- 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 130 SER 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 86 THR 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 173 SER 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 313 THR Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain L residue 52 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 133 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 147 optimal weight: 0.7980 chunk 156 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 112 optimal weight: 0.9980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.094736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.061748 restraints weight = 27248.814| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.14 r_work: 0.2793 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13107 Z= 0.115 Angle : 0.517 11.312 17778 Z= 0.261 Chirality : 0.041 0.225 2039 Planarity : 0.003 0.043 2282 Dihedral : 4.084 25.087 1809 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.67 % Favored : 95.03 % Rotamer: Outliers : 3.19 % Allowed : 21.36 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.22), residues: 1650 helix: 2.39 (0.20), residues: 705 sheet: -1.55 (0.35), residues: 226 loop : -1.48 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP Y 253 HIS 0.003 0.001 HIS f 37 PHE 0.012 0.001 PHE Y 157 TYR 0.008 0.001 TYR F 13 ARG 0.012 0.000 ARG L 66 Details of bonding type rmsd hydrogen bonds : bond 0.03426 ( 597) hydrogen bonds : angle 3.74877 ( 1704) metal coordination : bond 0.00323 ( 3) covalent geometry : bond 0.00270 (13104) covalent geometry : angle 0.51698 (17778) *********************** 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 154 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 111 time to evaluate : 1.397 Fit side-chains revert: symmetry clash REVERT: f 232 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7068 (tp30) REVERT: f 288 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8242 (mp0) REVERT: F 57 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: Y 82 ASP cc_start: 0.8863 (t70) cc_final: 0.8623 (t0) REVERT: Y 207 GLU cc_start: 0.5928 (tp30) cc_final: 0.5604 (tp30) REVERT: L 65 LYS cc_start: 0.9412 (OUTLIER) cc_final: 0.9041 (tmtt) REVERT: L 70 LYS cc_start: 0.8004 (mtmt) cc_final: 0.7775 (mtmt) REVERT: L 100 ARG cc_start: 0.8947 (mtm110) cc_final: 0.8715 (mtm110) outliers start: 43 outliers final: 31 residues processed: 146 average time/residue: 0.2259 time to fit residues: 49.3618 Evaluate side-chains 147 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain f residue 84 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 232 GLU 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 86 THR 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 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 295 PHE Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain L residue 52 ILE 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 154 LEU 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 161 optimal weight: 10.0000 chunk 148 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 54 optimal weight: 50.0000 chunk 48 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 196 ASN ** D 160 ASN ** 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 = 0.3590 r_free = 0.3590 target = 0.093239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.059554 restraints weight = 27341.703| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.17 r_work: 0.2773 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13107 Z= 0.222 Angle : 0.603 13.846 17778 Z= 0.301 Chirality : 0.043 0.233 2039 Planarity : 0.004 0.055 2282 Dihedral : 4.291 26.127 1809 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.82 % Favored : 93.88 % Rotamer: Outliers : 3.26 % Allowed : 21.36 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.22), residues: 1650 helix: 2.24 (0.20), residues: 707 sheet: -1.87 (0.36), residues: 208 loop : -1.46 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 352 HIS 0.003 0.001 HIS F 97 PHE 0.015 0.001 PHE Y 157 TYR 0.014 0.001 TYR D 204 ARG 0.013 0.000 ARG L 66 Details of bonding type rmsd hydrogen bonds : bond 0.04446 ( 597) hydrogen bonds : angle 4.01125 ( 1704) metal coordination : bond 0.00653 ( 3) covalent geometry : bond 0.00528 (13104) covalent geometry : angle 0.60274 (17778) *********************** 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 155 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 111 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: f 38 ASN cc_start: 0.8749 (m-40) cc_final: 0.8502 (m110) REVERT: f 288 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8262 (mp0) REVERT: F 57 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: Y 82 ASP cc_start: 0.8929 (t70) cc_final: 0.8652 (t0) REVERT: Y 207 GLU cc_start: 0.6016 (tp30) cc_final: 0.5693 (tp30) REVERT: L 65 LYS cc_start: 0.9432 (OUTLIER) cc_final: 0.9084 (tmtt) REVERT: L 70 LYS cc_start: 0.8154 (mtmt) cc_final: 0.7890 (mtmt) REVERT: L 100 ARG cc_start: 0.8898 (mtm110) cc_final: 0.8672 (mtm110) REVERT: L 155 ARG cc_start: 0.8908 (mmm-85) cc_final: 0.8697 (mmm-85) outliers start: 44 outliers final: 40 residues processed: 148 average time/residue: 0.2360 time to fit residues: 52.2997 Evaluate side-chains 152 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 109 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 72 VAL 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 232 GLU 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 201 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 86 THR 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 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 295 PHE Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 417 HIS Chi-restraints excluded: chain L residue 52 ILE 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 154 LEU Chi-restraints excluded: chain L residue 170 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 104 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 140 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 151 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.094616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.061004 restraints weight = 27175.625| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.17 r_work: 0.2831 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13107 Z= 0.144 Angle : 0.564 11.914 17778 Z= 0.282 Chirality : 0.042 0.211 2039 Planarity : 0.004 0.059 2282 Dihedral : 4.207 25.179 1809 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.79 % Favored : 94.91 % Rotamer: Outliers : 3.12 % Allowed : 21.66 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.22), residues: 1650 helix: 2.38 (0.20), residues: 704 sheet: -1.70 (0.35), residues: 222 loop : -1.40 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP y 211 HIS 0.003 0.001 HIS f 37 PHE 0.013 0.001 PHE Y 157 TYR 0.009 0.001 TYR D 204 ARG 0.014 0.000 ARG L 66 Details of bonding type rmsd hydrogen bonds : bond 0.03827 ( 597) hydrogen bonds : angle 3.94680 ( 1704) metal coordination : bond 0.00449 ( 3) covalent geometry : bond 0.00341 (13104) covalent geometry : angle 0.56443 (17778) ********************** 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 154 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 112 time to evaluate : 1.841 Fit side-chains REVERT: f 38 ASN cc_start: 0.8670 (m-40) cc_final: 0.8467 (m110) REVERT: f 232 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7070 (tp30) REVERT: f 288 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8312 (mp0) REVERT: F 57 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7392 (mp0) REVERT: F 224 ARG cc_start: 0.9055 (ttp-170) cc_final: 0.8753 (ttp-170) REVERT: Y 82 ASP cc_start: 0.8948 (t70) cc_final: 0.8663 (t0) REVERT: Y 207 GLU cc_start: 0.5979 (tp30) cc_final: 0.5667 (tp30) REVERT: L 65 LYS cc_start: 0.9461 (OUTLIER) cc_final: 0.9122 (tmtt) REVERT: L 70 LYS cc_start: 0.8236 (mtmt) cc_final: 0.7985 (mtmt) REVERT: L 100 ARG cc_start: 0.8916 (mtm110) cc_final: 0.8696 (mtm110) REVERT: L 155 ARG cc_start: 0.8968 (mmm-85) cc_final: 0.8750 (mmm-85) outliers start: 42 outliers final: 37 residues processed: 146 average time/residue: 0.2408 time to fit residues: 52.5876 Evaluate side-chains 152 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 111 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 72 VAL 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 232 GLU 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 201 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 86 THR 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 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 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 52 ILE 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 154 LEU Chi-restraints excluded: chain L residue 170 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 77 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 160 optimal weight: 20.0000 chunk 151 optimal weight: 0.2980 chunk 101 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.094022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.060298 restraints weight = 27237.811| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.18 r_work: 0.2790 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13107 Z= 0.170 Angle : 0.579 11.609 17778 Z= 0.290 Chirality : 0.042 0.208 2039 Planarity : 0.004 0.059 2282 Dihedral : 4.229 25.676 1809 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.45 % Favored : 94.24 % Rotamer: Outliers : 3.41 % Allowed : 21.51 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.22), residues: 1650 helix: 2.33 (0.20), residues: 705 sheet: -1.75 (0.36), residues: 212 loop : -1.38 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP y 211 HIS 0.003 0.001 HIS F 97 PHE 0.014 0.001 PHE Y 157 TYR 0.011 0.001 TYR D 204 ARG 0.014 0.000 ARG L 66 Details of bonding type rmsd hydrogen bonds : bond 0.04074 ( 597) hydrogen bonds : angle 3.98285 ( 1704) metal coordination : bond 0.00511 ( 3) covalent geometry : bond 0.00406 (13104) covalent geometry : angle 0.57888 (17778) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6855.73 seconds wall clock time: 125 minutes 17.58 seconds (7517.58 seconds total)