Starting phenix.real_space_refine on Sat Aug 23 23:04:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k0i_36765/08_2025/8k0i_36765.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k0i_36765/08_2025/8k0i_36765.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k0i_36765/08_2025/8k0i_36765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k0i_36765/08_2025/8k0i_36765.map" model { file = "/net/cci-nas-00/data/ceres_data/8k0i_36765/08_2025/8k0i_36765.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k0i_36765/08_2025/8k0i_36765.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.096 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 9828 2.51 5 N 2597 2.21 5 O 2867 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15372 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3242 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 23, 'TRANS': 375} Chain: "B" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2987 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 18, 'TRANS': 342} Chain: "C" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1407 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain: "a" Number of atoms: 3242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3242 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 23, 'TRANS': 375} Chain: "b" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2978 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 18, 'TRANS': 341} Chain: "c" Number of atoms: 1432 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 182, 1416 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 6, 'TRANS': 175} Conformer: "B" Number of residues, atoms: 182, 1416 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 6, 'TRANS': 175} bond proxies already assigned to first conformer: 1427 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.32, per 1000 atoms: 0.22 Number of scatterers: 15372 At special positions: 0 Unit cell: (112.2, 127.6, 184.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 2867 8.00 N 2597 7.00 C 9828 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 246 " - pdb=" SG CYS A 278 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 801 " - " ASN A 316 " " NAG B 501 " - " ASN B 87 " " NAG B 502 " - " ASN B 363 " " NAG a 801 " - " ASN a 316 " " NAG b 501 " - " ASN b 87 " " NAG b 502 " - " ASN b 363 " Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 703.2 milliseconds Enol-peptide restraints added in 1.2 microseconds 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3554 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 7 sheets defined 63.1% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 34 through 47 removed outlier: 3.560A pdb=" N LEU A 38 " --> pdb=" O THR A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 83 removed outlier: 4.080A pdb=" N ALA A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 125 removed outlier: 4.282A pdb=" N ALA A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY A 125 " --> pdb=" O ARG A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 142 Processing helix chain 'A' and resid 143 through 157 Processing helix chain 'A' and resid 158 through 173 removed outlier: 3.916A pdb=" N ALA A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 189 removed outlier: 3.721A pdb=" N MET A 189 " --> pdb=" O TYR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 Processing helix chain 'A' and resid 203 through 218 removed outlier: 3.906A pdb=" N PHE A 209 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU A 218 " --> pdb=" O ARG A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 244 removed outlier: 3.902A pdb=" N VAL A 225 " --> pdb=" O PRO A 221 " (cutoff:3.500A) Proline residue: A 226 - end of helix removed outlier: 4.189A pdb=" N ALA A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 259 removed outlier: 4.364A pdb=" N TYR A 257 " --> pdb=" O GLY A 254 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU A 258 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU A 259 " --> pdb=" O ASN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 282 removed outlier: 3.990A pdb=" N THR A 269 " --> pdb=" O PHE A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 Processing helix chain 'A' and resid 316 through 331 removed outlier: 3.728A pdb=" N ALA A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE A 330 " --> pdb=" O THR A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 348 Processing helix chain 'A' and resid 349 through 356 Processing helix chain 'A' and resid 359 through 383 removed outlier: 3.548A pdb=" N LYS A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 429 Processing helix chain 'B' and resid 37 through 41 removed outlier: 3.992A pdb=" N LEU B 41 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 57 Processing helix chain 'B' and resid 59 through 85 Processing helix chain 'B' and resid 97 through 102 Processing helix chain 'B' and resid 103 through 123 removed outlier: 4.153A pdb=" N PHE B 109 " --> pdb=" O GLU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 144 removed outlier: 3.905A pdb=" N LEU B 139 " --> pdb=" O SER B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 157 removed outlier: 4.241A pdb=" N PHE B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 175 removed outlier: 3.846A pdb=" N LYS B 174 " --> pdb=" O THR B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 191 Processing helix chain 'B' and resid 204 through 219 removed outlier: 3.914A pdb=" N SER B 208 " --> pdb=" O LYS B 204 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY B 219 " --> pdb=" O ARG B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 246 Proline residue: B 234 - end of helix Processing helix chain 'B' and resid 265 through 276 removed outlier: 3.768A pdb=" N GLU B 269 " --> pdb=" O ASP B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 308 removed outlier: 3.745A pdb=" N LEU B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 325 removed outlier: 3.835A pdb=" N CYS B 317 " --> pdb=" O ASN B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 341 removed outlier: 3.509A pdb=" N HIS B 341 " --> pdb=" O TYR B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 353 removed outlier: 3.649A pdb=" N GLN B 353 " --> pdb=" O GLU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 376 Processing helix chain 'C' and resid 40 through 50 removed outlier: 3.519A pdb=" N GLY C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 151 removed outlier: 3.660A pdb=" N VAL C 147 " --> pdb=" O GLY C 143 " (cutoff:3.500A) Processing helix chain 'a' and resid 34 through 49 removed outlier: 3.715A pdb=" N LEU a 38 " --> pdb=" O THR a 34 " (cutoff:3.500A) Processing helix chain 'a' and resid 50 through 83 removed outlier: 3.927A pdb=" N ALA a 66 " --> pdb=" O LEU a 62 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE a 83 " --> pdb=" O CYS a 79 " (cutoff:3.500A) Processing helix chain 'a' and resid 99 through 125 removed outlier: 3.916A pdb=" N ALA a 103 " --> pdb=" O SER a 99 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY a 125 " --> pdb=" O ARG a 121 " (cutoff:3.500A) Processing helix chain 'a' and resid 133 through 142 Processing helix chain 'a' and resid 143 through 156 removed outlier: 3.900A pdb=" N ASN a 147 " --> pdb=" O ARG a 143 " (cutoff:3.500A) Processing helix chain 'a' and resid 158 through 173 Processing helix chain 'a' and resid 176 through 189 Processing helix chain 'a' and resid 203 through 218 removed outlier: 3.592A pdb=" N GLN a 207 " --> pdb=" O GLN a 203 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE a 209 " --> pdb=" O HIS a 205 " (cutoff:3.500A) Processing helix chain 'a' and resid 220 through 224 Processing helix chain 'a' and resid 225 through 244 removed outlier: 4.133A pdb=" N ALA a 244 " --> pdb=" O GLU a 240 " (cutoff:3.500A) Processing helix chain 'a' and resid 263 through 281 removed outlier: 4.220A pdb=" N THR a 269 " --> pdb=" O PHE a 265 " (cutoff:3.500A) Processing helix chain 'a' and resid 300 through 315 Processing helix chain 'a' and resid 317 through 331 removed outlier: 3.709A pdb=" N PHE a 330 " --> pdb=" O THR a 326 " (cutoff:3.500A) Processing helix chain 'a' and resid 334 through 348 Processing helix chain 'a' and resid 349 through 356 Processing helix chain 'a' and resid 359 through 384 removed outlier: 3.683A pdb=" N LYS a 363 " --> pdb=" O ARG a 359 " (cutoff:3.500A) Processing helix chain 'a' and resid 400 through 429 Processing helix chain 'b' and resid 43 through 57 Processing helix chain 'b' and resid 59 through 89 removed outlier: 4.030A pdb=" N SER b 89 " --> pdb=" O HIS b 85 " (cutoff:3.500A) Processing helix chain 'b' and resid 98 through 102 removed outlier: 4.103A pdb=" N SER b 102 " --> pdb=" O GLY b 99 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 125 Processing helix chain 'b' and resid 126 through 131 removed outlier: 3.833A pdb=" N PHE b 129 " --> pdb=" O LEU b 126 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLN b 131 " --> pdb=" O ALA b 128 " (cutoff:3.500A) Processing helix chain 'b' and resid 135 through 144 Processing helix chain 'b' and resid 145 through 158 removed outlier: 3.936A pdb=" N LYS b 149 " --> pdb=" O ARG b 145 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE b 150 " --> pdb=" O GLU b 146 " (cutoff:3.500A) Processing helix chain 'b' and resid 160 through 172 Processing helix chain 'b' and resid 178 through 191 removed outlier: 3.831A pdb=" N LEU b 191 " --> pdb=" O TYR b 187 " (cutoff:3.500A) Processing helix chain 'b' and resid 193 through 197 Processing helix chain 'b' and resid 204 through 219 Processing helix chain 'b' and resid 221 through 246 removed outlier: 3.545A pdb=" N ILE b 226 " --> pdb=" O TRP b 222 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N THR b 227 " --> pdb=" O ARG b 223 " (cutoff:3.500A) Proline residue: b 234 - end of helix Processing helix chain 'b' and resid 258 through 275 Processing helix chain 'b' and resid 276 through 281 Processing helix chain 'b' and resid 292 through 308 Processing helix chain 'b' and resid 310 through 325 Proline residue: b 316 - end of helix Processing helix chain 'b' and resid 328 through 341 removed outlier: 4.246A pdb=" N HIS b 341 " --> pdb=" O TYR b 337 " (cutoff:3.500A) Processing helix chain 'b' and resid 349 through 353 removed outlier: 3.527A pdb=" N GLN b 353 " --> pdb=" O GLU b 350 " (cutoff:3.500A) Processing helix chain 'b' and resid 355 through 379 Processing helix chain 'c' and resid 37 through 50 Processing helix chain 'c' and resid 127 through 131 Processing helix chain 'c' and resid 144 through 152 removed outlier: 3.701A pdb=" N SER c 152 " --> pdb=" O ARG c 148 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 284 through 285 Processing sheet with id=AA2, first strand: chain 'B' and resid 384 through 385 removed outlier: 6.521A pdb=" N TYR C 15 " --> pdb=" O CYS C 170 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N CYS C 170 " --> pdb=" O TYR C 15 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP C 17 " --> pdb=" O ALA C 168 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 138 through 140 removed outlier: 3.507A pdb=" N GLY C 31 " --> pdb=" O LYS C 139 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY C 26 " --> pdb=" O LEU C 18 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL C 12 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 9.005A pdb=" N GLY C 7 " --> pdb=" O PHE C 179 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N PHE C 179 " --> pdb=" O GLY C 7 " (cutoff:3.500A) removed outlier: 9.408A pdb=" N LYS C 9 " --> pdb=" O LYS C 177 " (cutoff:3.500A) removed outlier: 10.842A pdb=" N LYS C 177 " --> pdb=" O LYS C 9 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N THR C 11 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL C 175 " --> pdb=" O THR C 11 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'b' and resid 284 through 285 removed outlier: 3.835A pdb=" N ILE b 285 " --> pdb=" O TYR b 288 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'b' and resid 384 through 386 removed outlier: 3.930A pdb=" N VAL c 12 " --> pdb=" O LEU c 32 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY c 26 " --> pdb=" O LEU c 18 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE c 20 " --> pdb=" O ASP c 24 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ASP c 24 " --> pdb=" O ILE c 20 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE c 29 " --> pdb=" O LEU c 141 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL c 136 " --> pdb=" O MET c 108 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N MET c 108 " --> pdb=" O VAL c 136 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLN c 119 " --> pdb=" O ALA c 109 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 384 through 386 removed outlier: 8.648A pdb=" N GLY c 7 " --> pdb=" O PHE c 179 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N PHE c 179 " --> pdb=" O GLY c 7 " (cutoff:3.500A) removed outlier: 9.647A pdb=" N LYS c 9 " --> pdb=" O LYS c 177 " (cutoff:3.500A) removed outlier: 10.687A pdb=" N LYS c 177 " --> pdb=" O LYS c 9 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR c 11 " --> pdb=" O VAL c 175 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL c 175 " --> pdb=" O THR c 11 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ARG c 19 " --> pdb=" O ILE c 167 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ILE c 167 " --> pdb=" O ARG c 19 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'c' and resid 63 through 65 868 hydrogen bonds defined for protein. 2540 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.11 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5024 1.35 - 1.47: 3950 1.47 - 1.59: 6675 1.59 - 1.72: 0 1.72 - 1.84: 122 Bond restraints: 15771 Sorted by residual: bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.50e+00 bond pdb=" C1 NAG b 502 " pdb=" O5 NAG b 502 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.65e+00 bond pdb=" C5 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.413 1.437 -0.024 2.00e-02 2.50e+03 1.41e+00 bond pdb=" CB ASP C 24 " pdb=" CG ASP C 24 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.35e+00 bond pdb=" C PHE A 299 " pdb=" N LEU A 300 " ideal model delta sigma weight residual 1.331 1.355 -0.024 2.07e-02 2.33e+03 1.34e+00 ... (remaining 15766 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 20944 2.10 - 4.21: 319 4.21 - 6.31: 44 6.31 - 8.41: 7 8.41 - 10.52: 3 Bond angle restraints: 21317 Sorted by residual: angle pdb=" C PHE a 299 " pdb=" N LEU a 300 " pdb=" CA LEU a 300 " ideal model delta sigma weight residual 121.80 132.23 -10.43 2.44e+00 1.68e-01 1.83e+01 angle pdb=" N ILE B 263 " pdb=" CA ILE B 263 " pdb=" C ILE B 263 " ideal model delta sigma weight residual 112.29 108.62 3.67 9.40e-01 1.13e+00 1.52e+01 angle pdb=" C PHE A 299 " pdb=" N LEU A 300 " pdb=" CA LEU A 300 " ideal model delta sigma weight residual 121.80 131.12 -9.32 2.44e+00 1.68e-01 1.46e+01 angle pdb=" C SER b 348 " pdb=" N ASP b 349 " pdb=" CA ASP b 349 " ideal model delta sigma weight residual 121.54 128.47 -6.93 1.91e+00 2.74e-01 1.32e+01 angle pdb=" N LYS c 133 " pdb=" CA LYS c 133 " pdb=" C LYS c 133 " ideal model delta sigma weight residual 114.56 110.65 3.91 1.27e+00 6.20e-01 9.48e+00 ... (remaining 21312 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.11: 8337 21.11 - 42.22: 966 42.22 - 63.33: 187 63.33 - 84.45: 35 84.45 - 105.56: 15 Dihedral angle restraints: 9540 sinusoidal: 3994 harmonic: 5546 Sorted by residual: dihedral pdb=" CB CYS A 246 " pdb=" SG CYS A 246 " pdb=" SG CYS A 278 " pdb=" CB CYS A 278 " ideal model delta sinusoidal sigma weight residual 93.00 20.40 72.60 1 1.00e+01 1.00e-02 6.73e+01 dihedral pdb=" CA PHE c 121 " pdb=" C PHE c 121 " pdb=" N ILE c 122 " pdb=" CA ILE c 122 " ideal model delta harmonic sigma weight residual 180.00 145.11 34.89 0 5.00e+00 4.00e-02 4.87e+01 dihedral pdb=" CA PHE C 120 " pdb=" C PHE C 120 " pdb=" N PHE C 121 " pdb=" CA PHE C 121 " ideal model delta harmonic sigma weight residual 180.00 153.99 26.01 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 9537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 2187 0.122 - 0.244: 22 0.244 - 0.366: 1 0.366 - 0.488: 0 0.488 - 0.610: 1 Chirality restraints: 2211 Sorted by residual: chirality pdb=" C1 NAG a 801 " pdb=" ND2 ASN a 316 " pdb=" C2 NAG a 801 " pdb=" O5 NAG a 801 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.29e+00 chirality pdb=" C1 NAG b 501 " pdb=" ND2 ASN b 87 " pdb=" C2 NAG b 501 " pdb=" O5 NAG b 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CG LEU b 335 " pdb=" CB LEU b 335 " pdb=" CD1 LEU b 335 " pdb=" CD2 LEU b 335 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.96e-01 ... (remaining 2208 not shown) Planarity restraints: 2802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN a 316 " 0.024 2.00e-02 2.50e+03 2.27e-02 6.46e+00 pdb=" CG ASN a 316 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN a 316 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN a 316 " -0.025 2.00e-02 2.50e+03 pdb=" C1 NAG a 801 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA b 91 " 0.035 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO b 92 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO b 92 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO b 92 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 152 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" C GLN B 152 " -0.034 2.00e-02 2.50e+03 pdb=" O GLN B 152 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE B 153 " 0.011 2.00e-02 2.50e+03 ... (remaining 2799 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 148 2.64 - 3.21: 13722 3.21 - 3.77: 22579 3.77 - 4.34: 29075 4.34 - 4.90: 49647 Nonbonded interactions: 115171 Sorted by model distance: nonbonded pdb=" OE2 GLU a 229 " pdb=" OH TYR a 311 " model vdw 2.077 3.040 nonbonded pdb=" O GLU A 175 " pdb=" OG SER a 190 " model vdw 2.122 3.040 nonbonded pdb=" OH TYR B 48 " pdb=" OE2 GLU B 146 " model vdw 2.195 3.040 nonbonded pdb=" O SER b 348 " pdb=" OG SER b 348 " model vdw 2.221 3.040 nonbonded pdb=" OD1 ASP b 258 " pdb=" N PHE b 259 " model vdw 2.230 3.120 ... (remaining 115166 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 'A' selection = chain 'a' } ncs_group { reference = (chain 'B' and resid 28 through 502) selection = chain 'b' } ncs_group { reference = (chain 'C' and (resid 6 through 64 or resid 66 through 112 or resid 114 through \ 165 or resid 167 through 186)) selection = (chain 'c' and (resid 6 through 64 or resid 66 through 112 or resid 114 through \ 165 or resid 167 through 186)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.200 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 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 0.038 15778 Z= 0.163 Angle : 0.650 10.518 21337 Z= 0.345 Chirality : 0.044 0.610 2211 Planarity : 0.004 0.053 2796 Dihedral : 18.377 105.558 5983 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.87 % Favored : 95.03 % Rotamer: Outliers : 0.37 % Allowed : 21.68 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.20), residues: 1873 helix: 1.32 (0.16), residues: 1106 sheet: -1.81 (0.54), residues: 94 loop : -1.52 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 74 TYR 0.018 0.001 TYR a 186 PHE 0.014 0.001 PHE C 30 TRP 0.010 0.001 TRP C 105 HIS 0.005 0.001 HIS b 266 Details of bonding type rmsd covalent geometry : bond 0.00356 (15771) covalent geometry : angle 0.64290 (21317) SS BOND : bond 0.00475 ( 1) SS BOND : angle 3.12557 ( 2) hydrogen bonds : bond 0.13272 ( 866) hydrogen bonds : angle 5.09098 ( 2540) link_NAG-ASN : bond 0.00426 ( 6) link_NAG-ASN : angle 3.17120 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 146 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 337 MET cc_start: 0.6741 (tpp) cc_final: 0.6140 (tpp) REVERT: B 297 MET cc_start: 0.7064 (ttm) cc_final: 0.6838 (ttm) REVERT: a 136 MET cc_start: 0.8399 (tpp) cc_final: 0.8136 (mmt) outliers start: 4 outliers final: 1 residues processed: 150 average time/residue: 0.1048 time to fit residues: 23.5972 Evaluate side-chains 139 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.0170 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.0000 overall best weight: 0.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN B 27 GLN ** B 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 173 ASN a 207 GLN a 280 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.217658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.200609 restraints weight = 41225.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.198751 restraints weight = 51340.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.197815 restraints weight = 39015.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.197522 restraints weight = 42176.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.196944 restraints weight = 36224.417| |-----------------------------------------------------------------------------| r_work (final): 0.4414 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4414 r_free = 0.4414 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4414 r_free = 0.4414 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.0822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15778 Z= 0.123 Angle : 0.554 10.706 21337 Z= 0.284 Chirality : 0.041 0.363 2211 Planarity : 0.004 0.046 2796 Dihedral : 6.701 67.346 2232 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.17 % Favored : 95.72 % Rotamer: Outliers : 1.93 % Allowed : 19.81 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.20), residues: 1873 helix: 1.70 (0.15), residues: 1130 sheet: -1.12 (0.60), residues: 80 loop : -1.55 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG b 30 TYR 0.014 0.001 TYR a 365 PHE 0.013 0.001 PHE C 30 TRP 0.010 0.001 TRP C 105 HIS 0.004 0.001 HIS b 50 Details of bonding type rmsd covalent geometry : bond 0.00265 (15771) covalent geometry : angle 0.54854 (21317) SS BOND : bond 0.00417 ( 1) SS BOND : angle 2.84815 ( 2) hydrogen bonds : bond 0.04890 ( 866) hydrogen bonds : angle 3.93228 ( 2540) link_NAG-ASN : bond 0.00976 ( 6) link_NAG-ASN : angle 2.48348 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: A 337 MET cc_start: 0.7204 (tpp) cc_final: 0.6886 (tpt) REVERT: B 297 MET cc_start: 0.7169 (ttm) cc_final: 0.6907 (ttm) REVERT: b 252 GLU cc_start: 0.7156 (pm20) cc_final: 0.6807 (pt0) outliers start: 29 outliers final: 9 residues processed: 169 average time/residue: 0.1106 time to fit residues: 27.9892 Evaluate side-chains 142 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain a residue 135 GLU Chi-restraints excluded: chain b residue 88 CYS Chi-restraints excluded: chain b residue 285 ILE Chi-restraints excluded: chain b residue 330 VAL Chi-restraints excluded: chain b residue 383 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 123 optimal weight: 0.9980 chunk 170 optimal weight: 0.0570 chunk 52 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 181 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 158 optimal weight: 0.4980 chunk 14 optimal weight: 0.0870 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN B 27 GLN B 302 GLN ** B 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 205 HIS ** a 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.219599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.200117 restraints weight = 56295.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.198227 restraints weight = 56808.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.197315 restraints weight = 41863.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.198034 restraints weight = 41281.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.197860 restraints weight = 29369.090| |-----------------------------------------------------------------------------| r_work (final): 0.4419 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4417 r_free = 0.4417 target_work(ls_wunit_k1) = 0.200 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4417 r_free = 0.4417 target_work(ls_wunit_k1) = 0.200 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15778 Z= 0.109 Angle : 0.515 10.647 21337 Z= 0.263 Chirality : 0.040 0.306 2211 Planarity : 0.004 0.043 2796 Dihedral : 5.033 53.756 2230 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.74 % Favored : 96.15 % Rotamer: Outliers : 2.12 % Allowed : 20.37 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.20), residues: 1873 helix: 1.92 (0.15), residues: 1130 sheet: -0.63 (0.59), residues: 73 loop : -1.50 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 74 TYR 0.016 0.001 TYR a 185 PHE 0.013 0.001 PHE C 44 TRP 0.008 0.001 TRP c 105 HIS 0.003 0.001 HIS a 227 Details of bonding type rmsd covalent geometry : bond 0.00233 (15771) covalent geometry : angle 0.50997 (21317) SS BOND : bond 0.00362 ( 1) SS BOND : angle 2.52936 ( 2) hydrogen bonds : bond 0.04144 ( 866) hydrogen bonds : angle 3.62987 ( 2540) link_NAG-ASN : bond 0.00823 ( 6) link_NAG-ASN : angle 2.26088 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: A 176 HIS cc_start: 0.5189 (OUTLIER) cc_final: 0.4089 (m-70) REVERT: A 232 LEU cc_start: 0.6542 (OUTLIER) cc_final: 0.6117 (mm) REVERT: A 337 MET cc_start: 0.7277 (tpp) cc_final: 0.6949 (tpt) REVERT: a 58 MET cc_start: 0.7785 (mtt) cc_final: 0.7491 (mtt) outliers start: 32 outliers final: 14 residues processed: 178 average time/residue: 0.1104 time to fit residues: 29.3448 Evaluate side-chains 150 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain a residue 135 GLU Chi-restraints excluded: chain b residue 88 CYS Chi-restraints excluded: chain b residue 383 ASP Chi-restraints excluded: chain b residue 386 GLU Chi-restraints excluded: chain c residue 174 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 176 optimal weight: 0.9980 chunk 87 optimal weight: 0.1980 chunk 170 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 179 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 156 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 167 HIS ** a 280 GLN ** 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 = 0.4602 r_free = 0.4602 target = 0.217459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.201488 restraints weight = 48668.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.199391 restraints weight = 54314.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.198289 restraints weight = 43302.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.198601 restraints weight = 46894.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.197816 restraints weight = 37086.574| |-----------------------------------------------------------------------------| r_work (final): 0.4385 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4386 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4386 r_free = 0.4386 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4386 r_free = 0.4386 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4386 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15778 Z= 0.126 Angle : 0.532 10.759 21337 Z= 0.269 Chirality : 0.041 0.353 2211 Planarity : 0.004 0.041 2796 Dihedral : 4.816 52.566 2230 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.28 % Favored : 95.61 % Rotamer: Outliers : 2.49 % Allowed : 20.81 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.20), residues: 1873 helix: 1.93 (0.15), residues: 1138 sheet: -0.76 (0.58), residues: 73 loop : -1.44 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 354 TYR 0.013 0.001 TYR a 365 PHE 0.013 0.001 PHE b 352 TRP 0.009 0.001 TRP C 105 HIS 0.004 0.001 HIS b 266 Details of bonding type rmsd covalent geometry : bond 0.00290 (15771) covalent geometry : angle 0.52775 (21317) SS BOND : bond 0.00639 ( 1) SS BOND : angle 1.92724 ( 2) hydrogen bonds : bond 0.04457 ( 866) hydrogen bonds : angle 3.60809 ( 2540) link_NAG-ASN : bond 0.00837 ( 6) link_NAG-ASN : angle 2.27274 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 139 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 176 HIS cc_start: 0.5097 (OUTLIER) cc_final: 0.3984 (m-70) REVERT: A 232 LEU cc_start: 0.6659 (OUTLIER) cc_final: 0.6218 (mm) REVERT: A 337 MET cc_start: 0.7276 (tpp) cc_final: 0.6912 (tpt) REVERT: B 185 MET cc_start: 0.7122 (tpt) cc_final: 0.6806 (tpt) REVERT: a 58 MET cc_start: 0.7848 (mtt) cc_final: 0.7516 (mtt) REVERT: a 292 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.6615 (mtp180) REVERT: a 328 LEU cc_start: 0.6437 (OUTLIER) cc_final: 0.6193 (mp) REVERT: c 115 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8411 (t) outliers start: 38 outliers final: 21 residues processed: 164 average time/residue: 0.1008 time to fit residues: 25.1359 Evaluate side-chains 158 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain a residue 135 GLU Chi-restraints excluded: chain a residue 176 HIS Chi-restraints excluded: chain a residue 292 ARG Chi-restraints excluded: chain a residue 328 LEU Chi-restraints excluded: chain b residue 88 CYS Chi-restraints excluded: chain b residue 282 THR Chi-restraints excluded: chain b residue 330 VAL Chi-restraints excluded: chain b residue 383 ASP Chi-restraints excluded: chain c residue 10 VAL Chi-restraints excluded: chain c residue 69 MET Chi-restraints excluded: chain c residue 115 THR Chi-restraints excluded: chain c residue 131 ASP Chi-restraints excluded: chain c residue 174 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 38 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 156 optimal weight: 0.0570 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 chunk 136 optimal weight: 7.9990 chunk 63 optimal weight: 0.3980 chunk 11 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** B 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 280 GLN ** 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 = 0.4623 r_free = 0.4623 target = 0.219750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.203289 restraints weight = 41555.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.201379 restraints weight = 51634.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.200130 restraints weight = 41418.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.199994 restraints weight = 43092.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.199455 restraints weight = 35902.236| |-----------------------------------------------------------------------------| r_work (final): 0.4453 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4453 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4453 r_free = 0.4453 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4453 r_free = 0.4453 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4453 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15778 Z= 0.106 Angle : 0.511 10.643 21337 Z= 0.259 Chirality : 0.040 0.346 2211 Planarity : 0.003 0.039 2796 Dihedral : 4.590 52.983 2230 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.53 % Favored : 96.36 % Rotamer: Outliers : 2.43 % Allowed : 21.00 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.20), residues: 1873 helix: 2.05 (0.15), residues: 1137 sheet: -0.89 (0.55), residues: 78 loop : -1.39 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 74 TYR 0.024 0.001 TYR a 185 PHE 0.009 0.001 PHE C 30 TRP 0.008 0.001 TRP C 105 HIS 0.003 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00228 (15771) covalent geometry : angle 0.50613 (21317) SS BOND : bond 0.00327 ( 1) SS BOND : angle 1.59752 ( 2) hydrogen bonds : bond 0.03925 ( 866) hydrogen bonds : angle 3.49917 ( 2540) link_NAG-ASN : bond 0.00766 ( 6) link_NAG-ASN : angle 2.29953 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 LYS cc_start: 0.7082 (OUTLIER) cc_final: 0.6836 (tptp) REVERT: A 176 HIS cc_start: 0.4991 (OUTLIER) cc_final: 0.3643 (m-70) REVERT: A 337 MET cc_start: 0.7311 (tpp) cc_final: 0.6916 (tpt) REVERT: B 185 MET cc_start: 0.7314 (tpt) cc_final: 0.7006 (tpt) REVERT: a 234 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6965 (mp0) REVERT: a 292 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.6509 (mtp180) REVERT: c 115 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8411 (t) outliers start: 37 outliers final: 22 residues processed: 169 average time/residue: 0.1021 time to fit residues: 26.1894 Evaluate side-chains 159 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain a residue 176 HIS Chi-restraints excluded: chain a residue 234 GLU Chi-restraints excluded: chain a residue 292 ARG Chi-restraints excluded: chain b residue 88 CYS Chi-restraints excluded: chain b residue 271 LEU Chi-restraints excluded: chain b residue 275 ILE Chi-restraints excluded: chain b residue 282 THR Chi-restraints excluded: chain b residue 331 MET Chi-restraints excluded: chain b residue 383 ASP Chi-restraints excluded: chain b residue 386 GLU Chi-restraints excluded: chain c residue 69 MET Chi-restraints excluded: chain c residue 115 THR Chi-restraints excluded: chain c residue 131 ASP Chi-restraints excluded: chain c residue 174 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 89 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 173 optimal weight: 0.2980 chunk 118 optimal weight: 4.9990 chunk 158 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 280 GLN ** 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 = 0.4606 r_free = 0.4606 target = 0.217988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.201579 restraints weight = 38706.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.199427 restraints weight = 48719.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.197893 restraints weight = 41164.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.197975 restraints weight = 41522.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.197530 restraints weight = 33601.221| |-----------------------------------------------------------------------------| r_work (final): 0.4419 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4420 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4420 r_free = 0.4420 target_work(ls_wunit_k1) = 0.200 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4420 r_free = 0.4420 target_work(ls_wunit_k1) = 0.200 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4420 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15778 Z= 0.125 Angle : 0.526 10.732 21337 Z= 0.268 Chirality : 0.041 0.298 2211 Planarity : 0.003 0.038 2796 Dihedral : 4.541 53.115 2230 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.44 % Favored : 95.45 % Rotamer: Outliers : 2.49 % Allowed : 21.50 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.20), residues: 1873 helix: 2.02 (0.15), residues: 1140 sheet: -0.96 (0.55), residues: 75 loop : -1.44 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 74 TYR 0.013 0.001 TYR a 365 PHE 0.010 0.001 PHE b 259 TRP 0.007 0.001 TRP C 105 HIS 0.004 0.001 HIS b 266 Details of bonding type rmsd covalent geometry : bond 0.00290 (15771) covalent geometry : angle 0.52233 (21317) SS BOND : bond 0.00339 ( 1) SS BOND : angle 1.74366 ( 2) hydrogen bonds : bond 0.04371 ( 866) hydrogen bonds : angle 3.53789 ( 2540) link_NAG-ASN : bond 0.00645 ( 6) link_NAG-ASN : angle 2.08981 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 155 LYS cc_start: 0.7086 (OUTLIER) cc_final: 0.6826 (tptp) REVERT: A 176 HIS cc_start: 0.5034 (OUTLIER) cc_final: 0.3754 (m-70) REVERT: A 232 LEU cc_start: 0.6635 (OUTLIER) cc_final: 0.6171 (mm) REVERT: A 337 MET cc_start: 0.7391 (tpp) cc_final: 0.6944 (tpt) REVERT: B 185 MET cc_start: 0.7190 (tpt) cc_final: 0.6853 (tpt) REVERT: a 234 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: a 292 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.6440 (mtp180) outliers start: 38 outliers final: 21 residues processed: 165 average time/residue: 0.1107 time to fit residues: 27.3524 Evaluate side-chains 156 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain a residue 132 LEU Chi-restraints excluded: chain a residue 176 HIS Chi-restraints excluded: chain a residue 234 GLU Chi-restraints excluded: chain a residue 292 ARG Chi-restraints excluded: chain b residue 88 CYS Chi-restraints excluded: chain b residue 271 LEU Chi-restraints excluded: chain b residue 282 THR Chi-restraints excluded: chain b residue 383 ASP Chi-restraints excluded: chain b residue 386 GLU Chi-restraints excluded: chain c residue 10 VAL Chi-restraints excluded: chain c residue 69 MET Chi-restraints excluded: chain c residue 131 ASP Chi-restraints excluded: chain c residue 174 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 184 optimal weight: 0.9980 chunk 152 optimal weight: 5.9990 chunk 163 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 149 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 207 GLN a 280 GLN ** b 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.211746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.193591 restraints weight = 46961.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.191492 restraints weight = 55131.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.189885 restraints weight = 45421.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.190121 restraints weight = 45599.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.189487 restraints weight = 36427.202| |-----------------------------------------------------------------------------| r_work (final): 0.4329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4330 r_free = 0.4330 target_work(ls_wunit_k1) = 0.191 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4330 r_free = 0.4330 target_work(ls_wunit_k1) = 0.191 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4330 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 15778 Z= 0.260 Angle : 0.675 10.903 21337 Z= 0.349 Chirality : 0.046 0.273 2211 Planarity : 0.004 0.041 2796 Dihedral : 5.127 51.129 2230 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.15 % Favored : 93.74 % Rotamer: Outliers : 2.99 % Allowed : 21.81 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.19), residues: 1873 helix: 1.54 (0.15), residues: 1132 sheet: -1.28 (0.56), residues: 73 loop : -1.68 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG a 354 TYR 0.022 0.002 TYR B 66 PHE 0.024 0.002 PHE b 259 TRP 0.007 0.002 TRP A 393 HIS 0.007 0.001 HIS b 266 Details of bonding type rmsd covalent geometry : bond 0.00637 (15771) covalent geometry : angle 0.67311 (21317) SS BOND : bond 0.00616 ( 1) SS BOND : angle 2.80653 ( 2) hydrogen bonds : bond 0.06766 ( 866) hydrogen bonds : angle 4.07748 ( 2540) link_NAG-ASN : bond 0.00463 ( 6) link_NAG-ASN : angle 1.82392 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 141 time to evaluate : 0.648 Fit side-chains REVERT: A 155 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.7126 (tptp) REVERT: A 176 HIS cc_start: 0.5684 (OUTLIER) cc_final: 0.4788 (m-70) REVERT: A 309 PHE cc_start: 0.5678 (OUTLIER) cc_final: 0.4771 (t80) REVERT: A 337 MET cc_start: 0.7697 (tpp) cc_final: 0.7174 (tpp) REVERT: B 355 ARG cc_start: 0.6591 (mtt180) cc_final: 0.6184 (ttp-170) REVERT: a 234 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: a 292 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.6486 (mtp180) outliers start: 46 outliers final: 29 residues processed: 173 average time/residue: 0.1007 time to fit residues: 26.6194 Evaluate side-chains 172 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 84 CYS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain a residue 132 LEU Chi-restraints excluded: chain a residue 176 HIS Chi-restraints excluded: chain a residue 234 GLU Chi-restraints excluded: chain a residue 274 GLN Chi-restraints excluded: chain a residue 292 ARG Chi-restraints excluded: chain b residue 88 CYS Chi-restraints excluded: chain b residue 203 THR Chi-restraints excluded: chain b residue 271 LEU Chi-restraints excluded: chain b residue 282 THR Chi-restraints excluded: chain b residue 330 VAL Chi-restraints excluded: chain b residue 381 ASP Chi-restraints excluded: chain b residue 383 ASP Chi-restraints excluded: chain c residue 10 VAL Chi-restraints excluded: chain c residue 69 MET Chi-restraints excluded: chain c residue 131 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 15 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 207 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.216977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.200787 restraints weight = 42713.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.198623 restraints weight = 47555.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.197340 restraints weight = 36703.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.197071 restraints weight = 41525.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.196401 restraints weight = 34885.804| |-----------------------------------------------------------------------------| r_work (final): 0.4371 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4370 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4370 r_free = 0.4370 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4370 r_free = 0.4370 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4370 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15778 Z= 0.134 Angle : 0.551 10.837 21337 Z= 0.282 Chirality : 0.041 0.260 2211 Planarity : 0.004 0.038 2796 Dihedral : 4.747 52.933 2230 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.39 % Favored : 95.51 % Rotamer: Outliers : 2.68 % Allowed : 22.31 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.20), residues: 1873 helix: 1.84 (0.15), residues: 1132 sheet: -1.36 (0.55), residues: 78 loop : -1.55 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 74 TYR 0.015 0.001 TYR a 365 PHE 0.012 0.001 PHE C 30 TRP 0.008 0.001 TRP C 105 HIS 0.004 0.001 HIS b 266 Details of bonding type rmsd covalent geometry : bond 0.00310 (15771) covalent geometry : angle 0.54825 (21317) SS BOND : bond 0.00406 ( 1) SS BOND : angle 2.10917 ( 2) hydrogen bonds : bond 0.04864 ( 866) hydrogen bonds : angle 3.69009 ( 2540) link_NAG-ASN : bond 0.00593 ( 6) link_NAG-ASN : angle 1.91124 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 139 time to evaluate : 0.579 Fit side-chains REVERT: A 155 LYS cc_start: 0.7221 (OUTLIER) cc_final: 0.6969 (tptp) REVERT: A 176 HIS cc_start: 0.5288 (OUTLIER) cc_final: 0.4117 (m-70) REVERT: A 309 PHE cc_start: 0.5573 (OUTLIER) cc_final: 0.4577 (t80) REVERT: B 185 MET cc_start: 0.7190 (tpt) cc_final: 0.6918 (tpt) REVERT: a 234 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6936 (mp0) REVERT: a 243 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.6892 (mtp85) REVERT: a 292 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.6633 (mtp180) REVERT: b 271 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8102 (tp) REVERT: b 297 MET cc_start: 0.7841 (ptm) cc_final: 0.7603 (ptm) outliers start: 41 outliers final: 26 residues processed: 170 average time/residue: 0.1088 time to fit residues: 27.7414 Evaluate side-chains 168 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 84 CYS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain a residue 132 LEU Chi-restraints excluded: chain a residue 176 HIS Chi-restraints excluded: chain a residue 200 LEU Chi-restraints excluded: chain a residue 234 GLU Chi-restraints excluded: chain a residue 243 ARG Chi-restraints excluded: chain a residue 274 GLN Chi-restraints excluded: chain a residue 292 ARG Chi-restraints excluded: chain b residue 88 CYS Chi-restraints excluded: chain b residue 233 LEU Chi-restraints excluded: chain b residue 271 LEU Chi-restraints excluded: chain b residue 282 THR Chi-restraints excluded: chain b residue 330 VAL Chi-restraints excluded: chain b residue 381 ASP Chi-restraints excluded: chain b residue 383 ASP Chi-restraints excluded: chain b residue 386 GLU Chi-restraints excluded: chain c residue 10 VAL Chi-restraints excluded: chain c residue 69 MET Chi-restraints excluded: chain c residue 131 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 54 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 chunk 180 optimal weight: 3.9990 chunk 75 optimal weight: 0.0770 chunk 67 optimal weight: 0.1980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 HIS ** 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 = 0.4611 r_free = 0.4611 target = 0.219170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.197746 restraints weight = 42246.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.196066 restraints weight = 53936.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.195716 restraints weight = 38664.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.196076 restraints weight = 39189.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.195657 restraints weight = 31984.026| |-----------------------------------------------------------------------------| r_work (final): 0.4398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4397 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4397 r_free = 0.4397 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4397 r_free = 0.4397 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15778 Z= 0.113 Angle : 0.529 10.755 21337 Z= 0.269 Chirality : 0.040 0.341 2211 Planarity : 0.004 0.037 2796 Dihedral : 4.558 52.664 2230 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.12 % Favored : 95.78 % Rotamer: Outliers : 2.37 % Allowed : 22.43 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.20), residues: 1873 helix: 2.00 (0.15), residues: 1132 sheet: -1.19 (0.55), residues: 78 loop : -1.46 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG a 354 TYR 0.019 0.001 TYR a 185 PHE 0.009 0.001 PHE C 30 TRP 0.009 0.001 TRP C 105 HIS 0.003 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00252 (15771) covalent geometry : angle 0.52471 (21317) SS BOND : bond 0.00332 ( 1) SS BOND : angle 1.67297 ( 2) hydrogen bonds : bond 0.04180 ( 866) hydrogen bonds : angle 3.52789 ( 2540) link_NAG-ASN : bond 0.00635 ( 6) link_NAG-ASN : angle 2.20890 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 0.639 Fit side-chains REVERT: A 136 MET cc_start: 0.7657 (tpp) cc_final: 0.7295 (tpp) REVERT: A 155 LYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6907 (tptp) REVERT: A 176 HIS cc_start: 0.5327 (OUTLIER) cc_final: 0.3866 (m-70) REVERT: A 232 LEU cc_start: 0.6641 (OUTLIER) cc_final: 0.6208 (mm) REVERT: A 309 PHE cc_start: 0.5519 (OUTLIER) cc_final: 0.4472 (t80) REVERT: a 292 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6548 (mtp180) REVERT: c 158 ARG cc_start: 0.7016 (mtm180) cc_final: 0.6814 (mtm-85) outliers start: 36 outliers final: 25 residues processed: 165 average time/residue: 0.1211 time to fit residues: 29.7549 Evaluate side-chains 167 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain a residue 132 LEU Chi-restraints excluded: chain a residue 176 HIS Chi-restraints excluded: chain a residue 200 LEU Chi-restraints excluded: chain a residue 274 GLN Chi-restraints excluded: chain a residue 292 ARG Chi-restraints excluded: chain b residue 88 CYS Chi-restraints excluded: chain b residue 233 LEU Chi-restraints excluded: chain b residue 282 THR Chi-restraints excluded: chain b residue 330 VAL Chi-restraints excluded: chain b residue 381 ASP Chi-restraints excluded: chain b residue 383 ASP Chi-restraints excluded: chain b residue 386 GLU Chi-restraints excluded: chain c residue 10 VAL Chi-restraints excluded: chain c residue 69 MET Chi-restraints excluded: chain c residue 131 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 118 optimal weight: 0.1980 chunk 21 optimal weight: 0.5980 chunk 87 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 162 optimal weight: 8.9990 chunk 173 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 180 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 HIS ** 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 = 0.4613 r_free = 0.4613 target = 0.218667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.202246 restraints weight = 43838.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.199974 restraints weight = 54363.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.198929 restraints weight = 42065.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.198981 restraints weight = 41944.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.198693 restraints weight = 34461.129| |-----------------------------------------------------------------------------| r_work (final): 0.4398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4397 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4397 r_free = 0.4397 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4397 r_free = 0.4397 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15778 Z= 0.114 Angle : 0.531 10.788 21337 Z= 0.269 Chirality : 0.040 0.363 2211 Planarity : 0.003 0.038 2796 Dihedral : 4.438 52.606 2230 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.06 % Favored : 95.83 % Rotamer: Outliers : 1.99 % Allowed : 22.62 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.20), residues: 1873 helix: 2.05 (0.15), residues: 1135 sheet: -1.07 (0.56), residues: 78 loop : -1.43 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 74 TYR 0.012 0.001 TYR a 365 PHE 0.013 0.001 PHE b 352 TRP 0.008 0.001 TRP b 60 HIS 0.003 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00256 (15771) covalent geometry : angle 0.52758 (21317) SS BOND : bond 0.00320 ( 1) SS BOND : angle 1.61304 ( 2) hydrogen bonds : bond 0.04143 ( 866) hydrogen bonds : angle 3.49929 ( 2540) link_NAG-ASN : bond 0.00675 ( 6) link_NAG-ASN : angle 2.20578 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.687 Fit side-chains REVERT: A 136 MET cc_start: 0.7649 (tpp) cc_final: 0.7421 (tpp) REVERT: A 155 LYS cc_start: 0.7209 (OUTLIER) cc_final: 0.6979 (tptp) REVERT: A 176 HIS cc_start: 0.5360 (OUTLIER) cc_final: 0.3877 (m-70) REVERT: A 232 LEU cc_start: 0.6627 (OUTLIER) cc_final: 0.6192 (mm) REVERT: A 309 PHE cc_start: 0.5481 (OUTLIER) cc_final: 0.4568 (t80) REVERT: a 292 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.6594 (mtp180) outliers start: 30 outliers final: 24 residues processed: 165 average time/residue: 0.1325 time to fit residues: 33.2126 Evaluate side-chains 168 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain a residue 176 HIS Chi-restraints excluded: chain a residue 200 LEU Chi-restraints excluded: chain a residue 292 ARG Chi-restraints excluded: chain b residue 88 CYS Chi-restraints excluded: chain b residue 233 LEU Chi-restraints excluded: chain b residue 282 THR Chi-restraints excluded: chain b residue 330 VAL Chi-restraints excluded: chain b residue 381 ASP Chi-restraints excluded: chain b residue 383 ASP Chi-restraints excluded: chain b residue 386 GLU Chi-restraints excluded: chain c residue 10 VAL Chi-restraints excluded: chain c residue 69 MET Chi-restraints excluded: chain c residue 131 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 5 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 167 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 129 optimal weight: 0.0970 chunk 70 optimal weight: 9.9990 chunk 163 optimal weight: 6.9990 chunk 115 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 HIS ** 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 = 0.4605 r_free = 0.4605 target = 0.217935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.201411 restraints weight = 39290.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.199361 restraints weight = 48957.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.198346 restraints weight = 37961.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.197980 restraints weight = 39713.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.197014 restraints weight = 36268.625| |-----------------------------------------------------------------------------| r_work (final): 0.4381 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4381 r_free = 0.4381 target_work(ls_wunit_k1) = 0.185 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4381 r_free = 0.4381 target_work(ls_wunit_k1) = 0.185 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15778 Z= 0.123 Angle : 0.542 10.802 21337 Z= 0.274 Chirality : 0.041 0.339 2211 Planarity : 0.004 0.038 2796 Dihedral : 4.435 52.392 2230 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.49 % Favored : 95.40 % Rotamer: Outliers : 2.12 % Allowed : 22.49 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.20), residues: 1873 helix: 2.03 (0.15), residues: 1135 sheet: -1.18 (0.55), residues: 80 loop : -1.41 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG a 354 TYR 0.023 0.001 TYR a 185 PHE 0.010 0.001 PHE C 30 TRP 0.008 0.001 TRP b 60 HIS 0.003 0.001 HIS b 266 Details of bonding type rmsd covalent geometry : bond 0.00285 (15771) covalent geometry : angle 0.53838 (21317) SS BOND : bond 0.00330 ( 1) SS BOND : angle 1.69704 ( 2) hydrogen bonds : bond 0.04302 ( 866) hydrogen bonds : angle 3.52888 ( 2540) link_NAG-ASN : bond 0.00650 ( 6) link_NAG-ASN : angle 2.11348 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2090.86 seconds wall clock time: 36 minutes 59.95 seconds (2219.95 seconds total)