Starting phenix.real_space_refine on Sat May 17 05:00:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k0i_36765/05_2025/8k0i_36765.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k0i_36765/05_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_36765/05_2025/8k0i_36765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k0i_36765/05_2025/8k0i_36765.map" model { file = "/net/cci-nas-00/data/ceres_data/8k0i_36765/05_2025/8k0i_36765.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k0i_36765/05_2025/8k0i_36765.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.24, per 1000 atoms: 0.60 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: 3.73 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.32 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: 3.96 Time building geometry restraints manager: 4.29 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 387 or resid 501 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: 0.830 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: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 33.220 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.460 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (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 TRP 0.010 0.001 TRP C 105 HIS 0.005 0.001 HIS b 266 PHE 0.014 0.001 PHE C 30 TYR 0.018 0.001 TYR a 186 ARG 0.004 0.000 ARG A 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 6) link_NAG-ASN : angle 3.17120 ( 18) hydrogen bonds : bond 0.13272 ( 866) hydrogen bonds : angle 5.09098 ( 2540) SS BOND : bond 0.00475 ( 1) SS BOND : angle 3.12557 ( 2) covalent geometry : bond 0.00356 (15771) covalent geometry : angle 0.64290 (21317) *********************** 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 : 1.849 Fit side-chains 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: 0.2726 time to fit residues: 61.0548 Evaluate side-chains 138 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 1.655 ------------------------------------------------------------------------------- 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 157 optimal weight: 6.9990 chunk 140 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 95 optimal weight: 0.4980 chunk 75 optimal weight: 0.8980 chunk 145 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 88 optimal weight: 0.0870 chunk 108 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 = 0.4597 r_free = 0.4597 target = 0.218061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.200558 restraints weight = 44185.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.199511 restraints weight = 56943.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.198247 restraints weight = 40825.212| |-----------------------------------------------------------------------------| r_work (final): 0.4423 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4422 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4422 r_free = 0.4422 target_work(ls_wunit_k1) = 0.200 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4422 r_free = 0.4422 target_work(ls_wunit_k1) = 0.200 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4422 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15778 Z= 0.125 Angle : 0.554 10.697 21337 Z= 0.284 Chirality : 0.041 0.370 2211 Planarity : 0.004 0.046 2796 Dihedral : 6.780 67.826 2232 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.17 % Favored : 95.72 % Rotamer: Outliers : 2.06 % Allowed : 20.06 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.20), residues: 1873 helix: 1.70 (0.15), residues: 1124 sheet: -1.12 (0.60), residues: 80 loop : -1.54 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 105 HIS 0.004 0.001 HIS C 62 PHE 0.016 0.001 PHE b 352 TYR 0.014 0.001 TYR a 365 ARG 0.004 0.000 ARG b 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00945 ( 6) link_NAG-ASN : angle 2.47717 ( 18) hydrogen bonds : bond 0.04971 ( 866) hydrogen bonds : angle 3.95113 ( 2540) SS BOND : bond 0.00426 ( 1) SS BOND : angle 2.85234 ( 2) covalent geometry : bond 0.00269 (15771) covalent geometry : angle 0.54914 (21317) *********************** 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 179 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 1.882 Fit side-chains revert: symmetry clash REVERT: A 232 LEU cc_start: 0.6611 (OUTLIER) cc_final: 0.6133 (mm) REVERT: A 337 MET cc_start: 0.7209 (tpp) cc_final: 0.6888 (tpt) REVERT: B 297 MET cc_start: 0.7172 (ttm) cc_final: 0.6906 (ttm) REVERT: b 252 GLU cc_start: 0.7184 (pm20) cc_final: 0.6812 (pt0) outliers start: 31 outliers final: 10 residues processed: 170 average time/residue: 0.2733 time to fit residues: 69.6270 Evaluate side-chains 143 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 1.752 ------------------------------------------------------------------------------- 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 B residue 243 CYS Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain a residue 135 GLU Chi-restraints excluded: chain a residue 316 ASN 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 59 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN B 27 GLN B 302 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.218410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.202721 restraints weight = 50687.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.201029 restraints weight = 55122.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.199802 restraints weight = 43885.444| |-----------------------------------------------------------------------------| r_work (final): 0.4425 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4428 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4428 r_free = 0.4428 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4428 r_free = 0.4428 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4428 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.1134 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= 0.121 Angle : 0.528 10.706 21337 Z= 0.271 Chirality : 0.040 0.349 2211 Planarity : 0.004 0.043 2796 Dihedral : 5.229 54.290 2230 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.17 % Favored : 95.72 % Rotamer: Outliers : 2.62 % Allowed : 20.37 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.20), residues: 1873 helix: 1.83 (0.15), residues: 1132 sheet: -0.70 (0.59), residues: 73 loop : -1.55 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 105 HIS 0.004 0.001 HIS a 227 PHE 0.011 0.001 PHE C 30 TYR 0.015 0.001 TYR a 185 ARG 0.005 0.000 ARG a 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00853 ( 6) link_NAG-ASN : angle 2.34257 ( 18) hydrogen bonds : bond 0.04589 ( 866) hydrogen bonds : angle 3.72363 ( 2540) SS BOND : bond 0.00386 ( 1) SS BOND : angle 2.64501 ( 2) covalent geometry : bond 0.00268 (15771) covalent geometry : angle 0.52335 (21317) *********************** 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: 40 poor density : 146 time to evaluate : 1.717 Fit side-chains REVERT: A 176 HIS cc_start: 0.5259 (OUTLIER) cc_final: 0.4318 (m-70) REVERT: A 232 LEU cc_start: 0.6568 (OUTLIER) cc_final: 0.6103 (mm) REVERT: A 337 MET cc_start: 0.7339 (tpp) cc_final: 0.6988 (tpt) REVERT: B 297 MET cc_start: 0.7235 (ttm) cc_final: 0.6986 (ttm) REVERT: a 58 MET cc_start: 0.7803 (mtt) cc_final: 0.7449 (mtt) REVERT: a 292 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.6549 (mtp180) outliers start: 40 outliers final: 19 residues processed: 174 average time/residue: 0.2856 time to fit residues: 73.0228 Evaluate side-chains 154 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 1.709 ------------------------------------------------------------------------------- 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 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 93 ASP Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 122 ILE 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 292 ARG Chi-restraints excluded: chain b residue 88 CYS Chi-restraints excluded: chain b residue 383 ASP Chi-restraints excluded: chain c residue 10 VAL Chi-restraints excluded: chain c residue 131 ASP 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 124 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 148 optimal weight: 9.9990 chunk 176 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 26 optimal weight: 0.0270 chunk 115 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 overall best weight: 1.1242 ------------------------------------------------------------------------------- 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 = 0.4589 r_free = 0.4589 target = 0.217285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.201830 restraints weight = 56130.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.199299 restraints weight = 52807.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.198131 restraints weight = 53098.669| |-----------------------------------------------------------------------------| r_work (final): 0.4415 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4416 r_free = 0.4416 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4416 r_free = 0.4416 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15778 Z= 0.133 Angle : 0.540 10.771 21337 Z= 0.274 Chirality : 0.041 0.358 2211 Planarity : 0.004 0.041 2796 Dihedral : 4.951 52.678 2230 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.65 % Favored : 95.24 % Rotamer: Outliers : 2.55 % Allowed : 21.25 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.20), residues: 1873 helix: 1.83 (0.15), residues: 1138 sheet: -0.88 (0.58), residues: 73 loop : -1.52 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 105 HIS 0.004 0.001 HIS b 266 PHE 0.013 0.001 PHE C 30 TYR 0.014 0.001 TYR a 365 ARG 0.003 0.000 ARG A 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00676 ( 6) link_NAG-ASN : angle 2.36550 ( 18) hydrogen bonds : bond 0.04708 ( 866) hydrogen bonds : angle 3.67989 ( 2540) SS BOND : bond 0.00585 ( 1) SS BOND : angle 2.15076 ( 2) covalent geometry : bond 0.00308 (15771) covalent geometry : angle 0.53590 (21317) *********************** 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 182 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 1.694 Fit side-chains REVERT: A 176 HIS cc_start: 0.5210 (OUTLIER) cc_final: 0.4140 (m-70) REVERT: A 232 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6265 (mm) REVERT: A 337 MET cc_start: 0.7405 (tpp) cc_final: 0.6985 (tpt) REVERT: B 297 MET cc_start: 0.7256 (ttm) cc_final: 0.7006 (ttm) REVERT: a 58 MET cc_start: 0.7852 (mtt) cc_final: 0.7467 (mtt) REVERT: a 234 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7057 (mp0) REVERT: a 292 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.6553 (mtp180) REVERT: a 328 LEU cc_start: 0.6611 (OUTLIER) cc_final: 0.6377 (mp) REVERT: c 115 THR cc_start: 0.9013 (OUTLIER) cc_final: 0.8554 (t) outliers start: 39 outliers final: 22 residues processed: 172 average time/residue: 0.2768 time to fit residues: 72.0238 Evaluate side-chains 160 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 1.751 ------------------------------------------------------------------------------- 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 113 LEU 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 14 VAL Chi-restraints excluded: chain C residue 93 ASP 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 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 234 GLU 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 b residue 386 GLU 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 137 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 51 optimal weight: 0.2980 chunk 113 optimal weight: 0.6980 chunk 119 optimal weight: 0.0470 chunk 52 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 71 optimal weight: 0.3980 chunk 170 optimal weight: 0.2980 chunk 19 optimal weight: 0.0570 chunk 181 optimal weight: 0.9980 overall best weight: 0.2196 ------------------------------------------------------------------------------- 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 205 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 = 0.4636 r_free = 0.4636 target = 0.221296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.201334 restraints weight = 43935.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.198955 restraints weight = 50385.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.197902 restraints weight = 38372.824| |-----------------------------------------------------------------------------| r_work (final): 0.4444 ------------------------------------------------------------------------------- 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 = 0.31 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 = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.1662 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= 0.101 Angle : 0.503 10.513 21337 Z= 0.256 Chirality : 0.039 0.293 2211 Planarity : 0.003 0.039 2796 Dihedral : 4.501 53.368 2230 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.48 % Favored : 96.42 % Rotamer: Outliers : 1.87 % Allowed : 21.81 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.20), residues: 1873 helix: 2.05 (0.15), residues: 1136 sheet: -0.78 (0.59), residues: 72 loop : -1.37 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 105 HIS 0.003 0.000 HIS b 351 PHE 0.009 0.001 PHE A 169 TYR 0.024 0.001 TYR a 185 ARG 0.007 0.000 ARG a 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00737 ( 6) link_NAG-ASN : angle 2.20330 ( 18) hydrogen bonds : bond 0.03601 ( 866) hydrogen bonds : angle 3.45859 ( 2540) SS BOND : bond 0.00282 ( 1) SS BOND : angle 1.44490 ( 2) covalent geometry : bond 0.00213 (15771) covalent geometry : angle 0.49904 (21317) *********************** 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 182 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 1.639 Fit side-chains revert: symmetry clash REVERT: A 155 LYS cc_start: 0.7039 (OUTLIER) cc_final: 0.6791 (tptp) REVERT: A 176 HIS cc_start: 0.5073 (OUTLIER) cc_final: 0.3692 (m-70) REVERT: A 232 LEU cc_start: 0.6405 (OUTLIER) cc_final: 0.6028 (mm) REVERT: A 337 MET cc_start: 0.7275 (tpp) cc_final: 0.6896 (tpt) REVERT: a 234 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: c 115 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8392 (t) outliers start: 28 outliers final: 12 residues processed: 174 average time/residue: 0.2465 time to fit residues: 65.4358 Evaluate side-chains 151 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 262 SER Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain a residue 176 HIS Chi-restraints excluded: chain a residue 234 GLU Chi-restraints excluded: chain b residue 271 LEU Chi-restraints excluded: chain b residue 282 THR 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 174 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 176 optimal weight: 0.6980 chunk 163 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 chunk 54 optimal weight: 7.9990 chunk 165 optimal weight: 3.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.218504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.202075 restraints weight = 43998.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.199869 restraints weight = 52686.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.198959 restraints weight = 43355.759| |-----------------------------------------------------------------------------| r_work (final): 0.4441 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4442 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4442 r_free = 0.4442 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4442 r_free = 0.4442 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4442 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.1630 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= 0.131 Angle : 0.534 10.741 21337 Z= 0.271 Chirality : 0.041 0.256 2211 Planarity : 0.004 0.039 2796 Dihedral : 4.494 52.566 2230 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.28 % Favored : 95.61 % Rotamer: Outliers : 2.31 % Allowed : 21.81 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.20), residues: 1873 helix: 2.01 (0.15), residues: 1143 sheet: -0.79 (0.59), residues: 73 loop : -1.46 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 105 HIS 0.004 0.001 HIS b 266 PHE 0.011 0.001 PHE b 352 TYR 0.020 0.001 TYR A 312 ARG 0.004 0.000 ARG A 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00615 ( 6) link_NAG-ASN : angle 1.91127 ( 18) hydrogen bonds : bond 0.04471 ( 866) hydrogen bonds : angle 3.53128 ( 2540) SS BOND : bond 0.00391 ( 1) SS BOND : angle 1.85397 ( 2) covalent geometry : bond 0.00305 (15771) covalent geometry : angle 0.53111 (21317) *********************** 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 170 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 1.662 Fit side-chains REVERT: A 155 LYS cc_start: 0.7111 (OUTLIER) cc_final: 0.6858 (tptp) REVERT: A 176 HIS cc_start: 0.5131 (OUTLIER) cc_final: 0.3807 (m-70) REVERT: A 232 LEU cc_start: 0.6685 (OUTLIER) cc_final: 0.6223 (mm) REVERT: A 309 PHE cc_start: 0.5643 (OUTLIER) cc_final: 0.4780 (t80) REVERT: A 337 MET cc_start: 0.7386 (tpp) cc_final: 0.6934 (tpt) REVERT: a 179 MET cc_start: 0.8276 (tpp) cc_final: 0.7804 (tpp) REVERT: a 234 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: a 292 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.6514 (mtp180) outliers start: 35 outliers final: 19 residues processed: 164 average time/residue: 0.2649 time to fit residues: 66.4591 Evaluate side-chains 155 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 262 SER Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 14 VAL 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 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 381 ASP 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 131 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 81 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 87 optimal weight: 0.0060 chunk 30 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 141 optimal weight: 0.8980 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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 = 0.4614 r_free = 0.4614 target = 0.220049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.204260 restraints weight = 48709.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.201948 restraints weight = 53634.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.201305 restraints weight = 45375.868| |-----------------------------------------------------------------------------| r_work (final): 0.4462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4464 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4464 r_free = 0.4464 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4464 r_free = 0.4464 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15778 Z= 0.110 Angle : 0.520 10.704 21337 Z= 0.261 Chirality : 0.040 0.369 2211 Planarity : 0.003 0.038 2796 Dihedral : 4.415 52.544 2230 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.85 % Favored : 96.04 % Rotamer: Outliers : 2.12 % Allowed : 22.18 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.20), residues: 1873 helix: 2.06 (0.15), residues: 1142 sheet: -0.88 (0.58), residues: 75 loop : -1.41 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP b 60 HIS 0.003 0.001 HIS b 266 PHE 0.010 0.001 PHE C 30 TYR 0.016 0.001 TYR A 312 ARG 0.007 0.000 ARG a 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00668 ( 6) link_NAG-ASN : angle 2.20910 ( 18) hydrogen bonds : bond 0.04047 ( 866) hydrogen bonds : angle 3.47652 ( 2540) SS BOND : bond 0.00318 ( 1) SS BOND : angle 1.60529 ( 2) covalent geometry : bond 0.00246 (15771) covalent geometry : angle 0.51590 (21317) *********************** 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 169 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 1.678 Fit side-chains REVERT: A 155 LYS cc_start: 0.7074 (OUTLIER) cc_final: 0.6837 (tptp) REVERT: A 176 HIS cc_start: 0.5081 (OUTLIER) cc_final: 0.3653 (m-70) REVERT: A 337 MET cc_start: 0.7332 (tpp) cc_final: 0.6906 (tpt) REVERT: a 234 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7166 (mp0) outliers start: 32 outliers final: 17 residues processed: 162 average time/residue: 0.2577 time to fit residues: 63.4434 Evaluate side-chains 153 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 14 VAL Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 123 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 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 386 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 134 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 143 optimal weight: 9.9990 chunk 101 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 174 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 1 optimal weight: 9.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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** ** b 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.217967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.201328 restraints weight = 42665.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.199494 restraints weight = 53735.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.198861 restraints weight = 41296.838| |-----------------------------------------------------------------------------| r_work (final): 0.4437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4436 r_free = 0.4436 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4436 r_free = 0.4436 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.1750 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 : 0.546 10.876 21337 Z= 0.277 Chirality : 0.041 0.313 2211 Planarity : 0.004 0.038 2796 Dihedral : 4.477 52.092 2230 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.76 % Favored : 95.13 % Rotamer: Outliers : 2.24 % Allowed : 21.87 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.20), residues: 1873 helix: 2.01 (0.15), residues: 1136 sheet: -0.89 (0.58), residues: 75 loop : -1.45 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP b 60 HIS 0.004 0.001 HIS b 266 PHE 0.011 0.001 PHE b 259 TYR 0.014 0.001 TYR a 365 ARG 0.004 0.000 ARG a 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00627 ( 6) link_NAG-ASN : angle 2.05454 ( 18) hydrogen bonds : bond 0.04594 ( 866) hydrogen bonds : angle 3.55689 ( 2540) SS BOND : bond 0.00410 ( 1) SS BOND : angle 1.89089 ( 2) covalent geometry : bond 0.00315 (15771) covalent geometry : angle 0.54250 (21317) *********************** 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 169 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 1.928 Fit side-chains REVERT: A 155 LYS cc_start: 0.7159 (OUTLIER) cc_final: 0.6906 (tptp) REVERT: A 176 HIS cc_start: 0.5219 (OUTLIER) cc_final: 0.3886 (m-70) REVERT: A 232 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6336 (mm) REVERT: A 309 PHE cc_start: 0.5725 (OUTLIER) cc_final: 0.4673 (t80) REVERT: A 337 MET cc_start: 0.7438 (tpp) cc_final: 0.7221 (mmm) REVERT: a 292 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.6577 (mtp180) outliers start: 34 outliers final: 26 residues processed: 161 average time/residue: 0.2624 time to fit residues: 64.3598 Evaluate side-chains 164 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 336 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 C residue 14 VAL 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 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 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 Chi-restraints excluded: chain c residue 174 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 152 optimal weight: 0.4980 chunk 167 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 155 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.216703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.200493 restraints weight = 45372.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.198529 restraints weight = 54005.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.197557 restraints weight = 43599.936| |-----------------------------------------------------------------------------| r_work (final): 0.4425 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4427 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4427 r_free = 0.4427 target_work(ls_wunit_k1) = 0.200 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4427 r_free = 0.4427 target_work(ls_wunit_k1) = 0.200 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4427 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15778 Z= 0.154 Angle : 0.567 10.899 21337 Z= 0.288 Chirality : 0.042 0.299 2211 Planarity : 0.004 0.038 2796 Dihedral : 4.584 51.782 2230 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.76 % Favored : 95.13 % Rotamer: Outliers : 2.49 % Allowed : 21.87 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.20), residues: 1873 helix: 1.94 (0.15), residues: 1133 sheet: -0.99 (0.58), residues: 75 loop : -1.50 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP b 60 HIS 0.005 0.001 HIS b 266 PHE 0.015 0.001 PHE C 44 TYR 0.018 0.001 TYR a 185 ARG 0.004 0.000 ARG A 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00617 ( 6) link_NAG-ASN : angle 1.96765 ( 18) hydrogen bonds : bond 0.04970 ( 866) hydrogen bonds : angle 3.64845 ( 2540) SS BOND : bond 0.00399 ( 1) SS BOND : angle 2.10252 ( 2) covalent geometry : bond 0.00368 (15771) covalent geometry : angle 0.56447 (21317) *********************** 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 178 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 140 time to evaluate : 1.667 Fit side-chains REVERT: A 155 LYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6938 (tptp) REVERT: A 176 HIS cc_start: 0.5331 (OUTLIER) cc_final: 0.4115 (m-70) REVERT: A 309 PHE cc_start: 0.5490 (OUTLIER) cc_final: 0.4526 (t80) REVERT: a 234 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6693 (mp0) REVERT: a 292 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.6564 (mtp180) outliers start: 38 outliers final: 29 residues processed: 169 average time/residue: 0.2577 time to fit residues: 65.9663 Evaluate side-chains 171 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 137 time to evaluate : 1.772 ------------------------------------------------------------------------------- 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 282 CYS Chi-restraints excluded: chain A residue 309 PHE 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 C residue 14 VAL 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 135 VAL 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 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 Chi-restraints excluded: chain c residue 174 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 73.4842 > 50: distance: 37 - 40: 34.248 distance: 41 - 42: 40.803 distance: 41 - 44: 39.267 distance: 42 - 50: 43.015 distance: 44 - 45: 10.924 distance: 45 - 46: 30.513 distance: 45 - 47: 29.224 distance: 46 - 48: 39.898 distance: 47 - 49: 39.157 distance: 50 - 51: 12.181 distance: 51 - 52: 43.802 distance: 52 - 53: 14.477 distance: 52 - 56: 40.310 distance: 54 - 55: 40.444 distance: 56 - 57: 32.711 distance: 57 - 58: 57.229 distance: 57 - 60: 28.904 distance: 58 - 64: 8.298 distance: 60 - 61: 41.890 distance: 61 - 62: 39.753 distance: 64 - 65: 51.438 distance: 65 - 66: 25.504 distance: 65 - 68: 41.181 distance: 66 - 67: 23.192 distance: 66 - 70: 22.929 distance: 67 - 96: 59.814 distance: 68 - 69: 13.158 distance: 71 - 72: 24.212 distance: 72 - 73: 5.032 distance: 72 - 79: 17.225 distance: 73 - 105: 41.207 distance: 74 - 75: 40.403 distance: 75 - 76: 43.398 distance: 76 - 77: 10.580 distance: 76 - 78: 29.884 distance: 79 - 80: 9.239 distance: 80 - 81: 9.182 distance: 80 - 83: 26.847 distance: 82 - 113: 42.132 distance: 83 - 84: 13.544 distance: 84 - 85: 25.940 distance: 85 - 87: 39.679 distance: 88 - 89: 20.022 distance: 89 - 90: 21.114 distance: 89 - 92: 45.155 distance: 90 - 91: 40.181 distance: 90 - 96: 40.354 distance: 91 - 122: 32.058 distance: 92 - 93: 47.849 distance: 93 - 94: 28.303 distance: 94 - 95: 40.290 distance: 96 - 97: 18.701 distance: 97 - 98: 58.390 distance: 97 - 100: 30.700 distance: 98 - 99: 49.552 distance: 99 - 131: 30.337 distance: 100 - 101: 15.974 distance: 101 - 102: 37.541 distance: 102 - 104: 56.641 distance: 106 - 107: 38.971 distance: 106 - 109: 39.058 distance: 107 - 108: 40.790 distance: 107 - 113: 37.586 distance: 108 - 142: 30.986 distance: 110 - 111: 39.379 distance: 113 - 114: 26.354 distance: 114 - 115: 15.380 distance: 114 - 117: 14.584 distance: 115 - 122: 35.206 distance: 117 - 118: 55.593 distance: 119 - 121: 6.895