Starting phenix.real_space_refine on Tue Dec 31 08:57:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k0i_36765/12_2024/8k0i_36765.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k0i_36765/12_2024/8k0i_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_36765/12_2024/8k0i_36765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k0i_36765/12_2024/8k0i_36765.map" model { file = "/net/cci-nas-00/data/ceres_data/8k0i_36765/12_2024/8k0i_36765.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k0i_36765/12_2024/8k0i_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 9.39, per 1000 atoms: 0.61 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: 4.23 Conformation dependent library (CDL) restraints added in 2.0 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: 1.45 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: 4.45 Time building geometry restraints manager: 4.78 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 35.020 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.400 ------------------------------------------------------------------------------- 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 15771 Z= 0.229 Angle : 0.643 10.518 21317 Z= 0.344 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 *********************** 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 : 1.768 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: 0.2888 time to fit residues: 64.5093 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 : 1.892 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 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 15771 Z= 0.173 Angle : 0.549 10.697 21317 Z= 0.283 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 : 5.33 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 *********************** 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 : 1.850 Fit side-chains revert: symmetry clash REVERT: A 232 LEU cc_start: 0.6603 (OUTLIER) cc_final: 0.6122 (mm) REVERT: A 337 MET cc_start: 0.7249 (tpp) cc_final: 0.6923 (tpt) REVERT: B 297 MET cc_start: 0.7192 (ttm) cc_final: 0.6921 (ttm) REVERT: b 252 GLU cc_start: 0.7207 (pm20) cc_final: 0.6830 (pt0) outliers start: 31 outliers final: 10 residues processed: 170 average time/residue: 0.2857 time to fit residues: 73.4713 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 : 1.755 ------------------------------------------------------------------------------- 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 93 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 46 optimal weight: 0.0670 chunk 169 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 167 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 135 optimal weight: 5.9990 overall best weight: 1.1720 ------------------------------------------------------------------------------- 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** b 221 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15771 Z= 0.207 Angle : 0.543 10.768 21317 Z= 0.280 Chirality : 0.041 0.351 2211 Planarity : 0.004 0.044 2796 Dihedral : 5.352 54.154 2230 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.60 % Favored : 95.29 % Rotamer: Outliers : 2.80 % Allowed : 20.69 % Favored : 76.51 % 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: 0.76 (0.20), residues: 1873 helix: 1.77 (0.15), residues: 1131 sheet: -0.82 (0.59), residues: 73 loop : -1.62 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 105 HIS 0.005 0.001 HIS b 266 PHE 0.012 0.001 PHE C 30 TYR 0.014 0.001 TYR a 365 ARG 0.005 0.000 ARG a 354 *********************** 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 187 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 144 time to evaluate : 1.726 Fit side-chains REVERT: A 176 HIS cc_start: 0.5397 (OUTLIER) cc_final: 0.4588 (m-70) REVERT: A 232 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6275 (mm) REVERT: A 337 MET cc_start: 0.7401 (tpp) cc_final: 0.7026 (tpt) REVERT: B 297 MET cc_start: 0.7240 (ttm) cc_final: 0.6980 (ttm) REVERT: a 292 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.6533 (mtp180) REVERT: b 252 GLU cc_start: 0.7155 (pm20) cc_final: 0.6901 (pt0) outliers start: 43 outliers final: 20 residues processed: 175 average time/residue: 0.2975 time to fit residues: 76.4835 Evaluate side-chains 152 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 1.894 ------------------------------------------------------------------------------- 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 155 THR Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain a residue 135 GLU Chi-restraints excluded: chain a residue 176 HIS Chi-restraints excluded: chain a residue 292 ARG Chi-restraints excluded: chain b residue 88 CYS Chi-restraints excluded: chain b residue 282 THR 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 167 optimal weight: 8.9990 chunk 127 optimal weight: 0.9990 chunk 87 optimal weight: 0.4980 chunk 18 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 169 optimal weight: 0.9990 chunk 179 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 160 optimal weight: 40.0000 chunk 48 optimal weight: 0.6980 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 205 HIS ** a 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15771 Z= 0.168 Angle : 0.524 10.695 21317 Z= 0.266 Chirality : 0.040 0.377 2211 Planarity : 0.004 0.041 2796 Dihedral : 4.925 52.957 2230 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.28 % Favored : 95.61 % Rotamer: Outliers : 2.37 % Allowed : 21.31 % 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: 0.92 (0.20), residues: 1873 helix: 1.87 (0.15), residues: 1137 sheet: -1.08 (0.56), residues: 78 loop : -1.48 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 105 HIS 0.003 0.001 HIS b 266 PHE 0.012 0.001 PHE C 30 TYR 0.013 0.001 TYR a 365 ARG 0.003 0.000 ARG A 74 *********************** 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: 36 poor density : 146 time to evaluate : 1.779 Fit side-chains REVERT: A 155 LYS cc_start: 0.7149 (OUTLIER) cc_final: 0.6872 (tptp) REVERT: A 176 HIS cc_start: 0.5189 (OUTLIER) cc_final: 0.4128 (m-70) REVERT: A 232 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6242 (mm) REVERT: A 337 MET cc_start: 0.7392 (tpp) cc_final: 0.6978 (tpt) REVERT: B 185 MET cc_start: 0.7302 (tpt) cc_final: 0.6932 (tpt) REVERT: B 297 MET cc_start: 0.7227 (ttm) cc_final: 0.6979 (ttm) REVERT: a 58 MET cc_start: 0.7858 (mtt) cc_final: 0.7490 (mtt) REVERT: a 234 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: a 292 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.6537 (mtp180) REVERT: a 328 LEU cc_start: 0.6569 (OUTLIER) cc_final: 0.6334 (mp) REVERT: b 252 GLU cc_start: 0.7069 (pm20) cc_final: 0.6860 (pt0) REVERT: c 115 THR cc_start: 0.8956 (OUTLIER) cc_final: 0.8450 (t) outliers start: 36 outliers final: 18 residues processed: 172 average time/residue: 0.2799 time to fit residues: 72.4817 Evaluate side-chains 159 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 1.973 ------------------------------------------------------------------------------- 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 336 VAL Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain a residue 135 GLU 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 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 149 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 133 optimal weight: 10.0000 chunk 74 optimal weight: 0.2980 chunk 153 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 161 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15771 Z= 0.215 Angle : 0.543 10.759 21317 Z= 0.279 Chirality : 0.041 0.302 2211 Planarity : 0.004 0.039 2796 Dihedral : 4.806 52.308 2230 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.81 % Favored : 95.08 % Rotamer: Outliers : 3.12 % Allowed : 21.56 % Favored : 75.33 % 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: 0.90 (0.20), residues: 1873 helix: 1.88 (0.15), residues: 1131 sheet: -0.98 (0.58), residues: 73 loop : -1.53 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 105 HIS 0.004 0.001 HIS b 266 PHE 0.014 0.001 PHE C 44 TYR 0.023 0.001 TYR a 185 ARG 0.006 0.000 ARG a 354 *********************** 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 189 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 141 time to evaluate : 1.755 Fit side-chains revert: symmetry clash REVERT: A 155 LYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6896 (tptp) REVERT: A 176 HIS cc_start: 0.5211 (OUTLIER) cc_final: 0.4091 (m-70) REVERT: A 232 LEU cc_start: 0.6791 (OUTLIER) cc_final: 0.6307 (mm) REVERT: A 309 PHE cc_start: 0.5706 (OUTLIER) cc_final: 0.4864 (t80) REVERT: A 337 MET cc_start: 0.7474 (tpp) cc_final: 0.7003 (tpt) REVERT: B 185 MET cc_start: 0.7253 (tpt) cc_final: 0.6844 (tpt) REVERT: B 297 MET cc_start: 0.7261 (ttm) cc_final: 0.7003 (ttm) REVERT: a 234 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7029 (mp0) REVERT: a 292 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.6548 (mtp180) REVERT: a 328 LEU cc_start: 0.6647 (OUTLIER) cc_final: 0.6430 (mp) outliers start: 48 outliers final: 28 residues processed: 177 average time/residue: 0.2667 time to fit residues: 71.3484 Evaluate side-chains 168 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 84 CYS Chi-restraints excluded: chain B residue 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 123 THR 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 271 LEU Chi-restraints excluded: chain b residue 282 THR Chi-restraints excluded: chain b residue 331 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 0.4980 chunk 161 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 149 optimal weight: 8.9990 chunk 83 optimal weight: 0.1980 chunk 14 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15771 Z= 0.218 Angle : 0.554 10.801 21317 Z= 0.283 Chirality : 0.041 0.264 2211 Planarity : 0.004 0.038 2796 Dihedral : 4.727 52.178 2230 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.81 % Favored : 95.08 % Rotamer: Outliers : 2.99 % Allowed : 21.93 % Favored : 75.08 % 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: 0.89 (0.20), residues: 1873 helix: 1.88 (0.15), residues: 1132 sheet: -1.18 (0.56), residues: 78 loop : -1.55 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 105 HIS 0.004 0.001 HIS b 266 PHE 0.014 0.001 PHE C 44 TYR 0.016 0.001 TYR a 365 ARG 0.003 0.000 ARG A 74 *********************** 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 189 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 143 time to evaluate : 1.744 Fit side-chains REVERT: A 155 LYS cc_start: 0.7192 (OUTLIER) cc_final: 0.6916 (tptp) REVERT: A 176 HIS cc_start: 0.5227 (OUTLIER) cc_final: 0.4109 (m-70) REVERT: A 232 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6326 (mm) REVERT: A 309 PHE cc_start: 0.5757 (OUTLIER) cc_final: 0.4729 (t80) REVERT: B 185 MET cc_start: 0.7271 (tpt) cc_final: 0.6926 (tpt) REVERT: B 297 MET cc_start: 0.7284 (ttm) cc_final: 0.7021 (ttm) REVERT: a 234 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7138 (mp0) REVERT: a 292 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.6544 (mtp180) REVERT: b 119 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7478 (tt) outliers start: 46 outliers final: 31 residues processed: 177 average time/residue: 0.2732 time to fit residues: 72.2253 Evaluate side-chains 171 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 84 CYS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 98 LEU 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 C residue 155 THR Chi-restraints excluded: chain a residue 132 LEU Chi-restraints excluded: chain a residue 176 HIS Chi-restraints excluded: chain a residue 200 LEU Chi-restraints excluded: chain a residue 234 GLU Chi-restraints excluded: chain a residue 292 ARG Chi-restraints excluded: chain a residue 322 GLU Chi-restraints excluded: chain b residue 88 CYS Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain b residue 270 VAL 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 383 ASP Chi-restraints excluded: chain b residue 386 GLU Chi-restraints excluded: chain c residue 10 VAL Chi-restraints excluded: chain c residue 69 MET Chi-restraints excluded: chain c residue 131 ASP Chi-restraints excluded: chain c residue 174 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 131 optimal weight: 8.9990 chunk 101 optimal weight: 0.8980 chunk 151 optimal weight: 7.9990 chunk 100 optimal weight: 0.1980 chunk 179 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15771 Z= 0.162 Angle : 0.519 10.682 21317 Z= 0.264 Chirality : 0.040 0.295 2211 Planarity : 0.003 0.038 2796 Dihedral : 4.558 52.524 2230 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.06 % Favored : 95.83 % Rotamer: Outliers : 2.93 % Allowed : 21.93 % Favored : 75.14 % 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: 1.04 (0.20), residues: 1873 helix: 1.99 (0.15), residues: 1136 sheet: -1.09 (0.57), residues: 78 loop : -1.48 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 105 HIS 0.003 0.001 HIS b 266 PHE 0.010 0.001 PHE C 44 TYR 0.017 0.001 TYR a 185 ARG 0.003 0.000 ARG a 354 *********************** 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 186 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 141 time to evaluate : 1.698 Fit side-chains revert: symmetry clash REVERT: A 155 LYS cc_start: 0.7141 (OUTLIER) cc_final: 0.6878 (tptp) REVERT: A 176 HIS cc_start: 0.5260 (OUTLIER) cc_final: 0.3913 (m-70) REVERT: A 232 LEU cc_start: 0.6723 (OUTLIER) cc_final: 0.6243 (mm) REVERT: A 309 PHE cc_start: 0.5706 (OUTLIER) cc_final: 0.4676 (t80) REVERT: A 337 MET cc_start: 0.6936 (mmm) cc_final: 0.6505 (tpt) REVERT: B 185 MET cc_start: 0.7296 (tpt) cc_final: 0.7039 (tpt) REVERT: a 234 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7147 (mp0) REVERT: a 292 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.6531 (mtp180) REVERT: b 119 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7476 (tt) outliers start: 45 outliers final: 29 residues processed: 174 average time/residue: 0.2578 time to fit residues: 68.7437 Evaluate side-chains 173 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain B residue 76 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 98 LEU Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain a residue 132 LEU Chi-restraints excluded: chain a residue 156 ILE 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 119 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 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 110 optimal weight: 0.9980 chunk 71 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 35 optimal weight: 0.2980 chunk 34 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 140 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15771 Z= 0.169 Angle : 0.523 10.815 21317 Z= 0.265 Chirality : 0.040 0.320 2211 Planarity : 0.003 0.038 2796 Dihedral : 4.457 52.525 2230 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.28 % Favored : 95.61 % Rotamer: Outliers : 3.05 % Allowed : 21.93 % Favored : 75.02 % 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: 2.04 (0.15), residues: 1135 sheet: -1.04 (0.57), residues: 78 loop : -1.48 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 105 HIS 0.003 0.001 HIS A 205 PHE 0.011 0.001 PHE C 30 TYR 0.013 0.001 TYR a 365 ARG 0.008 0.000 ARG a 354 *********************** 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 191 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 144 time to evaluate : 1.793 Fit side-chains REVERT: A 155 LYS cc_start: 0.7141 (OUTLIER) cc_final: 0.6891 (tptp) REVERT: A 176 HIS cc_start: 0.5169 (OUTLIER) cc_final: 0.3758 (m-70) REVERT: A 232 LEU cc_start: 0.6738 (OUTLIER) cc_final: 0.6254 (mm) REVERT: A 309 PHE cc_start: 0.5668 (OUTLIER) cc_final: 0.4591 (t80) REVERT: A 337 MET cc_start: 0.6937 (mmm) cc_final: 0.6486 (tpt) REVERT: a 234 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: a 292 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.6504 (mtp180) REVERT: b 119 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7489 (tt) REVERT: b 297 MET cc_start: 0.8084 (ptm) cc_final: 0.7855 (ptm) outliers start: 47 outliers final: 33 residues processed: 178 average time/residue: 0.2838 time to fit residues: 76.3874 Evaluate side-chains 178 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 76 LEU 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 98 LEU 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 156 ILE 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 274 GLN Chi-restraints excluded: chain a residue 292 ARG Chi-restraints excluded: chain a residue 322 GLU Chi-restraints excluded: chain b residue 88 CYS Chi-restraints excluded: chain b residue 119 LEU 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 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 163 optimal weight: 6.9990 chunk 171 optimal weight: 0.8980 chunk 156 optimal weight: 0.0010 chunk 167 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 131 optimal weight: 7.9990 chunk 51 optimal weight: 0.6980 chunk 150 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 overall best weight: 0.6386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15771 Z= 0.155 Angle : 0.518 10.690 21317 Z= 0.263 Chirality : 0.041 0.452 2211 Planarity : 0.003 0.038 2796 Dihedral : 4.452 52.634 2230 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.85 % Favored : 96.04 % Rotamer: Outliers : 2.55 % Allowed : 22.43 % Favored : 75.02 % 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: 2.12 (0.15), residues: 1129 sheet: -1.00 (0.57), residues: 78 loop : -1.44 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP b 60 HIS 0.003 0.000 HIS C 62 PHE 0.009 0.001 PHE C 30 TYR 0.019 0.001 TYR a 185 ARG 0.004 0.000 ARG A 74 *********************** 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 184 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 145 time to evaluate : 1.914 Fit side-chains REVERT: A 155 LYS cc_start: 0.7091 (OUTLIER) cc_final: 0.6871 (tptp) REVERT: A 176 HIS cc_start: 0.5247 (OUTLIER) cc_final: 0.3740 (m-70) REVERT: A 232 LEU cc_start: 0.6569 (OUTLIER) cc_final: 0.6123 (mm) REVERT: A 309 PHE cc_start: 0.5553 (OUTLIER) cc_final: 0.4491 (t80) REVERT: A 337 MET cc_start: 0.6933 (mmm) cc_final: 0.6486 (tpt) REVERT: b 119 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7494 (tt) outliers start: 39 outliers final: 28 residues processed: 171 average time/residue: 0.2606 time to fit residues: 67.7040 Evaluate side-chains 173 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 76 LEU 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 C residue 135 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain a residue 132 LEU Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 176 HIS Chi-restraints excluded: chain a residue 200 LEU Chi-restraints excluded: chain b residue 88 CYS Chi-restraints excluded: chain b residue 119 LEU 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 69 MET Chi-restraints excluded: chain c residue 131 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 4.9990 chunk 176 optimal weight: 0.1980 chunk 107 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 185 optimal weight: 5.9990 chunk 170 optimal weight: 0.8980 chunk 147 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 90 optimal weight: 0.0030 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15771 Z= 0.152 Angle : 0.526 10.725 21317 Z= 0.265 Chirality : 0.040 0.414 2211 Planarity : 0.003 0.038 2796 Dihedral : 4.353 52.649 2230 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.96 % Favored : 95.94 % Rotamer: Outliers : 2.18 % Allowed : 22.74 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.20), residues: 1873 helix: 2.16 (0.15), residues: 1129 sheet: -0.94 (0.57), residues: 78 loop : -1.40 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP b 60 HIS 0.003 0.000 HIS A 205 PHE 0.016 0.001 PHE b 352 TYR 0.012 0.001 TYR a 365 ARG 0.004 0.000 ARG A 74 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 1.909 Fit side-chains REVERT: A 136 MET cc_start: 0.7602 (tpp) cc_final: 0.7364 (tpp) REVERT: A 155 LYS cc_start: 0.7077 (OUTLIER) cc_final: 0.6862 (tptp) REVERT: A 176 HIS cc_start: 0.5197 (OUTLIER) cc_final: 0.3592 (m-70) REVERT: A 232 LEU cc_start: 0.6580 (OUTLIER) cc_final: 0.6152 (mm) REVERT: A 309 PHE cc_start: 0.5543 (OUTLIER) cc_final: 0.4479 (t80) REVERT: A 337 MET cc_start: 0.6923 (mmm) cc_final: 0.6484 (tpt) REVERT: b 119 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7488 (tt) outliers start: 33 outliers final: 27 residues processed: 166 average time/residue: 0.2673 time to fit residues: 67.5310 Evaluate side-chains 173 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 1.656 ------------------------------------------------------------------------------- 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 245 LEU Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 76 LEU 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 135 VAL Chi-restraints excluded: chain a residue 132 LEU Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 176 HIS Chi-restraints excluded: chain a residue 200 LEU Chi-restraints excluded: chain b residue 88 CYS Chi-restraints excluded: chain b residue 119 LEU 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 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 ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 0.9980 chunk 157 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.220003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.204459 restraints weight = 48628.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.202399 restraints weight = 52221.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.201128 restraints weight = 40848.835| |-----------------------------------------------------------------------------| r_work (final): 0.4458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4457 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4457 r_free = 0.4457 target_work(ls_wunit_k1) = 0.202 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4457 r_free = 0.4457 target_work(ls_wunit_k1) = 0.202 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4457 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15771 Z= 0.170 Angle : 0.526 10.782 21317 Z= 0.266 Chirality : 0.041 0.387 2211 Planarity : 0.003 0.038 2796 Dihedral : 4.350 52.412 2230 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.96 % Favored : 95.94 % Rotamer: Outliers : 2.49 % Allowed : 22.49 % Favored : 75.02 % 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: 1.21 (0.20), residues: 1873 helix: 2.14 (0.15), residues: 1129 sheet: -0.97 (0.57), residues: 78 loop : -1.41 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP b 60 HIS 0.003 0.001 HIS b 266 PHE 0.013 0.001 PHE b 352 TYR 0.019 0.001 TYR a 185 ARG 0.004 0.000 ARG A 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2653.96 seconds wall clock time: 49 minutes 54.65 seconds (2994.65 seconds total)