Starting phenix.real_space_refine on Mon Apr 6 00:07:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m6w_63665/04_2026/9m6w_63665.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m6w_63665/04_2026/9m6w_63665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m6w_63665/04_2026/9m6w_63665.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m6w_63665/04_2026/9m6w_63665.map" model { file = "/net/cci-nas-00/data/ceres_data/9m6w_63665/04_2026/9m6w_63665.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m6w_63665/04_2026/9m6w_63665.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 5 5.21 5 S 71 5.16 5 C 9027 2.51 5 N 2418 2.21 5 O 2733 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14269 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2333 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 13, 'TRANS': 281} Chain breaks: 1 Chain: "C" Number of atoms: 2354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2354 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 13, 'TRANS': 284} Chain breaks: 1 Chain: "D" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2342 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 13, 'TRANS': 282} Chain breaks: 1 Chain: "E" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2360 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 13, 'TRANS': 285} Chain breaks: 1 Chain: "F" Number of atoms: 2329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2329 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 13, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 2316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2316 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 13, 'TRANS': 279} Chain breaks: 1 Chain: "G" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 75 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'UNK:plan-1': 15} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.61, per 1000 atoms: 0.25 Number of scatterers: 14269 At special positions: 0 Unit cell: (96.35, 134.07, 138.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 71 16.00 P 15 15.00 Mg 5 11.99 O 2733 8.00 N 2418 7.00 C 9027 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 506.1 milliseconds 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3408 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 7 sheets defined 60.2% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'B' and resid 43 through 61 Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 70 through 78 Processing helix chain 'B' and resid 96 through 107 Processing helix chain 'B' and resid 107 through 113 Processing helix chain 'B' and resid 113 through 120 removed outlier: 4.199A pdb=" N TYR B 117 " --> pdb=" O MET B 113 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 124 Processing helix chain 'B' and resid 138 through 149 Processing helix chain 'B' and resid 158 through 163 removed outlier: 3.835A pdb=" N ILE B 162 " --> pdb=" O ARG B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 184 Processing helix chain 'B' and resid 193 through 198 removed outlier: 4.029A pdb=" N PHE B 197 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 221 Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.555A pdb=" N ARG B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 271 Processing helix chain 'B' and resid 282 through 290 removed outlier: 3.551A pdb=" N ILE B 286 " --> pdb=" O ASP B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 310 Processing helix chain 'B' and resid 310 through 319 Processing helix chain 'B' and resid 340 through 348 removed outlier: 3.653A pdb=" N LYS B 347 " --> pdb=" O ASP B 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 61 Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 70 through 78 Processing helix chain 'C' and resid 96 through 108 Processing helix chain 'C' and resid 108 through 113 Processing helix chain 'C' and resid 138 through 150 Processing helix chain 'C' and resid 168 through 184 Processing helix chain 'C' and resid 193 through 198 removed outlier: 4.039A pdb=" N PHE C 197 " --> pdb=" O GLN C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 221 removed outlier: 3.569A pdb=" N ASP C 221 " --> pdb=" O MET C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 249 Processing helix chain 'C' and resid 259 through 271 Processing helix chain 'C' and resid 282 through 290 removed outlier: 3.559A pdb=" N ILE C 286 " --> pdb=" O ASP C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 310 Processing helix chain 'C' and resid 310 through 320 Processing helix chain 'C' and resid 340 through 348 removed outlier: 3.638A pdb=" N PHE C 344 " --> pdb=" O LYS C 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 61 Processing helix chain 'D' and resid 62 through 66 removed outlier: 3.790A pdb=" N GLU D 66 " --> pdb=" O ALA D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 78 removed outlier: 3.618A pdb=" N SER D 78 " --> pdb=" O ARG D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'D' and resid 96 through 113 removed outlier: 5.441A pdb=" N TYR D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Proline residue: D 110 - end of helix Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 138 through 149 Processing helix chain 'D' and resid 168 through 184 Processing helix chain 'D' and resid 193 through 198 removed outlier: 4.022A pdb=" N PHE D 197 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 221 Processing helix chain 'D' and resid 237 through 241 removed outlier: 3.534A pdb=" N ASP D 240 " --> pdb=" O ARG D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 248 Processing helix chain 'D' and resid 259 through 271 Processing helix chain 'D' and resid 282 through 290 removed outlier: 3.517A pdb=" N ILE D 286 " --> pdb=" O ASP D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 310 Processing helix chain 'D' and resid 310 through 320 Processing helix chain 'D' and resid 340 through 346 Processing helix chain 'E' and resid 43 through 61 Processing helix chain 'E' and resid 62 through 66 removed outlier: 3.660A pdb=" N GLU E 66 " --> pdb=" O ALA E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 77 Processing helix chain 'E' and resid 89 through 93 Processing helix chain 'E' and resid 96 through 113 removed outlier: 4.816A pdb=" N TYR E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Proline residue: E 110 - end of helix Processing helix chain 'E' and resid 115 through 120 removed outlier: 4.255A pdb=" N ASN E 119 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER E 120 " --> pdb=" O TYR E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 149 Processing helix chain 'E' and resid 168 through 184 removed outlier: 3.502A pdb=" N LYS E 172 " --> pdb=" O GLY E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 198 removed outlier: 3.834A pdb=" N PHE E 197 " --> pdb=" O GLN E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 221 Processing helix chain 'E' and resid 237 through 241 Processing helix chain 'E' and resid 242 through 249 Processing helix chain 'E' and resid 259 through 271 Processing helix chain 'E' and resid 283 through 290 removed outlier: 3.650A pdb=" N THR E 290 " --> pdb=" O ILE E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 310 Processing helix chain 'E' and resid 310 through 321 Processing helix chain 'E' and resid 340 through 348 removed outlier: 4.256A pdb=" N PHE E 344 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS E 347 " --> pdb=" O ASP E 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 61 Processing helix chain 'F' and resid 70 through 78 Processing helix chain 'F' and resid 82 through 86 Processing helix chain 'F' and resid 96 through 113 removed outlier: 5.143A pdb=" N TYR F 109 " --> pdb=" O GLU F 105 " (cutoff:3.500A) Proline residue: F 110 - end of helix removed outlier: 3.586A pdb=" N MET F 113 " --> pdb=" O TYR F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 124 removed outlier: 3.843A pdb=" N GLN F 124 " --> pdb=" O PRO F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 149 Processing helix chain 'F' and resid 158 through 163 Processing helix chain 'F' and resid 169 through 184 Processing helix chain 'F' and resid 193 through 198 removed outlier: 4.079A pdb=" N PHE F 197 " --> pdb=" O GLN F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 221 Processing helix chain 'F' and resid 242 through 249 Processing helix chain 'F' and resid 260 through 271 Processing helix chain 'F' and resid 282 through 290 removed outlier: 3.699A pdb=" N ILE F 286 " --> pdb=" O ASP F 282 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR F 290 " --> pdb=" O ILE F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 310 Processing helix chain 'F' and resid 310 through 320 Processing helix chain 'F' and resid 340 through 348 removed outlier: 3.582A pdb=" N LYS F 347 " --> pdb=" O ASP F 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 61 Processing helix chain 'A' and resid 70 through 79 Processing helix chain 'A' and resid 96 through 107 Processing helix chain 'A' and resid 107 through 113 Processing helix chain 'A' and resid 138 through 149 Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 168 through 184 removed outlier: 3.897A pdb=" N LYS A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 198 removed outlier: 4.021A pdb=" N PHE A 197 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 221 Processing helix chain 'A' and resid 242 through 249 Processing helix chain 'A' and resid 259 through 272 Processing helix chain 'A' and resid 282 through 290 removed outlier: 3.702A pdb=" N ILE A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 310 Processing helix chain 'A' and resid 310 through 320 Processing helix chain 'A' and resid 341 through 348 Processing sheet with id=AA1, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.938A pdb=" N ALA B 234 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS B 251 " --> pdb=" O GLY B 128 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 153 through 155 Processing sheet with id=AA3, first strand: chain 'C' and resid 80 through 81 removed outlier: 3.998A pdb=" N PHE C 154 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ASP C 192 " --> pdb=" O ILE C 157 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET C 230 " --> pdb=" O CYS C 187 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA C 234 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLY C 128 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N PHE C 253 " --> pdb=" O GLY C 128 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU C 130 " --> pdb=" O PHE C 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 80 through 81 removed outlier: 3.962A pdb=" N PHE D 154 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N CYS D 187 " --> pdb=" O MET D 230 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ILE D 232 " --> pdb=" O CYS D 187 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ILE D 189 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ALA D 234 " --> pdb=" O ILE D 189 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE D 191 " --> pdb=" O ALA D 234 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLY D 128 " --> pdb=" O LYS D 251 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N PHE D 253 " --> pdb=" O GLY D 128 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU D 130 " --> pdb=" O PHE D 253 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 80 through 81 removed outlier: 4.038A pdb=" N PHE E 154 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ASN E 153 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N PHE E 190 " --> pdb=" O ASN E 153 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ILE E 155 " --> pdb=" O PHE E 190 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA E 234 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR E 235 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLY E 128 " --> pdb=" O LYS E 251 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N PHE E 253 " --> pdb=" O GLY E 128 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU E 130 " --> pdb=" O PHE E 253 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 80 through 81 removed outlier: 4.197A pdb=" N PHE F 154 " --> pdb=" O VAL F 81 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE F 190 " --> pdb=" O ILE F 155 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET F 230 " --> pdb=" O CYS F 187 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ALA F 234 " --> pdb=" O ILE F 191 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL F 129 " --> pdb=" O GLY F 233 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N THR F 235 " --> pdb=" O VAL F 129 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU F 131 " --> pdb=" O THR F 235 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY F 128 " --> pdb=" O LYS F 251 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N PHE F 253 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU F 130 " --> pdb=" O PHE F 253 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 153 through 157 removed outlier: 3.941A pdb=" N ASP A 192 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N ILE A 232 " --> pdb=" O CYS A 187 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE A 189 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N ALA A 234 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE A 191 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLY A 128 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N PHE A 253 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU A 130 " --> pdb=" O PHE A 253 " (cutoff:3.500A) 696 hydrogen bonds defined for protein. 2031 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2920 1.33 - 1.45: 3047 1.45 - 1.58: 8382 1.58 - 1.70: 22 1.70 - 1.83: 124 Bond restraints: 14495 Sorted by residual: bond pdb=" C4 ATP F 401 " pdb=" C5 ATP F 401 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.47e+01 bond pdb=" C5 ATP F 401 " pdb=" N7 ATP F 401 " ideal model delta sigma weight residual 1.387 1.333 0.054 1.00e-02 1.00e+04 2.89e+01 bond pdb=" C5 ATP F 401 " pdb=" C6 ATP F 401 " ideal model delta sigma weight residual 1.409 1.458 -0.049 1.00e-02 1.00e+04 2.44e+01 bond pdb=" C PRO A 134 " pdb=" N PRO A 135 " ideal model delta sigma weight residual 1.330 1.379 -0.049 1.19e-02 7.06e+03 1.70e+01 bond pdb=" C4 ATP F 401 " pdb=" N9 ATP F 401 " ideal model delta sigma weight residual 1.374 1.336 0.038 1.00e-02 1.00e+04 1.41e+01 ... (remaining 14490 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 19291 3.45 - 6.89: 219 6.89 - 10.34: 45 10.34 - 13.78: 9 13.78 - 17.23: 2 Bond angle restraints: 19566 Sorted by residual: angle pdb=" PB ATP F 401 " pdb=" O3B ATP F 401 " pdb=" PG ATP F 401 " ideal model delta sigma weight residual 139.87 122.64 17.23 1.00e+00 1.00e+00 2.97e+02 angle pdb=" PA ATP F 401 " pdb=" O3A ATP F 401 " pdb=" PB ATP F 401 " ideal model delta sigma weight residual 136.83 119.69 17.14 1.00e+00 1.00e+00 2.94e+02 angle pdb=" N3 ATP F 401 " pdb=" C4 ATP F 401 " pdb=" N9 ATP F 401 " ideal model delta sigma weight residual 127.04 137.74 -10.70 1.15e+00 7.59e-01 8.69e+01 angle pdb=" C5 ATP F 401 " pdb=" C4 ATP F 401 " pdb=" N3 ATP F 401 " ideal model delta sigma weight residual 126.80 117.84 8.96 1.00e+00 1.00e+00 8.02e+01 angle pdb=" C5 ATP F 401 " pdb=" C6 ATP F 401 " pdb=" N6 ATP F 401 " ideal model delta sigma weight residual 123.59 117.52 6.07 1.08e+00 8.64e-01 3.18e+01 ... (remaining 19561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 7602 17.90 - 35.81: 1120 35.81 - 53.71: 307 53.71 - 71.61: 49 71.61 - 89.52: 24 Dihedral angle restraints: 9102 sinusoidal: 3874 harmonic: 5228 Sorted by residual: dihedral pdb=" CA MET F 141 " pdb=" C MET F 141 " pdb=" N LEU F 142 " pdb=" CA LEU F 142 " ideal model delta harmonic sigma weight residual 180.00 156.88 23.12 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA ASP A 70 " pdb=" C ASP A 70 " pdb=" N ALA A 71 " pdb=" CA ALA A 71 " ideal model delta harmonic sigma weight residual -180.00 -159.71 -20.29 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA VAL A 107 " pdb=" C VAL A 107 " pdb=" N ILE A 108 " pdb=" CA ILE A 108 " ideal model delta harmonic sigma weight residual -180.00 -160.88 -19.12 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 9099 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1744 0.057 - 0.114: 388 0.114 - 0.171: 86 0.171 - 0.228: 19 0.228 - 0.285: 10 Chirality restraints: 2247 Sorted by residual: chirality pdb=" CA LEU B 246 " pdb=" N LEU B 246 " pdb=" C LEU B 246 " pdb=" CB LEU B 246 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA LEU B 184 " pdb=" N LEU B 184 " pdb=" C LEU B 184 " pdb=" CB LEU B 184 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CG LEU B 111 " pdb=" CB LEU B 111 " pdb=" CD1 LEU B 111 " pdb=" CD2 LEU B 111 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 2244 not shown) Planarity restraints: 2455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP F 273 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.78e+00 pdb=" C ASP F 273 " -0.054 2.00e-02 2.50e+03 pdb=" O ASP F 273 " 0.020 2.00e-02 2.50e+03 pdb=" N THR F 274 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 141 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.84e+00 pdb=" C MET A 141 " 0.048 2.00e-02 2.50e+03 pdb=" O MET A 141 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU A 142 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 111 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.58e+00 pdb=" C LEU B 111 " 0.048 2.00e-02 2.50e+03 pdb=" O LEU B 111 " -0.018 2.00e-02 2.50e+03 pdb=" N MET B 112 " -0.016 2.00e-02 2.50e+03 ... (remaining 2452 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 158 2.60 - 3.17: 12060 3.17 - 3.75: 24113 3.75 - 4.32: 31720 4.32 - 4.90: 51428 Nonbonded interactions: 119479 Sorted by model distance: nonbonded pdb=" O1B ATP F 401 " pdb="MG MG F 402 " model vdw 2.020 2.170 nonbonded pdb=" O2B ATP B 401 " pdb="MG MG B 402 " model vdw 2.052 2.170 nonbonded pdb=" O2G ATP C 401 " pdb="MG MG C 402 " model vdw 2.095 2.170 nonbonded pdb=" OG1 THR D 140 " pdb="MG MG D 402 " model vdw 2.108 2.170 nonbonded pdb=" OD2 ASP D 192 " pdb="MG MG D 402 " model vdw 2.162 2.170 ... (remaining 119474 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' and resid 43 through 349) selection = (chain 'B' and (resid 43 through 321 or resid 337 through 349)) selection = (chain 'C' and (resid 43 through 321 or resid 337 through 349)) selection = (chain 'D' and (resid 43 through 320 or resid 336 through 349)) selection = (chain 'E' and (resid 43 through 321 or resid 337 through 349)) selection = (chain 'F' and resid 43 through 349) } 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: 11.820 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.870 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.100 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 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 : 0.005 0.080 14495 Z= 0.264 Angle : 0.987 17.226 19566 Z= 0.542 Chirality : 0.054 0.285 2247 Planarity : 0.006 0.063 2455 Dihedral : 18.156 89.516 5694 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.83 % Allowed : 27.72 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.19), residues: 1752 helix: -0.22 (0.16), residues: 963 sheet: -0.88 (0.46), residues: 130 loop : -0.51 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 44 TYR 0.032 0.002 TYR C 132 PHE 0.047 0.002 PHE A 90 TRP 0.023 0.002 TRP B 54 HIS 0.004 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00463 (14495) covalent geometry : angle 0.98724 (19566) hydrogen bonds : bond 0.15996 ( 696) hydrogen bonds : angle 6.41635 ( 2031) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 410 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 MET cc_start: 0.7399 (pmm) cc_final: 0.6519 (mtt) REVERT: B 153 ASN cc_start: 0.8510 (m110) cc_final: 0.8244 (m-40) REVERT: B 195 ASP cc_start: 0.8918 (p0) cc_final: 0.8605 (p0) REVERT: C 193 GLN cc_start: 0.7869 (mm-40) cc_final: 0.7485 (mp-120) REVERT: C 301 LEU cc_start: 0.9119 (mp) cc_final: 0.8560 (mp) REVERT: D 198 LEU cc_start: 0.8664 (mt) cc_final: 0.8378 (mt) REVERT: D 319 GLN cc_start: 0.7779 (pp30) cc_final: 0.7554 (pp30) REVERT: E 50 GLN cc_start: 0.8893 (mt0) cc_final: 0.8679 (mt0) REVERT: E 277 ASP cc_start: 0.7383 (p0) cc_final: 0.7144 (p0) REVERT: E 285 LEU cc_start: 0.8548 (pt) cc_final: 0.7686 (mp) REVERT: E 300 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7588 (tm-30) REVERT: E 301 LEU cc_start: 0.8145 (tp) cc_final: 0.7774 (tt) REVERT: E 312 GLU cc_start: 0.8319 (mp0) cc_final: 0.8031 (tm-30) REVERT: A 64 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6883 (mt) REVERT: A 141 MET cc_start: 0.7865 (mtt) cc_final: 0.6801 (mmm) REVERT: A 163 MET cc_start: 0.7230 (tpp) cc_final: 0.4059 (ttt) outliers start: 13 outliers final: 3 residues processed: 415 average time/residue: 0.1154 time to fit residues: 71.8444 Evaluate side-chains 362 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 358 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 239 ASN Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain A residue 64 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 40.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 ASN B 182 ASN B 185 GLN E 153 ASN E 319 GLN ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.141655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.107775 restraints weight = 27316.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.111311 restraints weight = 13004.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.113595 restraints weight = 8303.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.114929 restraints weight = 6390.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.115672 restraints weight = 5531.882| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14495 Z= 0.159 Angle : 0.638 9.622 19566 Z= 0.309 Chirality : 0.042 0.163 2247 Planarity : 0.004 0.068 2455 Dihedral : 11.246 86.980 2094 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.89 % Allowed : 26.13 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.20), residues: 1752 helix: 0.41 (0.17), residues: 981 sheet: -1.08 (0.40), residues: 169 loop : -0.16 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 337 TYR 0.012 0.001 TYR E 313 PHE 0.012 0.001 PHE A 90 TRP 0.016 0.001 TRP F 220 HIS 0.004 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00365 (14495) covalent geometry : angle 0.63803 (19566) hydrogen bonds : bond 0.04136 ( 696) hydrogen bonds : angle 4.98792 ( 2031) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 374 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 MET cc_start: 0.7176 (ptp) cc_final: 0.6927 (ptp) REVERT: B 113 MET cc_start: 0.7322 (pmm) cc_final: 0.7069 (pmm) REVERT: C 237 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8596 (ptm160) REVERT: D 141 MET cc_start: 0.7331 (ttp) cc_final: 0.7086 (ttp) REVERT: D 219 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8606 (mm) REVERT: A 117 TYR cc_start: 0.7654 (m-80) cc_final: 0.7451 (m-80) REVERT: A 141 MET cc_start: 0.7780 (mtt) cc_final: 0.6074 (mpp) REVERT: A 298 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7112 (tt) outliers start: 61 outliers final: 31 residues processed: 407 average time/residue: 0.1057 time to fit residues: 66.1597 Evaluate side-chains 376 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 342 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 302 CYS Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 350 MET Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 163 MET Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 293 PHE Chi-restraints excluded: chain F residue 302 CYS Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 298 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 44 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 146 optimal weight: 0.0980 chunk 52 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 152 optimal weight: 0.0030 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 ASN C 104 HIS C 289 ASN F 124 GLN ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.144785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.111709 restraints weight = 27390.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.115315 restraints weight = 12821.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.117554 restraints weight = 8071.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.118960 restraints weight = 6194.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.119704 restraints weight = 5332.577| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14495 Z= 0.116 Angle : 0.609 8.089 19566 Z= 0.289 Chirality : 0.041 0.240 2247 Planarity : 0.004 0.050 2455 Dihedral : 10.964 86.650 2086 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.76 % Allowed : 27.09 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.20), residues: 1752 helix: 0.59 (0.17), residues: 1002 sheet: -1.08 (0.40), residues: 158 loop : -0.12 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 337 TYR 0.014 0.001 TYR F 109 PHE 0.017 0.001 PHE F 197 TRP 0.009 0.001 TRP B 54 HIS 0.003 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00258 (14495) covalent geometry : angle 0.60895 (19566) hydrogen bonds : bond 0.03524 ( 696) hydrogen bonds : angle 4.77997 ( 2031) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 374 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 MET cc_start: 0.7143 (ptp) cc_final: 0.6820 (ptm) REVERT: B 113 MET cc_start: 0.7299 (pmm) cc_final: 0.7079 (pmm) REVERT: C 91 GLN cc_start: 0.8624 (mm-40) cc_final: 0.8284 (tm-30) REVERT: C 265 LYS cc_start: 0.8674 (mmmt) cc_final: 0.8390 (mmmt) REVERT: C 284 GLN cc_start: 0.8890 (tp-100) cc_final: 0.8683 (tp-100) REVERT: D 141 MET cc_start: 0.7220 (ttp) cc_final: 0.6954 (ttp) REVERT: D 159 MET cc_start: 0.8162 (tpp) cc_final: 0.7785 (tpp) REVERT: D 219 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8623 (mm) REVERT: E 219 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8627 (mm) REVERT: F 141 MET cc_start: 0.7937 (mtt) cc_final: 0.7585 (mtt) REVERT: A 57 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.6936 (mt) REVERT: A 141 MET cc_start: 0.7677 (mtt) cc_final: 0.5959 (mpp) REVERT: A 252 ARG cc_start: 0.8129 (mmt-90) cc_final: 0.7879 (mmt-90) REVERT: A 298 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7321 (mp) outliers start: 59 outliers final: 31 residues processed: 403 average time/residue: 0.1013 time to fit residues: 63.0058 Evaluate side-chains 381 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 346 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 302 CYS Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 350 MET Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 163 MET Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 293 PHE Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 298 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 160 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 115 optimal weight: 20.0000 chunk 14 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 ASN B 171 ASN B 182 ASN C 206 HIS C 289 ASN D 119 ASN E 153 ASN F 124 GLN ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.139776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.105507 restraints weight = 27490.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.108973 restraints weight = 13001.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.111159 restraints weight = 8320.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.112438 restraints weight = 6453.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.113262 restraints weight = 5612.544| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14495 Z= 0.194 Angle : 0.637 11.352 19566 Z= 0.306 Chirality : 0.042 0.201 2247 Planarity : 0.004 0.060 2455 Dihedral : 11.053 84.000 2086 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 5.10 % Allowed : 26.90 % Favored : 68.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.20), residues: 1752 helix: 0.85 (0.17), residues: 982 sheet: -1.05 (0.40), residues: 168 loop : -0.01 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 247 TYR 0.021 0.002 TYR C 313 PHE 0.016 0.002 PHE E 154 TRP 0.015 0.001 TRP F 220 HIS 0.004 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00453 (14495) covalent geometry : angle 0.63713 (19566) hydrogen bonds : bond 0.03490 ( 696) hydrogen bonds : angle 4.70620 ( 2031) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 348 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 MET cc_start: 0.7334 (ptp) cc_final: 0.7092 (ptm) REVERT: C 91 GLN cc_start: 0.8650 (mm-40) cc_final: 0.8321 (tm-30) REVERT: C 108 ILE cc_start: 0.8525 (mm) cc_final: 0.8132 (mm) REVERT: C 113 MET cc_start: 0.8659 (mtm) cc_final: 0.8341 (pmm) REVERT: C 265 LYS cc_start: 0.8701 (mmmt) cc_final: 0.8440 (mmmt) REVERT: C 284 GLN cc_start: 0.8881 (tp-100) cc_final: 0.8656 (tp-100) REVERT: D 53 GLN cc_start: 0.8679 (mp10) cc_final: 0.8398 (mp10) REVERT: D 141 MET cc_start: 0.7697 (ttp) cc_final: 0.7493 (ttp) REVERT: D 219 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8622 (mm) REVERT: A 55 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7770 (tp30) REVERT: A 57 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.6947 (mt) REVERT: A 141 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.6050 (mpp) REVERT: A 252 ARG cc_start: 0.8168 (mmt-90) cc_final: 0.7908 (mmt-90) REVERT: A 298 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7135 (tt) outliers start: 80 outliers final: 48 residues processed: 398 average time/residue: 0.0997 time to fit residues: 62.3385 Evaluate side-chains 376 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 324 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 302 CYS Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 175 ASP Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 293 PHE Chi-restraints excluded: chain F residue 302 CYS Chi-restraints excluded: chain F residue 308 ASP Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 298 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 170 optimal weight: 0.4980 chunk 41 optimal weight: 0.0980 chunk 149 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 136 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 ASN B 185 GLN C 206 HIS C 289 ASN F 124 GLN ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.143145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.109453 restraints weight = 27535.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.112990 restraints weight = 13009.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.115176 restraints weight = 8302.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.116562 restraints weight = 6453.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.117197 restraints weight = 5588.453| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14495 Z= 0.119 Angle : 0.633 12.951 19566 Z= 0.296 Chirality : 0.042 0.281 2247 Planarity : 0.003 0.060 2455 Dihedral : 10.820 85.330 2086 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.27 % Allowed : 28.49 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.21), residues: 1752 helix: 0.88 (0.17), residues: 987 sheet: -1.04 (0.42), residues: 157 loop : 0.14 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 248 TYR 0.016 0.001 TYR F 109 PHE 0.015 0.001 PHE B 293 TRP 0.009 0.001 TRP B 54 HIS 0.005 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00269 (14495) covalent geometry : angle 0.63257 (19566) hydrogen bonds : bond 0.03170 ( 696) hydrogen bonds : angle 4.60954 ( 2031) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 359 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 MET cc_start: 0.7536 (pmm) cc_final: 0.7200 (mtt) REVERT: B 141 MET cc_start: 0.8244 (mtm) cc_final: 0.7795 (mtt) REVERT: C 91 GLN cc_start: 0.8601 (mm-40) cc_final: 0.8319 (tm-30) REVERT: C 265 LYS cc_start: 0.8658 (mmmt) cc_final: 0.8407 (mmmt) REVERT: C 284 GLN cc_start: 0.8894 (tp-100) cc_final: 0.8658 (tp-100) REVERT: D 141 MET cc_start: 0.7389 (ttp) cc_final: 0.7153 (ttp) REVERT: F 141 MET cc_start: 0.7980 (mtt) cc_final: 0.7555 (mtt) REVERT: A 57 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7330 (mp) REVERT: A 298 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7233 (tt) outliers start: 67 outliers final: 39 residues processed: 398 average time/residue: 0.0994 time to fit residues: 62.2689 Evaluate side-chains 373 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 332 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain D residue 53 GLN Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 293 PHE Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 298 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 102 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 115 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 154 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 ASN C 236 ASN C 289 ASN D 319 GLN F 124 GLN ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.140683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.107044 restraints weight = 27513.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.110509 restraints weight = 12907.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.112685 restraints weight = 8211.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.113970 restraints weight = 6347.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.114730 restraints weight = 5508.485| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14495 Z= 0.167 Angle : 0.643 11.717 19566 Z= 0.304 Chirality : 0.043 0.300 2247 Planarity : 0.004 0.056 2455 Dihedral : 10.818 84.106 2086 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.40 % Allowed : 29.25 % Favored : 66.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.21), residues: 1752 helix: 0.96 (0.17), residues: 976 sheet: -1.13 (0.40), residues: 177 loop : 0.26 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 247 TYR 0.017 0.001 TYR B 313 PHE 0.016 0.002 PHE B 293 TRP 0.011 0.001 TRP D 220 HIS 0.004 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00390 (14495) covalent geometry : angle 0.64273 (19566) hydrogen bonds : bond 0.03283 ( 696) hydrogen bonds : angle 4.63708 ( 2031) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 339 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 293 PHE cc_start: 0.7776 (OUTLIER) cc_final: 0.7150 (t80) REVERT: C 91 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8331 (tm-30) REVERT: C 193 GLN cc_start: 0.8425 (mm-40) cc_final: 0.7836 (mp-120) REVERT: C 265 LYS cc_start: 0.8674 (mmmt) cc_final: 0.8413 (mmmt) REVERT: C 284 GLN cc_start: 0.8895 (tp-100) cc_final: 0.8651 (tp-100) REVERT: D 141 MET cc_start: 0.7640 (ttp) cc_final: 0.7436 (ttp) REVERT: D 159 MET cc_start: 0.8535 (tpp) cc_final: 0.8273 (tpp) REVERT: D 219 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8677 (mm) REVERT: A 57 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.6912 (mt) REVERT: A 58 VAL cc_start: 0.8504 (t) cc_final: 0.8223 (p) REVERT: A 298 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7275 (tt) outliers start: 69 outliers final: 51 residues processed: 378 average time/residue: 0.0976 time to fit residues: 58.3216 Evaluate side-chains 381 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 326 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 236 ASN Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 78 SER Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 293 PHE Chi-restraints excluded: chain F residue 302 CYS Chi-restraints excluded: chain F residue 308 ASP Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 298 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 97 optimal weight: 0.7980 chunk 170 optimal weight: 7.9990 chunk 60 optimal weight: 0.0470 chunk 91 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 168 optimal weight: 20.0000 chunk 55 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 overall best weight: 1.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 ASN C 236 ASN C 289 ASN ** D 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 GLN ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.141339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.107325 restraints weight = 27418.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.110863 restraints weight = 12911.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.113075 restraints weight = 8240.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.114397 restraints weight = 6376.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.115018 restraints weight = 5536.665| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14495 Z= 0.148 Angle : 0.640 10.859 19566 Z= 0.304 Chirality : 0.042 0.259 2247 Planarity : 0.004 0.057 2455 Dihedral : 10.807 83.714 2086 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.46 % Allowed : 29.06 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.21), residues: 1752 helix: 1.00 (0.17), residues: 976 sheet: -1.19 (0.40), residues: 182 loop : 0.34 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 252 TYR 0.015 0.001 TYR F 264 PHE 0.019 0.001 PHE B 293 TRP 0.010 0.001 TRP B 54 HIS 0.004 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00347 (14495) covalent geometry : angle 0.64027 (19566) hydrogen bonds : bond 0.03191 ( 696) hydrogen bonds : angle 4.61092 ( 2031) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 338 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 MET cc_start: 0.7182 (ptm) cc_final: 0.6926 (ptp) REVERT: B 141 MET cc_start: 0.8082 (mtm) cc_final: 0.7860 (mtt) REVERT: B 293 PHE cc_start: 0.7833 (OUTLIER) cc_final: 0.7224 (t80) REVERT: C 91 GLN cc_start: 0.8611 (mm-40) cc_final: 0.8326 (tm-30) REVERT: C 265 LYS cc_start: 0.8677 (mmmt) cc_final: 0.8403 (mmmt) REVERT: C 284 GLN cc_start: 0.8897 (tp-100) cc_final: 0.8646 (tp-100) REVERT: D 53 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8231 (mp10) REVERT: D 141 MET cc_start: 0.7607 (ttp) cc_final: 0.7388 (ttp) REVERT: A 57 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7515 (mp) REVERT: A 58 VAL cc_start: 0.8472 (t) cc_final: 0.8226 (p) REVERT: A 64 LEU cc_start: 0.7426 (mt) cc_final: 0.7221 (mp) REVERT: A 254 LEU cc_start: 0.9123 (pt) cc_final: 0.8867 (mp) REVERT: A 298 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7294 (tt) outliers start: 70 outliers final: 53 residues processed: 383 average time/residue: 0.0975 time to fit residues: 59.3784 Evaluate side-chains 384 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 327 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain D residue 53 GLN Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 78 SER Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 175 ASP Chi-restraints excluded: chain F residue 293 PHE Chi-restraints excluded: chain F residue 302 CYS Chi-restraints excluded: chain F residue 308 ASP Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 298 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 76 optimal weight: 0.8980 chunk 171 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 167 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 chunk 144 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 ASN C 206 HIS ** D 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.142624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.109107 restraints weight = 27331.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.112653 restraints weight = 12872.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.114874 restraints weight = 8182.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.116218 restraints weight = 6316.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.116892 restraints weight = 5478.526| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14495 Z= 0.128 Angle : 0.645 10.761 19566 Z= 0.304 Chirality : 0.042 0.251 2247 Planarity : 0.004 0.059 2455 Dihedral : 10.724 83.973 2086 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.02 % Allowed : 29.70 % Favored : 66.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.21), residues: 1752 helix: 0.97 (0.17), residues: 988 sheet: -1.09 (0.40), residues: 175 loop : 0.40 (0.27), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 252 TYR 0.020 0.001 TYR D 72 PHE 0.018 0.001 PHE B 293 TRP 0.017 0.001 TRP D 220 HIS 0.003 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00298 (14495) covalent geometry : angle 0.64477 (19566) hydrogen bonds : bond 0.03099 ( 696) hydrogen bonds : angle 4.60037 ( 2031) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 338 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 141 MET cc_start: 0.7995 (mtm) cc_final: 0.7738 (mtt) REVERT: B 293 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.7218 (t80) REVERT: C 91 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8336 (tm-30) REVERT: C 193 GLN cc_start: 0.8351 (mm-40) cc_final: 0.7782 (mp-120) REVERT: C 265 LYS cc_start: 0.8664 (mmmt) cc_final: 0.8395 (mmmt) REVERT: C 284 GLN cc_start: 0.8907 (tp-100) cc_final: 0.8679 (tp-100) REVERT: D 53 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8261 (mp10) REVERT: D 141 MET cc_start: 0.7554 (ttp) cc_final: 0.7336 (ttp) REVERT: F 141 MET cc_start: 0.7968 (mtt) cc_final: 0.7575 (mtt) REVERT: A 57 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7541 (mp) REVERT: A 58 VAL cc_start: 0.8450 (t) cc_final: 0.8229 (p) REVERT: A 254 LEU cc_start: 0.9129 (pt) cc_final: 0.8877 (mp) outliers start: 63 outliers final: 52 residues processed: 374 average time/residue: 0.0962 time to fit residues: 57.1682 Evaluate side-chains 375 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 320 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain D residue 53 GLN Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 78 SER Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 175 ASP Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 293 PHE Chi-restraints excluded: chain F residue 302 CYS Chi-restraints excluded: chain F residue 308 ASP Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 211 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 5 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 134 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 ASN C 206 HIS ** D 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.142734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.109236 restraints weight = 27475.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.112764 restraints weight = 12892.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.114957 restraints weight = 8198.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.116292 restraints weight = 6322.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.116962 restraints weight = 5483.685| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14495 Z= 0.133 Angle : 0.650 10.863 19566 Z= 0.308 Chirality : 0.042 0.265 2247 Planarity : 0.004 0.060 2455 Dihedral : 10.687 84.544 2086 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.89 % Allowed : 30.21 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.21), residues: 1752 helix: 1.00 (0.17), residues: 993 sheet: -1.05 (0.40), residues: 176 loop : 0.43 (0.27), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 247 TYR 0.018 0.001 TYR F 264 PHE 0.018 0.001 PHE B 293 TRP 0.019 0.001 TRP D 220 HIS 0.003 0.000 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00310 (14495) covalent geometry : angle 0.65009 (19566) hydrogen bonds : bond 0.03067 ( 696) hydrogen bonds : angle 4.57080 ( 2031) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 331 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 141 MET cc_start: 0.7972 (mtm) cc_final: 0.7714 (mtt) REVERT: B 293 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.7283 (t80) REVERT: C 91 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8335 (tm-30) REVERT: C 219 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8366 (mm) REVERT: C 257 LEU cc_start: 0.8698 (mt) cc_final: 0.7778 (pt) REVERT: C 265 LYS cc_start: 0.8671 (mmmt) cc_final: 0.8398 (mmmt) REVERT: C 284 GLN cc_start: 0.8903 (tp-100) cc_final: 0.8667 (tp-100) REVERT: D 141 MET cc_start: 0.7554 (ttp) cc_final: 0.7352 (ttp) REVERT: D 149 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7260 (tt0) REVERT: E 207 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7402 (pt0) REVERT: F 113 MET cc_start: 0.8854 (ptp) cc_final: 0.8505 (ptp) REVERT: F 141 MET cc_start: 0.8028 (mtt) cc_final: 0.7610 (mtt) REVERT: A 57 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7616 (mp) REVERT: A 254 LEU cc_start: 0.9124 (pt) cc_final: 0.8867 (mp) outliers start: 61 outliers final: 50 residues processed: 368 average time/residue: 0.1057 time to fit residues: 60.4515 Evaluate side-chains 373 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 318 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 78 SER Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 175 ASP Chi-restraints excluded: chain F residue 293 PHE Chi-restraints excluded: chain F residue 308 ASP Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 211 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 48 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 153 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 chunk 154 optimal weight: 0.0980 chunk 87 optimal weight: 0.0370 overall best weight: 1.0264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 ASN ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 HIS ** D 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.143271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.110114 restraints weight = 27236.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.113582 restraints weight = 12892.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.115852 restraints weight = 8199.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.117227 restraints weight = 6314.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.117904 restraints weight = 5446.737| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14495 Z= 0.132 Angle : 0.671 15.376 19566 Z= 0.315 Chirality : 0.043 0.260 2247 Planarity : 0.004 0.059 2455 Dihedral : 10.644 85.124 2086 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.76 % Allowed : 30.78 % Favored : 65.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.21), residues: 1752 helix: 1.00 (0.17), residues: 999 sheet: -1.00 (0.40), residues: 175 loop : 0.40 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 252 TYR 0.018 0.001 TYR F 264 PHE 0.017 0.001 PHE F 190 TRP 0.021 0.001 TRP D 220 HIS 0.003 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00308 (14495) covalent geometry : angle 0.67055 (19566) hydrogen bonds : bond 0.03083 ( 696) hydrogen bonds : angle 4.59407 ( 2031) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 324 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 MET cc_start: 0.7133 (ptm) cc_final: 0.6206 (ptm) REVERT: B 113 MET cc_start: 0.8418 (mtt) cc_final: 0.7829 (mpp) REVERT: B 141 MET cc_start: 0.7959 (mtm) cc_final: 0.7694 (mtt) REVERT: B 293 PHE cc_start: 0.7685 (OUTLIER) cc_final: 0.7264 (t80) REVERT: C 91 GLN cc_start: 0.8608 (mm-40) cc_final: 0.8335 (tm-30) REVERT: C 219 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8369 (mm) REVERT: C 257 LEU cc_start: 0.8689 (mt) cc_final: 0.7762 (pt) REVERT: C 265 LYS cc_start: 0.8646 (mmmt) cc_final: 0.8389 (mmmt) REVERT: C 284 GLN cc_start: 0.8881 (tp-100) cc_final: 0.8650 (tp-100) REVERT: D 149 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7224 (tt0) REVERT: E 207 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7348 (pt0) REVERT: F 113 MET cc_start: 0.8769 (ptp) cc_final: 0.8501 (ptp) REVERT: F 141 MET cc_start: 0.7978 (mtt) cc_final: 0.7556 (mtt) REVERT: A 55 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7726 (tp30) REVERT: A 123 LEU cc_start: 0.7154 (mt) cc_final: 0.6923 (mt) REVERT: A 254 LEU cc_start: 0.9139 (pt) cc_final: 0.8878 (mp) outliers start: 59 outliers final: 51 residues processed: 362 average time/residue: 0.1004 time to fit residues: 56.7838 Evaluate side-chains 371 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 316 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 78 SER Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 175 ASP Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 293 PHE Chi-restraints excluded: chain F residue 308 ASP Chi-restraints excluded: chain F residue 341 THR Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 246 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 123 optimal weight: 0.2980 chunk 136 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 chunk 173 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 ASN ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 HIS ** D 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.142314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.108505 restraints weight = 27571.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.112070 restraints weight = 13003.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.114322 restraints weight = 8277.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.115658 restraints weight = 6385.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.116469 restraints weight = 5520.835| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14495 Z= 0.146 Angle : 0.677 13.445 19566 Z= 0.320 Chirality : 0.043 0.255 2247 Planarity : 0.004 0.058 2455 Dihedral : 10.612 85.562 2086 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.02 % Allowed : 30.59 % Favored : 65.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.21), residues: 1752 helix: 1.04 (0.17), residues: 1004 sheet: -0.95 (0.41), residues: 167 loop : 0.37 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 252 TYR 0.018 0.002 TYR F 264 PHE 0.016 0.001 PHE B 293 TRP 0.025 0.001 TRP D 220 HIS 0.003 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00345 (14495) covalent geometry : angle 0.67673 (19566) hydrogen bonds : bond 0.03105 ( 696) hydrogen bonds : angle 4.59868 ( 2031) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4689.95 seconds wall clock time: 80 minutes 58.83 seconds (4858.83 seconds total)