Starting phenix.real_space_refine on Wed Aug 5 16:32:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vxu_65441/08_2026/9vxu_65441.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vxu_65441/08_2026/9vxu_65441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vxu_65441/08_2026/9vxu_65441.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vxu_65441/08_2026/9vxu_65441.map" model { file = "/net/cci-nas-00/data/ceres_data/9vxu_65441/08_2026/9vxu_65441.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vxu_65441/08_2026/9vxu_65441.cif" } resolution = 3.2 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= 0.006 sd= 0.089 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 52 5.16 5 C 6673 2.51 5 N 1875 2.21 5 O 1925 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10533 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2588 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 16, 'TRANS': 311} Chain breaks: 1 Chain: "B" Number of atoms: 2588 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 327, 2580 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 16, 'TRANS': 310} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 327, 2580 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 16, 'TRANS': 310} Chain breaks: 1 bond proxies already assigned to first conformer: 2627 Chain: "C" Number of atoms: 2581 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 327, 2573 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 310} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 327, 2573 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 310} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 2619 Chain: "D" Number of atoms: 2596 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 328, 2588 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 16, 'TRANS': 311} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 328, 2588 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 16, 'TRANS': 311} Chain breaks: 1 bond proxies already assigned to first conformer: 2635 Chain: "B" Number of atoms: 90 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 90 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" C1'A1SY B 401 " occ=0.50 ... (88 atoms not shown) pdb=" P27B1SY B 401 " occ=0.50 residue: pdb=" C1'A1SY C 401 " occ=0.50 ... (88 atoms not shown) pdb=" P27B1SY C 401 " occ=0.50 Time building chain proxies: 3.61, per 1000 atoms: 0.34 Number of scatterers: 10533 At special positions: 0 Unit cell: (87.36, 88.2, 105, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 P 8 15.00 O 1925 8.00 N 1875 7.00 C 6673 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: 0.89 Conformation dependent library (CDL) restraints added in 712.1 milliseconds 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2450 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 11 sheets defined 59.2% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 17 through 36 Processing helix chain 'A' and resid 39 through 70 removed outlier: 3.720A pdb=" N THR A 43 " --> pdb=" O PRO A 39 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU A 68 " --> pdb=" O CYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 80 through 89 removed outlier: 3.555A pdb=" N THR A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 109 Processing helix chain 'A' and resid 117 through 135 removed outlier: 3.842A pdb=" N LEU A 121 " --> pdb=" O PHE A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 152 Processing helix chain 'A' and resid 154 through 186 removed outlier: 5.016A pdb=" N ARG A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU A 170 " --> pdb=" O GLY A 166 " (cutoff:3.500A) Proline residue: A 173 - end of helix removed outlier: 4.269A pdb=" N GLN A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ALA A 177 " --> pdb=" O PRO A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 272 removed outlier: 3.509A pdb=" N GLN A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 301 removed outlier: 3.956A pdb=" N LEU A 285 " --> pdb=" O ARG A 281 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP A 301 " --> pdb=" O ASP A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.880A pdb=" N GLU A 328 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 36 Processing helix chain 'B' and resid 39 through 70 removed outlier: 3.825A pdb=" N THR B 43 " --> pdb=" O PRO B 39 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU B 68 " --> pdb=" O CYS B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 80 through 90 removed outlier: 3.732A pdb=" N THR B 84 " --> pdb=" O SER B 80 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 89 " --> pdb=" O VAL B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 107 removed outlier: 4.188A pdb=" N ARG B 95 " --> pdb=" O CYS B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 135 removed outlier: 4.506A pdb=" N LEU B 121 " --> pdb=" O PHE B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 151 removed outlier: 4.130A pdb=" N ALA B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 172 removed outlier: 4.690A pdb=" N ARG B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LEU B 170 " --> pdb=" O GLY B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.890A pdb=" N ARG B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 272 removed outlier: 3.648A pdb=" N GLN B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 301 removed outlier: 3.613A pdb=" N ALA B 288 " --> pdb=" O ARG B 284 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP B 301 " --> pdb=" O ASP B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 324 through 335 removed outlier: 3.738A pdb=" N GLU B 328 " --> pdb=" O SER B 324 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLN B 335 " --> pdb=" O ARG B 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 36 Processing helix chain 'C' and resid 39 through 70 removed outlier: 4.016A pdb=" N THR C 43 " --> pdb=" O PRO C 39 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C 67 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLU C 68 " --> pdb=" O CYS C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 80 through 90 removed outlier: 4.026A pdb=" N THR C 84 " --> pdb=" O SER C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 105 removed outlier: 4.005A pdb=" N PHE C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 135 removed outlier: 3.720A pdb=" N LEU C 121 " --> pdb=" O PHE C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 151 Processing helix chain 'C' and resid 154 through 167 Processing helix chain 'C' and resid 167 through 186 Proline residue: C 173 - end of helix removed outlier: 4.342A pdb=" N GLN C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ALA C 177 " --> pdb=" O PRO C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 274 removed outlier: 3.611A pdb=" N GLN C 266 " --> pdb=" O ALA C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 301 removed outlier: 3.783A pdb=" N LEU C 285 " --> pdb=" O ARG C 281 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP C 301 " --> pdb=" O ASP C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 335 removed outlier: 3.654A pdb=" N GLU C 328 " --> pdb=" O SER C 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 36 Processing helix chain 'D' and resid 39 through 70 removed outlier: 3.615A pdb=" N THR D 43 " --> pdb=" O PRO D 39 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU D 68 " --> pdb=" O CYS D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 73 No H-bonds generated for 'chain 'D' and resid 71 through 73' Processing helix chain 'D' and resid 80 through 89 removed outlier: 3.508A pdb=" N THR D 84 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 108 removed outlier: 3.720A pdb=" N SER D 108 " --> pdb=" O TYR D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 135 removed outlier: 3.933A pdb=" N LEU D 121 " --> pdb=" O PHE D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 151 removed outlier: 3.638A pdb=" N GLY D 151 " --> pdb=" O VAL D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 167 Processing helix chain 'D' and resid 167 through 172 Processing helix chain 'D' and resid 174 through 187 removed outlier: 3.600A pdb=" N ARG D 178 " --> pdb=" O GLU D 174 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN D 187 " --> pdb=" O ASN D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 272 removed outlier: 3.851A pdb=" N GLN D 266 " --> pdb=" O ALA D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 301 removed outlier: 4.288A pdb=" N LEU D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP D 301 " --> pdb=" O ASP D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 335 removed outlier: 3.970A pdb=" N GLU D 328 " --> pdb=" O SER D 324 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN D 335 " --> pdb=" O ARG D 331 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 259 through 260 removed outlier: 3.728A pdb=" N TYR A 314 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 219 through 224 removed outlier: 3.661A pdb=" N ARG A 220 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A 246 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 222 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ILE A 244 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LEU A 247 " --> pdb=" O ALA A 254 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 228 through 232 removed outlier: 6.508A pdb=" N ARG A 232 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LYS A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 259 through 260 removed outlier: 3.865A pdb=" N TYR B 314 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 219 through 224 removed outlier: 7.316A pdb=" N ILE B 244 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N TYR B 245 " --> pdb=" O THR B 256 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N THR B 256 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU B 247 " --> pdb=" O ALA B 254 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 228 through 232 removed outlier: 6.352A pdb=" N ARG B 232 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LYS B 236 " --> pdb=" O ARG B 232 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 219 through 224 removed outlier: 7.485A pdb=" N ILE C 244 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N SER C 243 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N VAL C 258 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N TYR C 245 " --> pdb=" O THR C 256 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N THR C 256 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU C 247 " --> pdb=" O ALA C 254 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU C 260 " --> pdb=" O TYR C 199 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR C 314 " --> pdb=" O LEU C 202 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 228 through 232 removed outlier: 6.940A pdb=" N ARG C 232 " --> pdb=" O LYS C 236 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N LYS C 236 " --> pdb=" O ARG C 232 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 198 through 203 removed outlier: 6.204A pdb=" N LEU D 198 " --> pdb=" O ARG D 310 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ILE D 312 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE D 200 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N TYR D 314 " --> pdb=" O ILE D 200 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU D 202 " --> pdb=" O TYR D 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 220 through 223 removed outlier: 3.764A pdb=" N LEU D 222 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ILE D 244 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU D 247 " --> pdb=" O ALA D 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 228 through 232 removed outlier: 6.526A pdb=" N ARG D 232 " --> pdb=" O LYS D 236 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N LYS D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) 577 hydrogen bonds defined for protein. 1703 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: 1.57 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1666 1.31 - 1.44: 2945 1.44 - 1.56: 6092 1.56 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 10783 Sorted by residual: bond pdb=" C40A1SY B 401 " pdb=" N39A1SY B 401 " ideal model delta sigma weight residual 1.304 1.442 -0.138 2.00e-02 2.50e+03 4.75e+01 bond pdb=" C40B1SY B 401 " pdb=" N39B1SY B 401 " ideal model delta sigma weight residual 1.304 1.442 -0.138 2.00e-02 2.50e+03 4.73e+01 bond pdb=" C40A1SY C 401 " pdb=" N39A1SY C 401 " ideal model delta sigma weight residual 1.304 1.442 -0.138 2.00e-02 2.50e+03 4.73e+01 bond pdb=" C40B1SY C 401 " pdb=" N39B1SY C 401 " ideal model delta sigma weight residual 1.304 1.441 -0.137 2.00e-02 2.50e+03 4.69e+01 bond pdb=" C36A1SY B 401 " pdb=" N42A1SY B 401 " ideal model delta sigma weight residual 1.357 1.492 -0.135 2.00e-02 2.50e+03 4.58e+01 ... (remaining 10778 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.72: 14511 3.72 - 7.43: 120 7.43 - 11.15: 31 11.15 - 14.87: 16 14.87 - 18.58: 8 Bond angle restraints: 14686 Sorted by residual: angle pdb=" O19A1SY B 401 " pdb=" P18A1SY B 401 " pdb=" O44A1SY B 401 " ideal model delta sigma weight residual 123.21 104.63 18.58 3.00e+00 1.11e-01 3.84e+01 angle pdb=" O19B1SY C 401 " pdb=" P18B1SY C 401 " pdb=" O44B1SY C 401 " ideal model delta sigma weight residual 123.21 104.72 18.49 3.00e+00 1.11e-01 3.80e+01 angle pdb=" O19B1SY B 401 " pdb=" P18B1SY B 401 " pdb=" O44B1SY B 401 " ideal model delta sigma weight residual 123.21 104.96 18.25 3.00e+00 1.11e-01 3.70e+01 angle pdb=" O19A1SY C 401 " pdb=" P18A1SY C 401 " pdb=" O44A1SY C 401 " ideal model delta sigma weight residual 123.21 104.99 18.22 3.00e+00 1.11e-01 3.69e+01 angle pdb=" O29A1SY B 401 " pdb=" P27A1SY B 401 " pdb=" O30A1SY B 401 " ideal model delta sigma weight residual 123.47 107.05 16.42 3.00e+00 1.11e-01 3.00e+01 ... (remaining 14681 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.42: 6299 28.42 - 56.84: 282 56.84 - 85.26: 24 85.26 - 113.68: 11 113.68 - 142.10: 14 Dihedral angle restraints: 6630 sinusoidal: 2805 harmonic: 3825 Sorted by residual: dihedral pdb=" C3'B1SY C 401 " pdb=" O28B1SY C 401 " pdb=" P27B1SY C 401 " pdb=" O29B1SY C 401 " ideal model delta sinusoidal sigma weight residual -15.81 -157.91 142.10 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" C3'A1SY C 401 " pdb=" O28A1SY C 401 " pdb=" P27A1SY C 401 " pdb=" O29A1SY C 401 " ideal model delta sinusoidal sigma weight residual -15.81 -150.77 134.96 1 3.00e+01 1.11e-03 1.82e+01 dihedral pdb=" C3'B1SY B 401 " pdb=" O28B1SY B 401 " pdb=" P27B1SY B 401 " pdb=" O29B1SY B 401 " ideal model delta sinusoidal sigma weight residual -15.81 -148.65 132.84 1 3.00e+01 1.11e-03 1.79e+01 ... (remaining 6627 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1202 0.039 - 0.079: 338 0.079 - 0.118: 79 0.118 - 0.158: 12 0.158 - 0.197: 12 Chirality restraints: 1643 Sorted by residual: chirality pdb=" C22A1SY C 401 " pdb=" C21A1SY C 401 " pdb=" C24A1SY C 401 " pdb=" O23A1SY C 401 " both_signs ideal model delta sigma weight residual False -2.70 -2.50 -0.20 2.00e-01 2.50e+01 9.70e-01 chirality pdb=" C22B1SY B 401 " pdb=" C21B1SY B 401 " pdb=" C24B1SY B 401 " pdb=" O23B1SY B 401 " both_signs ideal model delta sigma weight residual False -2.70 -2.50 -0.20 2.00e-01 2.50e+01 9.65e-01 chirality pdb=" C2'B1SY C 401 " pdb=" C1'B1SY C 401 " pdb=" C3'B1SY C 401 " pdb=" O2'B1SY C 401 " both_signs ideal model delta sigma weight residual False -2.74 -2.55 -0.19 2.00e-01 2.50e+01 9.36e-01 ... (remaining 1640 not shown) Planarity restraints: 1863 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 208 " 0.039 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO A 209 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 209 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 209 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 140 " -0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO B 141 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 141 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 141 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 7 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO C 8 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 8 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 8 " -0.026 5.00e-02 4.00e+02 ... (remaining 1860 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 212 2.69 - 3.24: 10283 3.24 - 3.80: 16513 3.80 - 4.35: 20800 4.35 - 4.90: 35158 Nonbonded interactions: 82966 Sorted by model distance: nonbonded pdb=" OH TYR D 167 " pdb=" OD1 ASN D 242 " model vdw 2.138 3.040 nonbonded pdb=" OE1 GLU B 69 " pdb=" OH TYR B 77 " model vdw 2.139 3.040 nonbonded pdb=" NH1 ARG A 14 " pdb=" OE2 GLU B 69 " model vdw 2.161 3.120 nonbonded pdb=" ND2 ASN A 242 " pdb=" OE2 GLU A 260 " model vdw 2.164 3.120 nonbonded pdb=" OG SER C 75 " pdb=" O SER D 9 " model vdw 2.232 3.040 ... (remaining 82961 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 4 through 70 or resid 72 through 85 or resid 87 through 10 \ 6 or (resid 107 and (name N or name CA or name C or name O or name CB )) or resi \ d 108 or resid 116 through 337)) selection = (chain 'B' and (resid 4 through 70 or resid 72 through 85 or resid 87 through 10 \ 6 or (resid 107 and (name N or name CA or name C or name O or name CB )) or resi \ d 108 through 337)) selection = (chain 'C' and (resid 4 through 70 or resid 72 through 85 or resid 87 through 33 \ 7)) selection = (chain 'D' and (resid 4 through 70 or resid 72 through 85 or resid 87 through 10 \ 6 or (resid 107 and (name N or name CA or name C or name O or name CB )) or resi \ d 108 or resid 116 through 337)) } 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.910 Find NCS groups from input model: 0.250 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 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 : 0.009 0.138 10783 Z= 0.444 Angle : 1.030 18.584 14686 Z= 0.407 Chirality : 0.041 0.197 1643 Planarity : 0.005 0.060 1863 Dihedral : 17.129 142.103 4180 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.36 % Allowed : 0.81 % Favored : 98.83 % 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: 0.73 (0.24), residues: 1297 helix: 1.78 (0.20), residues: 701 sheet: -1.41 (0.49), residues: 112 loop : -0.97 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 76 TYR 0.015 0.001 TYR B 167 PHE 0.009 0.001 PHE B 279 TRP 0.013 0.002 TRP D 119 HIS 0.004 0.001 HIS D 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00898 / 0.44 (10783) covalent geometry : angle 1.02978 / 0.41 (14686) hydrogen bonds : bond 0.13683 / 9.54 ( 577) hydrogen bonds : angle 6.02190 / 4.42 ( 1703) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 153 time to evaluate : 0.403 Fit side-chains REVERT: A 246 GLU cc_start: 0.5158 (pp20) cc_final: 0.4666 (pp20) REVERT: D 174 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7107 (mp0) outliers start: 2 outliers final: 0 residues processed: 154 average time/residue: 0.1105 time to fit residues: 23.5168 Evaluate side-chains 127 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 150 ASN ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 HIS D 131 ASN ** D 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 GLN D 242 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.231241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.174488 restraints weight = 21646.651| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 4.04 r_work: 0.3924 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3952 r_free = 0.3952 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3952 r_free = 0.3952 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10783 Z= 0.161 Angle : 0.652 10.332 14686 Z= 0.311 Chirality : 0.039 0.188 1643 Planarity : 0.006 0.052 1863 Dihedral : 14.470 158.593 1734 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.26 % Allowed : 8.45 % Favored : 90.29 % 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: 0.83 (0.24), residues: 1297 helix: 1.82 (0.20), residues: 699 sheet: -0.53 (0.44), residues: 156 loop : -1.12 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 197 TYR 0.014 0.001 TYR D 163 PHE 0.012 0.001 PHE B 279 TRP 0.011 0.001 TRP D 119 HIS 0.002 0.001 HIS D 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (10783) covalent geometry : angle 0.65162 / 0.31 (14686) hydrogen bonds : bond 0.03963 / 2.74 ( 577) hydrogen bonds : angle 4.67401 / 3.43 ( 1703) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.325 Fit side-chains REVERT: A 246 GLU cc_start: 0.5326 (pp20) cc_final: 0.4724 (pp20) REVERT: A 297 ASP cc_start: 0.7860 (t0) cc_final: 0.7634 (t0) REVERT: C 94 ARG cc_start: 0.5759 (ttp80) cc_final: 0.4210 (mtp180) REVERT: D 78 ARG cc_start: 0.7044 (mmp80) cc_final: 0.6481 (mmp80) REVERT: D 174 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7284 (mp0) outliers start: 12 outliers final: 12 residues processed: 144 average time/residue: 0.1075 time to fit residues: 21.5737 Evaluate side-chains 135 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 263 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 91 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN C 150 ASN D 42 HIS ** D 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.229480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.171962 restraints weight = 28778.515| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 5.21 r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4093 r_free = 0.4093 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4093 r_free = 0.4093 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.4093 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10783 Z= 0.178 Angle : 0.643 10.512 14686 Z= 0.309 Chirality : 0.039 0.215 1643 Planarity : 0.005 0.051 1863 Dihedral : 14.503 165.214 1734 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 1.80 % Allowed : 10.16 % Favored : 88.04 % 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: 0.65 (0.24), residues: 1297 helix: 1.69 (0.19), residues: 703 sheet: -0.63 (0.44), residues: 152 loop : -1.24 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 281 TYR 0.014 0.001 TYR D 163 PHE 0.014 0.001 PHE B 279 TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS A 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (10783) covalent geometry : angle 0.64330 / 0.31 (14686) hydrogen bonds : bond 0.03975 / 2.74 ( 577) hydrogen bonds : angle 4.56867 / 3.34 ( 1703) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.393 Fit side-chains REVERT: A 235 ILE cc_start: 0.8554 (mt) cc_final: 0.8293 (mt) REVERT: A 246 GLU cc_start: 0.5106 (pp20) cc_final: 0.4432 (pp20) REVERT: B 214 MET cc_start: 0.7298 (mpp) cc_final: 0.7036 (mpp) REVERT: D 174 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7057 (mp0) outliers start: 18 outliers final: 17 residues processed: 140 average time/residue: 0.1047 time to fit residues: 20.9339 Evaluate side-chains 139 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 263 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 86 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 113 optimal weight: 8.9990 chunk 112 optimal weight: 0.2980 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 ASN B 152 ASN ** B 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 ASN D 42 HIS D 61 ASN D 128 GLN ** D 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.229261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.174336 restraints weight = 28884.554| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 4.89 r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4122 r_free = 0.4122 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4122 r_free = 0.4122 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10783 Z= 0.171 Angle : 0.628 10.645 14686 Z= 0.302 Chirality : 0.039 0.218 1643 Planarity : 0.005 0.054 1863 Dihedral : 14.367 164.288 1734 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 2.07 % Allowed : 12.41 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.65 (0.24), residues: 1297 helix: 1.68 (0.19), residues: 705 sheet: -0.64 (0.44), residues: 152 loop : -1.23 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 281 TYR 0.014 0.001 TYR D 163 PHE 0.013 0.001 PHE A 153 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS D 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (10783) covalent geometry : angle 0.62768 / 0.30 (14686) hydrogen bonds : bond 0.03793 / 2.60 ( 577) hydrogen bonds : angle 4.51703 / 3.30 ( 1703) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.377 Fit side-chains REVERT: A 235 ILE cc_start: 0.8509 (mt) cc_final: 0.8286 (mt) REVERT: A 246 GLU cc_start: 0.5302 (pp20) cc_final: 0.4646 (pp20) REVERT: B 214 MET cc_start: 0.7343 (mpp) cc_final: 0.7108 (mpp) REVERT: B 266 GLN cc_start: 0.7870 (tt0) cc_final: 0.7651 (tt0) REVERT: D 174 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7143 (mp0) REVERT: D 214 MET cc_start: 0.7725 (mtm) cc_final: 0.7389 (mmm) outliers start: 21 outliers final: 17 residues processed: 144 average time/residue: 0.0978 time to fit residues: 20.1505 Evaluate side-chains 136 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 263 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 53 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 ASN D 42 HIS D 128 GLN ** D 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.226227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.171243 restraints weight = 28712.536| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 5.25 r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4081 r_free = 0.4081 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4081 r_free = 0.4081 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10783 Z= 0.229 Angle : 0.701 12.114 14686 Z= 0.337 Chirality : 0.041 0.219 1643 Planarity : 0.006 0.052 1863 Dihedral : 14.332 159.915 1734 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.34 % Allowed : 14.21 % Favored : 83.45 % 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: 0.34 (0.23), residues: 1297 helix: 1.42 (0.19), residues: 703 sheet: -0.80 (0.44), residues: 148 loop : -1.34 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 281 TYR 0.020 0.002 TYR C 245 PHE 0.016 0.002 PHE A 153 TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS A 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.23 (10783) covalent geometry : angle 0.70110 / 0.34 (14686) hydrogen bonds : bond 0.04200 / 2.89 ( 577) hydrogen bonds : angle 4.74116 / 3.46 ( 1703) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.380 Fit side-chains REVERT: A 72 HIS cc_start: 0.8040 (OUTLIER) cc_final: 0.7557 (m-70) REVERT: A 235 ILE cc_start: 0.8516 (mt) cc_final: 0.8262 (mt) REVERT: A 246 GLU cc_start: 0.5375 (pp20) cc_final: 0.4687 (pp20) REVERT: B 214 MET cc_start: 0.7403 (mpp) cc_final: 0.7171 (mpp) REVERT: D 174 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7119 (mp0) REVERT: D 214 MET cc_start: 0.7693 (mtm) cc_final: 0.7335 (mmm) outliers start: 24 outliers final: 20 residues processed: 135 average time/residue: 0.1003 time to fit residues: 19.4881 Evaluate side-chains 139 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 263 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 127 optimal weight: 0.0060 chunk 114 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 52 optimal weight: 0.0870 chunk 46 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 250 ASN C 150 ASN D 42 HIS D 72 HIS ** D 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.235663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.181529 restraints weight = 30114.878| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 4.61 r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4169 r_free = 0.4169 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4169 r_free = 0.4169 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10783 Z= 0.102 Angle : 0.571 10.275 14686 Z= 0.272 Chirality : 0.036 0.209 1643 Planarity : 0.005 0.058 1863 Dihedral : 14.237 162.440 1734 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.89 % Allowed : 14.93 % Favored : 83.18 % 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: 0.98 (0.24), residues: 1297 helix: 1.98 (0.20), residues: 705 sheet: -0.51 (0.44), residues: 152 loop : -1.14 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 281 TYR 0.015 0.001 TYR C 245 PHE 0.009 0.001 PHE A 291 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.000 HIS A 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (10783) covalent geometry : angle 0.57097 / 0.27 (14686) hydrogen bonds : bond 0.03197 / 2.20 ( 577) hydrogen bonds : angle 4.23106 / 3.09 ( 1703) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.403 Fit side-chains REVERT: A 246 GLU cc_start: 0.5427 (pp20) cc_final: 0.4837 (pp20) REVERT: B 214 MET cc_start: 0.7260 (mpp) cc_final: 0.7056 (mpp) REVERT: D 174 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7147 (mp0) REVERT: D 214 MET cc_start: 0.7645 (mtm) cc_final: 0.7410 (mmm) outliers start: 19 outliers final: 16 residues processed: 132 average time/residue: 0.1123 time to fit residues: 20.9210 Evaluate side-chains 131 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 72 HIS Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 263 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 104 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 116 optimal weight: 0.0970 chunk 80 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 266 GLN C 150 ASN D 72 HIS ** D 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 GLN D 242 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.235576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.177655 restraints weight = 27428.932| |-----------------------------------------------------------------------------| r_work (start): 0.4140 rms_B_bonded: 5.08 r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4141 r_free = 0.4141 target_work(ls_wunit_k1) = 0.177 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4141 r_free = 0.4141 target_work(ls_wunit_k1) = 0.177 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.4141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10783 Z= 0.104 Angle : 0.581 9.881 14686 Z= 0.274 Chirality : 0.036 0.197 1643 Planarity : 0.005 0.057 1863 Dihedral : 14.100 160.944 1734 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.34 % Allowed : 15.38 % Favored : 82.28 % 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: 1.19 (0.24), residues: 1297 helix: 2.16 (0.20), residues: 701 sheet: -0.40 (0.43), residues: 156 loop : -1.03 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 281 TYR 0.013 0.001 TYR C 245 PHE 0.009 0.001 PHE A 153 TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS A 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (10783) covalent geometry : angle 0.58082 / 0.27 (14686) hydrogen bonds : bond 0.03212 / 2.20 ( 577) hydrogen bonds : angle 4.17162 / 3.05 ( 1703) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.444 Fit side-chains REVERT: A 72 HIS cc_start: 0.7659 (OUTLIER) cc_final: 0.6908 (m-70) REVERT: A 95 ARG cc_start: 0.7301 (tpp-160) cc_final: 0.7084 (tpp-160) REVERT: A 246 GLU cc_start: 0.5309 (pp20) cc_final: 0.4690 (pp20) REVERT: B 249 GLU cc_start: 0.7143 (tt0) cc_final: 0.6015 (tp30) REVERT: D 174 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7189 (mp0) REVERT: D 214 MET cc_start: 0.7671 (mtm) cc_final: 0.7318 (mmm) outliers start: 24 outliers final: 20 residues processed: 135 average time/residue: 0.1020 time to fit residues: 19.8018 Evaluate side-chains 140 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 7 HIS Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 263 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 72 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 6 optimal weight: 0.1980 chunk 83 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 150 ASN ** D 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.237406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.182114 restraints weight = 20672.725| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 4.30 r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4179 r_free = 0.4179 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4179 r_free = 0.4179 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10783 Z= 0.098 Angle : 0.564 10.051 14686 Z= 0.266 Chirality : 0.036 0.190 1643 Planarity : 0.005 0.057 1863 Dihedral : 14.013 159.750 1734 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.25 % Allowed : 15.83 % Favored : 81.92 % 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: 1.32 (0.24), residues: 1297 helix: 2.27 (0.20), residues: 701 sheet: -0.27 (0.44), residues: 152 loop : -1.02 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 281 TYR 0.012 0.001 TYR C 245 PHE 0.009 0.001 PHE C 291 TRP 0.010 0.001 TRP D 119 HIS 0.003 0.000 HIS A 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (10783) covalent geometry : angle 0.56416 / 0.27 (14686) hydrogen bonds : bond 0.03033 / 2.09 ( 577) hydrogen bonds : angle 4.09836 / 2.98 ( 1703) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.380 Fit side-chains REVERT: A 72 HIS cc_start: 0.7559 (OUTLIER) cc_final: 0.6784 (m-70) REVERT: A 95 ARG cc_start: 0.7258 (tpp-160) cc_final: 0.7051 (tpp-160) REVERT: A 236 LYS cc_start: 0.8345 (mptt) cc_final: 0.8025 (mmtt) REVERT: A 246 GLU cc_start: 0.5305 (pp20) cc_final: 0.4690 (pp20) REVERT: B 249 GLU cc_start: 0.7276 (tt0) cc_final: 0.6234 (tp30) REVERT: D 174 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7124 (mp0) REVERT: D 214 MET cc_start: 0.7744 (mtm) cc_final: 0.7427 (mmm) REVERT: D 236 LYS cc_start: 0.7599 (mmtt) cc_final: 0.6826 (mmmm) outliers start: 23 outliers final: 21 residues processed: 142 average time/residue: 0.1116 time to fit residues: 22.3560 Evaluate side-chains 141 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain D residue 7 HIS Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 263 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 59 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 chunk 83 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 150 ASN C 266 GLN ** D 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.234880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.177592 restraints weight = 30376.601| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 5.26 r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4132 r_free = 0.4132 target_work(ls_wunit_k1) = 0.176 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4132 r_free = 0.4132 target_work(ls_wunit_k1) = 0.176 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10783 Z= 0.120 Angle : 0.586 9.985 14686 Z= 0.276 Chirality : 0.036 0.176 1643 Planarity : 0.005 0.056 1863 Dihedral : 13.991 158.350 1734 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.34 % Allowed : 16.19 % Favored : 81.47 % 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: 1.26 (0.24), residues: 1297 helix: 2.19 (0.20), residues: 701 sheet: -0.28 (0.45), residues: 152 loop : -0.98 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 281 TYR 0.011 0.001 TYR D 163 PHE 0.009 0.001 PHE D 279 TRP 0.012 0.001 TRP D 119 HIS 0.003 0.001 HIS A 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (10783) covalent geometry : angle 0.58618 / 0.28 (14686) hydrogen bonds : bond 0.03241 / 2.23 ( 577) hydrogen bonds : angle 4.18198 / 3.04 ( 1703) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.405 Fit side-chains REVERT: A 72 HIS cc_start: 0.7645 (OUTLIER) cc_final: 0.6878 (m-70) REVERT: A 95 ARG cc_start: 0.7357 (tpp-160) cc_final: 0.7155 (tpp-160) REVERT: A 236 LYS cc_start: 0.8363 (mptt) cc_final: 0.8145 (mmtt) REVERT: A 246 GLU cc_start: 0.5410 (pp20) cc_final: 0.4810 (pp20) REVERT: C 89 LEU cc_start: 0.7320 (mt) cc_final: 0.6715 (mt) REVERT: D 174 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7241 (mp0) REVERT: D 214 MET cc_start: 0.7723 (mtm) cc_final: 0.7362 (mmm) REVERT: D 236 LYS cc_start: 0.7661 (mmtt) cc_final: 0.6826 (mmmm) outliers start: 24 outliers final: 20 residues processed: 135 average time/residue: 0.1112 time to fit residues: 21.3085 Evaluate side-chains 141 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 263 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 69 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 150 ASN D 42 HIS ** D 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.234967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.178808 restraints weight = 19945.312| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 3.91 r_work: 0.3958 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3990 r_free = 0.3990 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3990 r_free = 0.3990 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10783 Z= 0.119 Angle : 0.585 10.117 14686 Z= 0.276 Chirality : 0.036 0.178 1643 Planarity : 0.005 0.056 1863 Dihedral : 13.996 157.665 1734 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.16 % Allowed : 16.46 % Favored : 81.38 % 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: 1.24 (0.24), residues: 1297 helix: 2.16 (0.20), residues: 701 sheet: -0.29 (0.45), residues: 152 loop : -0.99 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 281 TYR 0.011 0.001 TYR C 245 PHE 0.009 0.001 PHE C 279 TRP 0.010 0.001 TRP D 119 HIS 0.003 0.001 HIS D 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (10783) covalent geometry : angle 0.58530 / 0.28 (14686) hydrogen bonds : bond 0.03226 / 2.22 ( 577) hydrogen bonds : angle 4.18819 / 3.05 ( 1703) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.415 Fit side-chains REVERT: A 72 HIS cc_start: 0.7725 (OUTLIER) cc_final: 0.6886 (m-70) REVERT: A 95 ARG cc_start: 0.7512 (tpp-160) cc_final: 0.7260 (tpp-160) REVERT: A 236 LYS cc_start: 0.8310 (mptt) cc_final: 0.8070 (mmtt) REVERT: A 246 GLU cc_start: 0.5628 (pp20) cc_final: 0.4986 (pp20) REVERT: C 89 LEU cc_start: 0.7734 (mt) cc_final: 0.7047 (mt) REVERT: D 174 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7442 (mp0) REVERT: D 214 MET cc_start: 0.7895 (mtm) cc_final: 0.7461 (mmm) REVERT: D 236 LYS cc_start: 0.7617 (mmtt) cc_final: 0.6772 (mmmm) outliers start: 22 outliers final: 19 residues processed: 136 average time/residue: 0.1128 time to fit residues: 21.8551 Evaluate side-chains 142 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 263 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 116 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 74 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 ASN D 42 HIS ** D 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.227740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.169961 restraints weight = 24660.348| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 4.26 r_work: 0.3881 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3909 r_free = 0.3909 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3909 r_free = 0.3909 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10783 Z= 0.217 Angle : 0.692 11.198 14686 Z= 0.330 Chirality : 0.041 0.175 1643 Planarity : 0.005 0.052 1863 Dihedral : 14.121 157.864 1734 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.16 % Allowed : 16.73 % Favored : 81.12 % 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: 0.76 (0.24), residues: 1297 helix: 1.75 (0.19), residues: 703 sheet: -0.61 (0.44), residues: 152 loop : -1.11 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 281 TYR 0.018 0.002 TYR D 163 PHE 0.014 0.002 PHE C 279 TRP 0.011 0.001 TRP C 161 HIS 0.005 0.001 HIS D 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.22 (10783) covalent geometry : angle 0.69231 / 0.33 (14686) hydrogen bonds : bond 0.03981 / 2.74 ( 577) hydrogen bonds : angle 4.56460 / 3.32 ( 1703) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2174.82 seconds wall clock time: 38 minutes 10.39 seconds (2290.39 seconds total)