Starting phenix.real_space_refine on Tue Nov 18 06:57:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6djm_7936/11_2025/6djm_7936.cif Found real_map, /net/cci-nas-00/data/ceres_data/6djm_7936/11_2025/6djm_7936.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6djm_7936/11_2025/6djm_7936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6djm_7936/11_2025/6djm_7936.map" model { file = "/net/cci-nas-00/data/ceres_data/6djm_7936/11_2025/6djm_7936.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6djm_7936/11_2025/6djm_7936.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 84 5.16 5 C 7408 2.51 5 N 1984 2.21 5 O 2276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11768 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.94, per 1000 atoms: 0.25 Number of scatterers: 11768 At special positions: 0 Unit cell: (101.365, 78.375, 165.11, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 84 16.00 P 12 15.00 Mg 4 11.99 O 2276 8.00 N 1984 7.00 C 7408 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: 0.91 Conformation dependent library (CDL) restraints added in 518.0 milliseconds 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 20 sheets defined 42.7% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 91 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.831A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 144 removed outlier: 4.065A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.580A pdb=" N LYS A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.670A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 230 removed outlier: 3.865A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 4.063A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 283 removed outlier: 3.504A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.531A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.527A pdb=" N THR A 304 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 319 removed outlier: 3.505A pdb=" N ARG A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR A 318 " --> pdb=" O GLN A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 347 Processing helix chain 'A' and resid 359 through 364 removed outlier: 3.655A pdb=" N GLU A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 4.146A pdb=" N SER A 368 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A 369 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N HIS A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 371' Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 91 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.832A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 144 removed outlier: 4.066A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 193 removed outlier: 3.580A pdb=" N LYS B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.670A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 230 removed outlier: 3.865A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 removed outlier: 4.063A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 283 removed outlier: 3.504A pdb=" N TYR B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.531A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.526A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 319 removed outlier: 3.505A pdb=" N ARG B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR B 318 " --> pdb=" O GLN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 359 through 364 removed outlier: 3.656A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 4.146A pdb=" N SER B 368 " --> pdb=" O ALA B 365 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE B 369 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS B 371 " --> pdb=" O SER B 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 371' Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 91 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.832A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 144 removed outlier: 4.065A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 193 removed outlier: 3.581A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.670A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS C 215 " --> pdb=" O ASP C 211 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 230 removed outlier: 3.865A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 removed outlier: 4.063A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 283 removed outlier: 3.504A pdb=" N TYR C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.532A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.526A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 319 removed outlier: 3.505A pdb=" N ARG C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR C 318 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 359 through 364 removed outlier: 3.655A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 removed outlier: 4.146A pdb=" N SER C 368 " --> pdb=" O ALA C 365 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE C 369 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS C 371 " --> pdb=" O SER C 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 371' Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 91 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.832A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 144 removed outlier: 4.065A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 193 removed outlier: 3.580A pdb=" N LYS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.670A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS D 215 " --> pdb=" O ASP D 211 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 230 removed outlier: 3.865A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 257 removed outlier: 4.063A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 283 removed outlier: 3.505A pdb=" N TYR D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.531A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 removed outlier: 3.525A pdb=" N THR D 304 " --> pdb=" O GLY D 301 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 319 removed outlier: 3.505A pdb=" N ARG D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR D 318 " --> pdb=" O GLN D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 359 through 364 removed outlier: 3.655A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 371 removed outlier: 4.146A pdb=" N SER D 368 " --> pdb=" O ALA D 365 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE D 369 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS D 371 " --> pdb=" O SER D 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 365 through 371' Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.550A pdb=" N PHE A 31 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.547A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 removed outlier: 5.971A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.550A pdb=" N PHE B 31 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.547A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA9, first strand: chain 'B' and resid 176 through 178 removed outlier: 5.971A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB2, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.551A pdb=" N PHE C 31 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.547A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB5, first strand: chain 'C' and resid 176 through 178 removed outlier: 5.971A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB7, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.551A pdb=" N PHE D 31 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.547A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC1, first strand: chain 'D' and resid 176 through 178 removed outlier: 5.970A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 238 through 241 424 hydrogen bonds defined for protein. 1092 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: 1.45 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3633 1.33 - 1.45: 1729 1.45 - 1.57: 6494 1.57 - 1.68: 12 1.68 - 1.80: 152 Bond restraints: 12020 Sorted by residual: bond pdb=" O3A ANP C 802 " pdb=" PB ANP C 802 " ideal model delta sigma weight residual 1.700 1.538 0.162 2.00e-02 2.50e+03 6.59e+01 bond pdb=" O3A ANP A 802 " pdb=" PB ANP A 802 " ideal model delta sigma weight residual 1.700 1.539 0.161 2.00e-02 2.50e+03 6.51e+01 bond pdb=" O3A ANP B 802 " pdb=" PB ANP B 802 " ideal model delta sigma weight residual 1.700 1.539 0.161 2.00e-02 2.50e+03 6.51e+01 bond pdb=" O3A ANP D 802 " pdb=" PB ANP D 802 " ideal model delta sigma weight residual 1.700 1.541 0.159 2.00e-02 2.50e+03 6.33e+01 bond pdb=" O5' ANP C 802 " pdb=" PA ANP C 802 " ideal model delta sigma weight residual 1.655 1.549 0.106 2.00e-02 2.50e+03 2.81e+01 ... (remaining 12015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.68: 16153 3.68 - 7.37: 149 7.37 - 11.05: 10 11.05 - 14.74: 4 14.74 - 18.42: 4 Bond angle restraints: 16320 Sorted by residual: angle pdb=" PB ANP A 802 " pdb=" N3B ANP A 802 " pdb=" PG ANP A 802 " ideal model delta sigma weight residual 126.95 108.53 18.42 3.00e+00 1.11e-01 3.77e+01 angle pdb=" PB ANP B 802 " pdb=" N3B ANP B 802 " pdb=" PG ANP B 802 " ideal model delta sigma weight residual 126.95 109.57 17.38 3.00e+00 1.11e-01 3.36e+01 angle pdb=" PB ANP D 802 " pdb=" N3B ANP D 802 " pdb=" PG ANP D 802 " ideal model delta sigma weight residual 126.95 110.79 16.16 3.00e+00 1.11e-01 2.90e+01 angle pdb=" PB ANP C 802 " pdb=" N3B ANP C 802 " pdb=" PG ANP C 802 " ideal model delta sigma weight residual 126.95 111.66 15.29 3.00e+00 1.11e-01 2.60e+01 angle pdb=" O1B ANP C 802 " pdb=" PB ANP C 802 " pdb=" O2B ANP C 802 " ideal model delta sigma weight residual 120.08 108.34 11.74 3.00e+00 1.11e-01 1.53e+01 ... (remaining 16315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.13: 7184 30.13 - 60.26: 108 60.26 - 90.38: 8 90.38 - 120.51: 0 120.51 - 150.64: 4 Dihedral angle restraints: 7304 sinusoidal: 3004 harmonic: 4300 Sorted by residual: dihedral pdb=" CA TYR A 166 " pdb=" C TYR A 166 " pdb=" N GLU A 167 " pdb=" CA GLU A 167 " ideal model delta harmonic sigma weight residual -180.00 -155.05 -24.95 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA TYR C 166 " pdb=" C TYR C 166 " pdb=" N GLU C 167 " pdb=" CA GLU C 167 " ideal model delta harmonic sigma weight residual -180.00 -155.06 -24.94 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA TYR B 166 " pdb=" C TYR B 166 " pdb=" N GLU B 167 " pdb=" CA GLU B 167 " ideal model delta harmonic sigma weight residual -180.00 -155.08 -24.92 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 7301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1284 0.060 - 0.120: 470 0.120 - 0.179: 34 0.179 - 0.239: 17 0.239 - 0.299: 3 Chirality restraints: 1808 Sorted by residual: chirality pdb=" C3' ANP A 802 " pdb=" C2' ANP A 802 " pdb=" C4' ANP A 802 " pdb=" O3' ANP A 802 " both_signs ideal model delta sigma weight residual False -2.36 -2.66 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C3' ANP B 802 " pdb=" C2' ANP B 802 " pdb=" C4' ANP B 802 " pdb=" O3' ANP B 802 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C3' ANP D 802 " pdb=" C2' ANP D 802 " pdb=" C4' ANP D 802 " pdb=" O3' ANP D 802 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 1805 not shown) Planarity restraints: 2084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 242 " 0.039 5.00e-02 4.00e+02 5.91e-02 5.59e+00 pdb=" N PRO B 243 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 243 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 243 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 242 " -0.039 5.00e-02 4.00e+02 5.89e-02 5.55e+00 pdb=" N PRO D 243 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO D 243 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 243 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 242 " 0.039 5.00e-02 4.00e+02 5.89e-02 5.55e+00 pdb=" N PRO C 243 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO C 243 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 243 " 0.033 5.00e-02 4.00e+02 ... (remaining 2081 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 146 2.64 - 3.20: 9964 3.20 - 3.77: 17846 3.77 - 4.33: 26546 4.33 - 4.90: 43172 Nonbonded interactions: 97674 Sorted by model distance: nonbonded pdb="MG MG B 801 " pdb=" O2G ANP B 802 " model vdw 2.069 2.170 nonbonded pdb="MG MG A 801 " pdb=" O3G ANP A 802 " model vdw 2.078 2.170 nonbonded pdb="MG MG D 801 " pdb=" O2G ANP D 802 " model vdw 2.078 2.170 nonbonded pdb="MG MG C 801 " pdb=" O2G ANP C 802 " model vdw 2.087 2.170 nonbonded pdb="MG MG C 801 " pdb=" O2B ANP C 802 " model vdw 2.093 2.170 ... (remaining 97669 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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=1.00 max=1.00 mean=1.00 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: 2.290 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.400 Find NCS groups from input model: 0.100 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 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 : 0.010 0.162 12020 Z= 0.430 Angle : 1.005 18.422 16320 Z= 0.505 Chirality : 0.060 0.299 1808 Planarity : 0.007 0.059 2084 Dihedral : 11.490 150.638 4552 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % 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: -4.16 (0.18), residues: 1468 helix: -4.37 (0.10), residues: 568 sheet: -1.57 (0.35), residues: 196 loop : -1.50 (0.21), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 335 TYR 0.012 0.002 TYR A 218 PHE 0.024 0.003 PHE A 124 TRP 0.034 0.005 TRP A 340 HIS 0.011 0.003 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00984 (12020) covalent geometry : angle 1.00508 (16320) hydrogen bonds : bond 0.29843 ( 424) hydrogen bonds : angle 10.62089 ( 1092) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.8090 (m-30) cc_final: 0.7878 (m-30) REVERT: B 227 MET cc_start: 0.8515 (mmm) cc_final: 0.8275 (mmm) REVERT: C 44 MET cc_start: 0.8306 (mmt) cc_final: 0.8038 (mmm) REVERT: C 305 MET cc_start: 0.8099 (mmm) cc_final: 0.7838 (mmt) REVERT: D 24 ASP cc_start: 0.7452 (m-30) cc_final: 0.7206 (m-30) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.1363 time to fit residues: 55.5828 Evaluate side-chains 142 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN A 161 HIS A 162 ASN B 161 HIS B 162 ASN C 49 GLN C 161 HIS C 263 GLN D 49 GLN D 161 HIS D 353 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.103645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.089662 restraints weight = 18545.758| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.95 r_work: 0.3046 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12020 Z= 0.133 Angle : 0.574 7.247 16320 Z= 0.299 Chirality : 0.044 0.143 1808 Planarity : 0.005 0.044 2084 Dihedral : 10.122 157.502 1756 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.96 % Allowed : 8.44 % Favored : 90.61 % 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: -2.68 (0.20), residues: 1468 helix: -2.72 (0.17), residues: 580 sheet: -1.43 (0.32), residues: 236 loop : -0.73 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 37 TYR 0.010 0.001 TYR A 143 PHE 0.009 0.001 PHE A 255 TRP 0.015 0.002 TRP C 340 HIS 0.004 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00298 (12020) covalent geometry : angle 0.57444 (16320) hydrogen bonds : bond 0.03767 ( 424) hydrogen bonds : angle 5.52485 ( 1092) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 170 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 GLN cc_start: 0.8105 (tp-100) cc_final: 0.7860 (pm20) REVERT: A 227 MET cc_start: 0.8740 (mmt) cc_final: 0.8440 (mmt) REVERT: A 286 ASP cc_start: 0.7379 (t0) cc_final: 0.7029 (m-30) REVERT: B 176 MET cc_start: 0.8476 (mmm) cc_final: 0.8048 (mmt) REVERT: B 227 MET cc_start: 0.8841 (mmm) cc_final: 0.8614 (mmm) REVERT: B 316 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7929 (mt-10) REVERT: C 305 MET cc_start: 0.8789 (mmm) cc_final: 0.8541 (mmt) REVERT: C 324 THR cc_start: 0.8763 (t) cc_final: 0.8531 (p) REVERT: C 372 ARG cc_start: 0.7914 (ptt-90) cc_final: 0.7664 (ptt90) REVERT: D 47 MET cc_start: 0.7614 (ppp) cc_final: 0.7279 (ppp) REVERT: D 81 ASP cc_start: 0.8622 (m-30) cc_final: 0.8303 (m-30) outliers start: 12 outliers final: 5 residues processed: 180 average time/residue: 0.0907 time to fit residues: 24.9119 Evaluate side-chains 140 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 134 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 180 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 44 optimal weight: 2.9990 chunk 82 optimal weight: 0.3980 chunk 56 optimal weight: 0.9980 chunk 130 optimal weight: 0.0000 chunk 15 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.103278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.089189 restraints weight = 18483.845| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.97 r_work: 0.3039 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12020 Z= 0.117 Angle : 0.513 6.813 16320 Z= 0.263 Chirality : 0.043 0.135 1808 Planarity : 0.004 0.033 2084 Dihedral : 9.942 165.894 1756 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.27 % Allowed : 9.87 % Favored : 88.85 % 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: -1.68 (0.21), residues: 1468 helix: -1.66 (0.20), residues: 580 sheet: -1.05 (0.33), residues: 236 loop : -0.34 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 147 TYR 0.011 0.001 TYR B 279 PHE 0.009 0.001 PHE A 375 TRP 0.011 0.002 TRP A 340 HIS 0.006 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00269 (12020) covalent geometry : angle 0.51295 (16320) hydrogen bonds : bond 0.03043 ( 424) hydrogen bonds : angle 4.85720 ( 1092) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 227 MET cc_start: 0.8699 (mmt) cc_final: 0.8454 (mmt) REVERT: B 86 TRP cc_start: 0.8976 (m-10) cc_final: 0.8728 (m-10) REVERT: B 305 MET cc_start: 0.8536 (mmt) cc_final: 0.8215 (mmt) REVERT: C 6 THR cc_start: 0.7772 (t) cc_final: 0.7550 (m) REVERT: C 325 MET cc_start: 0.7684 (mmp) cc_final: 0.7464 (mmp) REVERT: D 47 MET cc_start: 0.7646 (ppp) cc_final: 0.6986 (ppp) REVERT: D 81 ASP cc_start: 0.8590 (m-30) cc_final: 0.8264 (m-30) REVERT: D 107 GLU cc_start: 0.7960 (pt0) cc_final: 0.7529 (pt0) REVERT: D 355 MET cc_start: 0.8829 (mmm) cc_final: 0.8573 (mmm) outliers start: 16 outliers final: 8 residues processed: 160 average time/residue: 0.0972 time to fit residues: 23.5391 Evaluate side-chains 133 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 51 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 108 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 142 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 173 HIS B 115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.101535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.087717 restraints weight = 18650.963| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.92 r_work: 0.3016 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12020 Z= 0.170 Angle : 0.541 7.877 16320 Z= 0.275 Chirality : 0.045 0.141 1808 Planarity : 0.004 0.045 2084 Dihedral : 9.831 168.668 1756 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.75 % Allowed : 9.63 % Favored : 88.61 % 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 (0.22), residues: 1468 helix: -1.18 (0.21), residues: 584 sheet: -0.80 (0.34), residues: 236 loop : -0.13 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 116 TYR 0.010 0.001 TYR A 143 PHE 0.008 0.001 PHE D 262 TRP 0.012 0.002 TRP B 79 HIS 0.006 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00399 (12020) covalent geometry : angle 0.54055 (16320) hydrogen bonds : bond 0.02866 ( 424) hydrogen bonds : angle 4.69389 ( 1092) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: B 176 MET cc_start: 0.8539 (mmm) cc_final: 0.8143 (mmt) REVERT: B 305 MET cc_start: 0.8533 (mmt) cc_final: 0.8243 (mmt) REVERT: C 6 THR cc_start: 0.7710 (t) cc_final: 0.7479 (m) REVERT: C 241 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7559 (tm-30) REVERT: C 325 MET cc_start: 0.7770 (mmp) cc_final: 0.7490 (mmp) REVERT: D 47 MET cc_start: 0.7605 (ppp) cc_final: 0.7216 (ppp) REVERT: D 81 ASP cc_start: 0.8597 (m-30) cc_final: 0.8265 (m-30) REVERT: D 107 GLU cc_start: 0.8005 (pt0) cc_final: 0.7663 (pt0) outliers start: 22 outliers final: 10 residues processed: 144 average time/residue: 0.0943 time to fit residues: 20.7724 Evaluate side-chains 133 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain D residue 51 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 78 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 88 optimal weight: 0.0770 chunk 137 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 136 optimal weight: 0.6980 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN B 87 HIS B 115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.102273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.088500 restraints weight = 18519.750| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.92 r_work: 0.3028 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12020 Z= 0.118 Angle : 0.498 6.555 16320 Z= 0.254 Chirality : 0.044 0.129 1808 Planarity : 0.004 0.041 2084 Dihedral : 9.683 167.294 1756 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.35 % Allowed : 10.43 % Favored : 88.22 % 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 (0.22), residues: 1468 helix: -0.66 (0.22), residues: 564 sheet: -0.39 (0.33), residues: 244 loop : -0.01 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 147 TYR 0.008 0.001 TYR A 143 PHE 0.006 0.001 PHE B 127 TRP 0.010 0.002 TRP A 340 HIS 0.006 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00279 (12020) covalent geometry : angle 0.49769 (16320) hydrogen bonds : bond 0.02530 ( 424) hydrogen bonds : angle 4.53915 ( 1092) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 176 MET cc_start: 0.8550 (mmm) cc_final: 0.8187 (mmt) REVERT: C 6 THR cc_start: 0.7722 (t) cc_final: 0.7511 (m) REVERT: C 241 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7553 (tm-30) REVERT: C 314 GLN cc_start: 0.8700 (tp40) cc_final: 0.8237 (tt0) REVERT: C 372 ARG cc_start: 0.7945 (ptt-90) cc_final: 0.7718 (ptt90) REVERT: D 47 MET cc_start: 0.7597 (ppp) cc_final: 0.7152 (ppp) REVERT: D 81 ASP cc_start: 0.8605 (m-30) cc_final: 0.8260 (m-30) REVERT: D 107 GLU cc_start: 0.7961 (pt0) cc_final: 0.7602 (pt0) REVERT: D 176 MET cc_start: 0.8958 (mmm) cc_final: 0.8739 (mtp) REVERT: D 355 MET cc_start: 0.8895 (mmm) cc_final: 0.8679 (mmm) outliers start: 17 outliers final: 11 residues processed: 145 average time/residue: 0.0882 time to fit residues: 19.8618 Evaluate side-chains 137 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain D residue 51 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 26 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 2 optimal weight: 0.0070 chunk 35 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 84 optimal weight: 0.0770 chunk 32 optimal weight: 0.7980 chunk 126 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN B 115 ASN B 162 ASN C 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.102812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.089139 restraints weight = 18589.733| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.90 r_work: 0.3038 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12020 Z= 0.107 Angle : 0.485 6.291 16320 Z= 0.246 Chirality : 0.043 0.127 1808 Planarity : 0.003 0.036 2084 Dihedral : 9.567 166.451 1756 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.43 % Allowed : 10.51 % Favored : 88.06 % 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 (0.22), residues: 1468 helix: -0.36 (0.22), residues: 568 sheet: -0.26 (0.34), residues: 244 loop : 0.15 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 116 TYR 0.007 0.001 TYR C 143 PHE 0.006 0.001 PHE B 127 TRP 0.009 0.002 TRP A 340 HIS 0.003 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00249 (12020) covalent geometry : angle 0.48472 (16320) hydrogen bonds : bond 0.02389 ( 424) hydrogen bonds : angle 4.41909 ( 1092) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 176 MET cc_start: 0.8565 (mmm) cc_final: 0.8226 (mmt) REVERT: C 6 THR cc_start: 0.7708 (t) cc_final: 0.7493 (m) REVERT: C 47 MET cc_start: 0.7149 (ppp) cc_final: 0.6773 (ppp) REVERT: C 325 MET cc_start: 0.7783 (mmp) cc_final: 0.7481 (mmp) REVERT: D 47 MET cc_start: 0.7633 (ppp) cc_final: 0.7178 (ppp) REVERT: D 81 ASP cc_start: 0.8642 (m-30) cc_final: 0.8305 (m-30) REVERT: D 107 GLU cc_start: 0.7972 (pt0) cc_final: 0.7607 (pt0) REVERT: D 283 MET cc_start: 0.9003 (mmm) cc_final: 0.8786 (mmm) REVERT: D 355 MET cc_start: 0.8916 (mmm) cc_final: 0.8683 (mmm) outliers start: 18 outliers final: 10 residues processed: 142 average time/residue: 0.0842 time to fit residues: 18.8445 Evaluate side-chains 139 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 83 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 112 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN B 87 HIS B 115 ASN B 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.102235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.088552 restraints weight = 18503.550| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.90 r_work: 0.3030 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12020 Z= 0.126 Angle : 0.493 6.705 16320 Z= 0.250 Chirality : 0.044 0.128 1808 Planarity : 0.003 0.035 2084 Dihedral : 9.528 166.553 1756 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.19 % Allowed : 11.23 % Favored : 87.58 % 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: -0.20 (0.22), residues: 1468 helix: -0.18 (0.22), residues: 568 sheet: -0.18 (0.34), residues: 244 loop : 0.16 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 116 TYR 0.007 0.001 TYR D 143 PHE 0.006 0.001 PHE B 127 TRP 0.017 0.002 TRP D 79 HIS 0.008 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00299 (12020) covalent geometry : angle 0.49260 (16320) hydrogen bonds : bond 0.02444 ( 424) hydrogen bonds : angle 4.36657 ( 1092) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7285 (ppp) cc_final: 0.6907 (ppp) REVERT: B 176 MET cc_start: 0.8594 (mmm) cc_final: 0.8265 (mmt) REVERT: C 6 THR cc_start: 0.7718 (t) cc_final: 0.7491 (m) REVERT: C 47 MET cc_start: 0.7109 (ppp) cc_final: 0.6697 (ppp) REVERT: C 316 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7861 (mt-10) REVERT: D 47 MET cc_start: 0.7613 (ppp) cc_final: 0.7125 (ppp) REVERT: D 81 ASP cc_start: 0.8628 (m-30) cc_final: 0.8274 (m-30) REVERT: D 107 GLU cc_start: 0.7992 (pt0) cc_final: 0.7627 (pt0) REVERT: D 355 MET cc_start: 0.8928 (mmm) cc_final: 0.8682 (mmm) outliers start: 15 outliers final: 13 residues processed: 142 average time/residue: 0.0936 time to fit residues: 20.5891 Evaluate side-chains 141 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 84 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 76 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 26 optimal weight: 0.0020 chunk 120 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 110 optimal weight: 0.2980 chunk 90 optimal weight: 0.9980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN B 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.102547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.088906 restraints weight = 18434.883| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.90 r_work: 0.3033 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12020 Z= 0.112 Angle : 0.482 6.164 16320 Z= 0.245 Chirality : 0.043 0.129 1808 Planarity : 0.003 0.034 2084 Dihedral : 9.471 165.891 1756 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.27 % Allowed : 11.31 % Favored : 87.42 % 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: -0.06 (0.22), residues: 1468 helix: -0.00 (0.23), residues: 568 sheet: -0.13 (0.34), residues: 244 loop : 0.19 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 372 TYR 0.007 0.001 TYR A 143 PHE 0.005 0.001 PHE B 127 TRP 0.017 0.002 TRP D 79 HIS 0.004 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00264 (12020) covalent geometry : angle 0.48236 (16320) hydrogen bonds : bond 0.02375 ( 424) hydrogen bonds : angle 4.31344 ( 1092) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7307 (ppp) cc_final: 0.6998 (ppp) REVERT: B 107 GLU cc_start: 0.8425 (pt0) cc_final: 0.8167 (pt0) REVERT: B 176 MET cc_start: 0.8595 (mmm) cc_final: 0.8264 (mmt) REVERT: C 6 THR cc_start: 0.7720 (t) cc_final: 0.7480 (m) REVERT: C 47 MET cc_start: 0.7079 (ppp) cc_final: 0.6616 (ppp) REVERT: D 47 MET cc_start: 0.7496 (ppp) cc_final: 0.6968 (ppp) REVERT: D 81 ASP cc_start: 0.8645 (m-30) cc_final: 0.8287 (m-30) REVERT: D 107 GLU cc_start: 0.7995 (pt0) cc_final: 0.7640 (pt0) REVERT: D 355 MET cc_start: 0.8963 (mmm) cc_final: 0.8712 (mmm) outliers start: 16 outliers final: 11 residues processed: 148 average time/residue: 0.0921 time to fit residues: 21.6113 Evaluate side-chains 141 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 84 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.8980 chunk 69 optimal weight: 0.0980 chunk 36 optimal weight: 0.1980 chunk 33 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 115 ASN B 115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.102912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.089346 restraints weight = 18196.475| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.89 r_work: 0.3042 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12020 Z= 0.104 Angle : 0.481 6.152 16320 Z= 0.243 Chirality : 0.043 0.126 1808 Planarity : 0.003 0.033 2084 Dihedral : 9.409 165.287 1756 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.27 % Allowed : 11.39 % Favored : 87.34 % 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: 0.07 (0.23), residues: 1468 helix: 0.15 (0.23), residues: 568 sheet: -0.07 (0.34), residues: 244 loop : 0.23 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 147 TYR 0.007 0.001 TYR A 143 PHE 0.006 0.001 PHE C 223 TRP 0.017 0.002 TRP D 79 HIS 0.003 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00244 (12020) covalent geometry : angle 0.48068 (16320) hydrogen bonds : bond 0.02304 ( 424) hydrogen bonds : angle 4.27010 ( 1092) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7263 (ppp) cc_final: 0.6978 (ppp) REVERT: B 107 GLU cc_start: 0.8433 (pt0) cc_final: 0.8153 (pt0) REVERT: C 6 THR cc_start: 0.7502 (t) cc_final: 0.7231 (m) REVERT: C 47 MET cc_start: 0.7042 (ppp) cc_final: 0.6612 (ppp) REVERT: D 47 MET cc_start: 0.7550 (ppp) cc_final: 0.7027 (ppp) REVERT: D 81 ASP cc_start: 0.8657 (m-30) cc_final: 0.8294 (m-30) REVERT: D 107 GLU cc_start: 0.7994 (pt0) cc_final: 0.7641 (pt0) REVERT: D 355 MET cc_start: 0.8969 (mmm) cc_final: 0.8713 (mmm) outliers start: 16 outliers final: 12 residues processed: 144 average time/residue: 0.0889 time to fit residues: 20.2598 Evaluate side-chains 142 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 84 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 84 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 115 ASN B 115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.101748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.088183 restraints weight = 18525.552| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.90 r_work: 0.3020 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12020 Z= 0.145 Angle : 0.503 6.162 16320 Z= 0.255 Chirality : 0.044 0.126 1808 Planarity : 0.004 0.037 2084 Dihedral : 9.457 166.197 1756 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.19 % Allowed : 11.54 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.22), residues: 1468 helix: 0.11 (0.23), residues: 568 sheet: -0.01 (0.34), residues: 244 loop : 0.21 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 147 TYR 0.009 0.001 TYR A 143 PHE 0.007 0.001 PHE C 223 TRP 0.022 0.002 TRP D 79 HIS 0.005 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00344 (12020) covalent geometry : angle 0.50269 (16320) hydrogen bonds : bond 0.02471 ( 424) hydrogen bonds : angle 4.30153 ( 1092) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.7314 (ppp) cc_final: 0.7049 (ppp) REVERT: C 6 THR cc_start: 0.7714 (t) cc_final: 0.7471 (m) REVERT: C 47 MET cc_start: 0.7086 (ppp) cc_final: 0.6670 (ppp) REVERT: C 207 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8257 (mm-30) REVERT: D 47 MET cc_start: 0.7591 (ppp) cc_final: 0.7057 (ppp) REVERT: D 81 ASP cc_start: 0.8681 (m-30) cc_final: 0.8317 (m-30) REVERT: D 107 GLU cc_start: 0.8017 (pt0) cc_final: 0.7656 (pt0) outliers start: 15 outliers final: 12 residues processed: 142 average time/residue: 0.0878 time to fit residues: 19.7736 Evaluate side-chains 141 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 84 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 59 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 115 ASN B 115 ASN C 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.101740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.088202 restraints weight = 18562.093| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.90 r_work: 0.3020 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12020 Z= 0.141 Angle : 0.512 7.504 16320 Z= 0.259 Chirality : 0.044 0.127 1808 Planarity : 0.003 0.037 2084 Dihedral : 9.455 166.222 1756 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.11 % Allowed : 11.70 % Favored : 87.18 % 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: 0.07 (0.22), residues: 1468 helix: 0.12 (0.22), residues: 568 sheet: 0.01 (0.34), residues: 244 loop : 0.22 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 147 TYR 0.009 0.001 TYR A 143 PHE 0.006 0.001 PHE C 223 TRP 0.021 0.002 TRP D 79 HIS 0.005 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00335 (12020) covalent geometry : angle 0.51152 (16320) hydrogen bonds : bond 0.02486 ( 424) hydrogen bonds : angle 4.31450 ( 1092) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2662.32 seconds wall clock time: 46 minutes 29.21 seconds (2789.21 seconds total)