Starting phenix.real_space_refine on Thu Feb 5 19:46:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vye_65449/02_2026/9vye_65449.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vye_65449/02_2026/9vye_65449.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/9vye_65449/02_2026/9vye_65449.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vye_65449/02_2026/9vye_65449.map" model { file = "/net/cci-nas-00/data/ceres_data/9vye_65449/02_2026/9vye_65449.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vye_65449/02_2026/9vye_65449.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= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 12174 2.51 5 N 3369 2.21 5 O 3867 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19478 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2792 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 7, 'TRANS': 360} Chain: "B" Number of atoms: 2793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2793 Classifications: {'peptide': 368} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 360} Chain: "C" Number of atoms: 2792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2792 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 7, 'TRANS': 360} Chain: "D" Number of atoms: 2793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2793 Classifications: {'peptide': 368} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 360} Chain: "E" Number of atoms: 2792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2792 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 7, 'TRANS': 360} Chain: "F" Number of atoms: 2793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2793 Classifications: {'peptide': 368} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 360} Chain: "G" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2723 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 7, 'TRANS': 351} Chain breaks: 2 Time building chain proxies: 4.53, per 1000 atoms: 0.23 Number of scatterers: 19478 At special positions: 0 Unit cell: (167.99, 193.67, 135.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 3867 8.00 N 3369 7.00 C 12174 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 899.9 milliseconds 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4672 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 32 sheets defined 32.1% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 7 through 11 removed outlier: 3.697A pdb=" N VAL A 11 " --> pdb=" O THR A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 31 removed outlier: 3.622A pdb=" N ALA A 31 " --> pdb=" O GLY A 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 28 through 31' Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.556A pdb=" N LYS A 49 " --> pdb=" O ASP A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 107 Processing helix chain 'A' and resid 110 through 136 Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 147 through 158 Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 189 through 203 Processing helix chain 'A' and resid 225 through 238 removed outlier: 4.146A pdb=" N ASN A 238 " --> pdb=" O ASP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 252 removed outlier: 3.591A pdb=" N LYS A 252 " --> pdb=" O MET A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.589A pdb=" N THR A 283 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'B' and resid 7 through 11 removed outlier: 3.738A pdb=" N VAL B 11 " --> pdb=" O THR B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 31 No H-bonds generated for 'chain 'B' and resid 29 through 31' Processing helix chain 'B' and resid 101 through 107 Processing helix chain 'B' and resid 110 through 136 Processing helix chain 'B' and resid 147 through 158 Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 173 through 179 Processing helix chain 'B' and resid 189 through 203 Processing helix chain 'B' and resid 225 through 237 Processing helix chain 'B' and resid 246 through 252 removed outlier: 3.758A pdb=" N LYS B 252 " --> pdb=" O MET B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 283 Processing helix chain 'B' and resid 362 through 367 Processing helix chain 'C' and resid 7 through 11 removed outlier: 3.585A pdb=" N VAL C 11 " --> pdb=" O THR C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 101 through 107 Processing helix chain 'C' and resid 110 through 136 Processing helix chain 'C' and resid 142 through 146 Processing helix chain 'C' and resid 147 through 158 Processing helix chain 'C' and resid 173 through 179 Processing helix chain 'C' and resid 189 through 203 Processing helix chain 'C' and resid 225 through 236 Processing helix chain 'C' and resid 246 through 251 Processing helix chain 'C' and resid 251 through 256 Processing helix chain 'C' and resid 279 through 283 removed outlier: 3.676A pdb=" N THR C 283 " --> pdb=" O ALA C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 315 No H-bonds generated for 'chain 'C' and resid 313 through 315' Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'D' and resid 7 through 11 removed outlier: 3.743A pdb=" N VAL D 11 " --> pdb=" O THR D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'D' and resid 101 through 107 Processing helix chain 'D' and resid 110 through 136 Processing helix chain 'D' and resid 142 through 146 Processing helix chain 'D' and resid 147 through 158 Processing helix chain 'D' and resid 173 through 179 Processing helix chain 'D' and resid 189 through 202 Processing helix chain 'D' and resid 225 through 238 removed outlier: 4.491A pdb=" N ASN D 238 " --> pdb=" O ASP D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 251 Processing helix chain 'D' and resid 251 through 256 Processing helix chain 'D' and resid 279 through 283 removed outlier: 3.854A pdb=" N THR D 283 " --> pdb=" O ALA D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 315 No H-bonds generated for 'chain 'D' and resid 313 through 315' Processing helix chain 'D' and resid 362 through 367 Processing helix chain 'E' and resid 7 through 11 removed outlier: 3.832A pdb=" N VAL E 11 " --> pdb=" O THR E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 45 through 50 removed outlier: 4.264A pdb=" N LYS E 49 " --> pdb=" O GLU E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 107 Processing helix chain 'E' and resid 110 through 136 Processing helix chain 'E' and resid 147 through 158 Processing helix chain 'E' and resid 173 through 179 Processing helix chain 'E' and resid 189 through 203 Processing helix chain 'E' and resid 225 through 238 removed outlier: 4.623A pdb=" N ASN E 238 " --> pdb=" O ASP E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 256 removed outlier: 3.738A pdb=" N LEU E 253 " --> pdb=" O GLN E 249 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE E 254 " --> pdb=" O ALA E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 283 removed outlier: 3.680A pdb=" N THR E 283 " --> pdb=" O ALA E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 367 Processing helix chain 'F' and resid 7 through 11 removed outlier: 3.858A pdb=" N VAL F 11 " --> pdb=" O THR F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 4.173A pdb=" N LEU F 32 " --> pdb=" O GLY F 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 32' Processing helix chain 'F' and resid 45 through 49 Processing helix chain 'F' and resid 101 through 107 Processing helix chain 'F' and resid 110 through 136 Processing helix chain 'F' and resid 142 through 146 Processing helix chain 'F' and resid 147 through 158 Processing helix chain 'F' and resid 164 through 168 Processing helix chain 'F' and resid 173 through 180 Processing helix chain 'F' and resid 189 through 203 Processing helix chain 'F' and resid 225 through 237 Processing helix chain 'F' and resid 246 through 252 removed outlier: 3.743A pdb=" N LYS F 252 " --> pdb=" O MET F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 283 removed outlier: 3.664A pdb=" N THR F 283 " --> pdb=" O ALA F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 367 Processing helix chain 'G' and resid 7 through 11 removed outlier: 3.818A pdb=" N VAL G 11 " --> pdb=" O THR G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 31 No H-bonds generated for 'chain 'G' and resid 29 through 31' Processing helix chain 'G' and resid 45 through 49 Processing helix chain 'G' and resid 101 through 107 Processing helix chain 'G' and resid 110 through 136 Processing helix chain 'G' and resid 142 through 146 removed outlier: 3.631A pdb=" N ARG G 146 " --> pdb=" O PHE G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 158 Processing helix chain 'G' and resid 173 through 179 Processing helix chain 'G' and resid 189 through 202 Processing helix chain 'G' and resid 225 through 236 Processing helix chain 'G' and resid 279 through 283 removed outlier: 3.941A pdb=" N THR G 283 " --> pdb=" O ALA G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 367 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 21 removed outlier: 5.592A pdb=" N ALA F 58 " --> pdb=" O GLU A 16 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LYS A 18 " --> pdb=" O ALA F 58 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N VAL F 60 " --> pdb=" O LYS A 18 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE A 20 " --> pdb=" O VAL F 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 34 removed outlier: 6.170A pdb=" N GLN A 42 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N TYR A 301 " --> pdb=" O GLN A 42 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LYS A 44 " --> pdb=" O TYR A 301 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N LYS A 303 " --> pdb=" O LYS A 44 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ALA A 300 " --> pdb=" O ARG A 329 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ARG A 329 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ALA A 302 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 9.285A pdb=" N GLY A 327 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ARG A 304 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE A 325 " --> pdb=" O ARG A 304 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 89 removed outlier: 6.910A pdb=" N SER A 54 " --> pdb=" O GLN B 14 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N GLU B 16 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N THR A 56 " --> pdb=" O GLU B 16 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N LYS B 18 " --> pdb=" O THR A 56 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA A 58 " --> pdb=" O LYS B 18 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 162 through 164 removed outlier: 4.179A pdb=" N GLU A 285 " --> pdb=" O THR A 355 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LYS A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG A 211 " --> pdb=" O TYR A 219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 162 through 164 removed outlier: 4.179A pdb=" N GLU A 285 " --> pdb=" O THR A 355 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE A 265 " --> pdb=" O ARG A 218 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TYR A 220 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LYS A 267 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA A 222 " --> pdb=" O LYS A 267 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 332 through 334 Processing sheet with id=AA7, first strand: chain 'B' and resid 33 through 34 removed outlier: 6.130A pdb=" N GLN B 42 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N TYR B 301 " --> pdb=" O GLN B 42 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LYS B 44 " --> pdb=" O TYR B 301 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N LYS B 303 " --> pdb=" O LYS B 44 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ALA B 300 " --> pdb=" O ARG B 329 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ARG B 329 " --> pdb=" O ALA B 300 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ALA B 302 " --> pdb=" O GLY B 327 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N GLY B 327 " --> pdb=" O ALA B 302 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ARG B 304 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ILE B 325 " --> pdb=" O ARG B 304 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 83 through 89 removed outlier: 6.662A pdb=" N SER B 54 " --> pdb=" O GLN C 14 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 83 through 89 removed outlier: 9.090A pdb=" N PHE C 20 " --> pdb=" O THR B 56 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ALA B 58 " --> pdb=" O PHE C 20 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 68 through 69 removed outlier: 6.922A pdb=" N LYS C 317 " --> pdb=" O GLU C 310 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLU C 310 " --> pdb=" O LYS C 317 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLY C 319 " --> pdb=" O VAL C 308 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL C 308 " --> pdb=" O GLY C 319 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA C 321 " --> pdb=" O LYS C 306 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LYS C 306 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ASP C 323 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ARG C 304 " --> pdb=" O ASP C 323 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE C 325 " --> pdb=" O ALA C 302 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLN C 42 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N TYR C 301 " --> pdb=" O GLN C 42 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS C 44 " --> pdb=" O TYR C 301 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N LYS C 303 " --> pdb=" O LYS C 44 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 162 through 164 removed outlier: 3.828A pdb=" N GLU B 285 " --> pdb=" O THR B 355 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TYR B 220 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N LYS B 267 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA B 222 " --> pdb=" O LYS B 267 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 332 through 334 Processing sheet with id=AB4, first strand: chain 'C' and resid 83 through 89 removed outlier: 13.391A pdb=" N SER C 54 " --> pdb=" O GLU D 16 " (cutoff:3.500A) removed outlier: 13.176A pdb=" N LYS D 18 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N THR C 56 " --> pdb=" O LYS D 18 " (cutoff:3.500A) removed outlier: 9.190A pdb=" N PHE D 20 " --> pdb=" O THR C 56 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ALA C 58 " --> pdb=" O PHE D 20 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 68 through 69 removed outlier: 6.984A pdb=" N LYS D 317 " --> pdb=" O GLU D 310 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLU D 310 " --> pdb=" O LYS D 317 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLY D 319 " --> pdb=" O VAL D 308 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL D 308 " --> pdb=" O GLY D 319 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALA D 321 " --> pdb=" O LYS D 306 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LYS D 306 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASP D 323 " --> pdb=" O ARG D 304 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ARG D 304 " --> pdb=" O ASP D 323 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE D 325 " --> pdb=" O ALA D 302 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLN D 42 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N TYR D 301 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LYS D 44 " --> pdb=" O TYR D 301 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LYS D 303 " --> pdb=" O LYS D 44 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 162 through 164 removed outlier: 3.982A pdb=" N GLU C 285 " --> pdb=" O THR C 355 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TYR C 220 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N LYS C 267 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA C 222 " --> pdb=" O LYS C 267 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 332 through 333 Processing sheet with id=AB8, first strand: chain 'D' and resid 83 through 89 removed outlier: 6.744A pdb=" N SER D 54 " --> pdb=" O GLN E 14 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLU E 16 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N THR D 56 " --> pdb=" O GLU E 16 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N LYS E 18 " --> pdb=" O THR D 56 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA D 58 " --> pdb=" O LYS E 18 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 68 through 69 removed outlier: 3.524A pdb=" N ARG E 94 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ILE E 325 " --> pdb=" O ARG E 304 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ARG E 304 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 9.542A pdb=" N GLY E 327 " --> pdb=" O ALA E 302 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ALA E 302 " --> pdb=" O GLY E 327 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ARG E 329 " --> pdb=" O ALA E 300 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ALA E 300 " --> pdb=" O ARG E 329 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLN E 42 " --> pdb=" O VAL E 299 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N TYR E 301 " --> pdb=" O GLN E 42 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS E 44 " --> pdb=" O TYR E 301 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N LYS E 303 " --> pdb=" O LYS E 44 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLY E 34 " --> pdb=" O VAL E 43 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 162 through 164 removed outlier: 4.014A pdb=" N GLU D 285 " --> pdb=" O THR D 355 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TYR D 220 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N LYS D 267 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA D 222 " --> pdb=" O LYS D 267 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 332 through 334 Processing sheet with id=AC3, first strand: chain 'E' and resid 83 through 89 removed outlier: 13.607A pdb=" N SER E 54 " --> pdb=" O GLU F 16 " (cutoff:3.500A) removed outlier: 13.430A pdb=" N LYS F 18 " --> pdb=" O SER E 54 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N THR E 56 " --> pdb=" O LYS F 18 " (cutoff:3.500A) removed outlier: 9.267A pdb=" N PHE F 20 " --> pdb=" O THR E 56 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ALA E 58 " --> pdb=" O PHE F 20 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 137 through 138 Processing sheet with id=AC5, first strand: chain 'E' and resid 162 through 164 removed outlier: 3.924A pdb=" N GLU E 285 " --> pdb=" O THR E 355 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR E 220 " --> pdb=" O ILE E 265 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LYS E 267 " --> pdb=" O TYR E 220 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA E 222 " --> pdb=" O LYS E 267 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 332 through 334 Processing sheet with id=AC7, first strand: chain 'F' and resid 33 through 34 removed outlier: 6.288A pdb=" N GLN F 42 " --> pdb=" O VAL F 299 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N TYR F 301 " --> pdb=" O GLN F 42 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS F 44 " --> pdb=" O TYR F 301 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LYS F 303 " --> pdb=" O LYS F 44 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ALA F 300 " --> pdb=" O ARG F 329 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ARG F 329 " --> pdb=" O ALA F 300 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ALA F 302 " --> pdb=" O GLY F 327 " (cutoff:3.500A) removed outlier: 9.273A pdb=" N GLY F 327 " --> pdb=" O ALA F 302 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ARG F 304 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ILE F 325 " --> pdb=" O ARG F 304 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 259 through 261 removed outlier: 6.595A pdb=" N TYR F 220 " --> pdb=" O ILE F 265 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LYS F 267 " --> pdb=" O TYR F 220 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA F 222 " --> pdb=" O LYS F 267 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU F 285 " --> pdb=" O THR F 355 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 332 through 333 Processing sheet with id=AD1, first strand: chain 'G' and resid 33 through 34 removed outlier: 7.471A pdb=" N ALA G 300 " --> pdb=" O ARG G 329 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ARG G 329 " --> pdb=" O ALA G 300 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ALA G 302 " --> pdb=" O GLY G 327 " (cutoff:3.500A) removed outlier: 9.308A pdb=" N GLY G 327 " --> pdb=" O ALA G 302 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ARG G 304 " --> pdb=" O ILE G 325 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ILE G 325 " --> pdb=" O ARG G 304 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 54 through 60 Processing sheet with id=AD3, first strand: chain 'G' and resid 162 through 164 removed outlier: 6.536A pdb=" N TYR G 163 " --> pdb=" O PHE G 352 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N ALA G 354 " --> pdb=" O TYR G 163 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU G 285 " --> pdb=" O THR G 355 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ILE G 265 " --> pdb=" O ARG G 218 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TYR G 220 " --> pdb=" O ILE G 265 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LYS G 267 " --> pdb=" O TYR G 220 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA G 222 " --> pdb=" O LYS G 267 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 210 through 211 Processing sheet with id=AD5, first strand: chain 'G' and resid 332 through 334 810 hydrogen bonds defined for protein. 2232 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.57 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6674 1.34 - 1.46: 3799 1.46 - 1.57: 9189 1.57 - 1.69: 0 1.69 - 1.81: 122 Bond restraints: 19784 Sorted by residual: bond pdb=" N ASP B 341 " pdb=" CA ASP B 341 " ideal model delta sigma weight residual 1.460 1.487 -0.027 8.20e-03 1.49e+04 1.06e+01 bond pdb=" N LEU B 343 " pdb=" CA LEU B 343 " ideal model delta sigma weight residual 1.455 1.489 -0.033 1.22e-02 6.72e+03 7.45e+00 bond pdb=" N LEU G 343 " pdb=" CA LEU G 343 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.23e-02 6.61e+03 7.29e+00 bond pdb=" N ASP G 341 " pdb=" CA ASP G 341 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.10e+00 bond pdb=" N THR E 172 " pdb=" CA THR E 172 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.17e-02 7.31e+03 6.08e+00 ... (remaining 19779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 26404 1.47 - 2.94: 359 2.94 - 4.42: 47 4.42 - 5.89: 10 5.89 - 7.36: 2 Bond angle restraints: 26822 Sorted by residual: angle pdb=" C SER G 251 " pdb=" CA SER G 251 " pdb=" CB SER G 251 " ideal model delta sigma weight residual 116.54 111.66 4.88 1.15e+00 7.56e-01 1.80e+01 angle pdb=" CA GLU A 101 " pdb=" CB GLU A 101 " pdb=" CG GLU A 101 " ideal model delta sigma weight residual 114.10 121.46 -7.36 2.00e+00 2.50e-01 1.36e+01 angle pdb=" C ASP G 339 " pdb=" CA ASP G 339 " pdb=" CB ASP G 339 " ideal model delta sigma weight residual 110.67 103.74 6.93 1.92e+00 2.71e-01 1.30e+01 angle pdb=" N ASP B 339 " pdb=" CA ASP B 339 " pdb=" C ASP B 339 " ideal model delta sigma weight residual 110.97 107.22 3.75 1.09e+00 8.42e-01 1.18e+01 angle pdb=" N ASP G 339 " pdb=" CA ASP G 339 " pdb=" C ASP G 339 " ideal model delta sigma weight residual 111.82 115.81 -3.99 1.16e+00 7.43e-01 1.18e+01 ... (remaining 26817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 10348 17.84 - 35.68: 1050 35.68 - 53.52: 265 53.52 - 71.36: 59 71.36 - 89.20: 22 Dihedral angle restraints: 11744 sinusoidal: 4430 harmonic: 7314 Sorted by residual: dihedral pdb=" CA ASN D 204 " pdb=" C ASN D 204 " pdb=" N PRO D 205 " pdb=" CA PRO D 205 " ideal model delta harmonic sigma weight residual 180.00 161.11 18.89 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA ASN E 204 " pdb=" C ASN E 204 " pdb=" N PRO E 205 " pdb=" CA PRO E 205 " ideal model delta harmonic sigma weight residual 180.00 162.35 17.65 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA ASN F 204 " pdb=" C ASN F 204 " pdb=" N PRO F 205 " pdb=" CA PRO F 205 " ideal model delta harmonic sigma weight residual 180.00 162.48 17.52 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 11741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2470 0.048 - 0.097: 407 0.097 - 0.145: 169 0.145 - 0.194: 0 0.194 - 0.242: 1 Chirality restraints: 3047 Sorted by residual: chirality pdb=" CA THR B 340 " pdb=" N THR B 340 " pdb=" C THR B 340 " pdb=" CB THR B 340 " both_signs ideal model delta sigma weight residual False 2.53 2.77 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ILE E 272 " pdb=" N ILE E 272 " pdb=" C ILE E 272 " pdb=" CB ILE E 272 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA ILE F 88 " pdb=" N ILE F 88 " pdb=" C ILE F 88 " pdb=" CB ILE F 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 3044 not shown) Planarity restraints: 3531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP G 339 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" C ASP G 339 " -0.037 2.00e-02 2.50e+03 pdb=" O ASP G 339 " 0.014 2.00e-02 2.50e+03 pdb=" N THR G 340 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN E 225 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO E 226 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO E 226 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 226 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 225 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO C 226 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 226 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 226 " 0.026 5.00e-02 4.00e+02 ... (remaining 3528 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1033 2.74 - 3.28: 18422 3.28 - 3.82: 31892 3.82 - 4.36: 39134 4.36 - 4.90: 68184 Nonbonded interactions: 158665 Sorted by model distance: nonbonded pdb=" O LEU C 232 " pdb=" OG SER C 235 " model vdw 2.196 3.040 nonbonded pdb=" NZ LYS B 92 " pdb=" OD2 ASP B 323 " model vdw 2.270 3.120 nonbonded pdb=" OD2 ASP G 182 " pdb=" OG SER G 184 " model vdw 2.280 3.040 nonbonded pdb=" OG SER A 335 " pdb=" O ASP A 342 " model vdw 2.283 3.040 nonbonded pdb=" OE2 GLU C 133 " pdb=" NE ARG C 142 " model vdw 2.300 3.120 ... (remaining 158660 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 2 through 241 or resid 250 through 259 or resid 261 throug \ h 369)) selection = (chain 'B' and (resid 2 through 241 or resid 250 through 259 or resid 261 throug \ h 368 or (resid 369 and (name N or name CA or name C or name O or name CB or nam \ e CG or name OD1 or name ND2)))) selection = (chain 'C' and (resid 2 through 241 or resid 250 through 259 or resid 261 throug \ h 369)) selection = (chain 'D' and (resid 2 through 241 or resid 250 through 259 or resid 261 throug \ h 368 or (resid 369 and (name N or name CA or name C or name O or name CB or nam \ e CG or name OD1 or name ND2)))) selection = (chain 'E' and (resid 2 through 241 or resid 250 through 259 or resid 261 throug \ h 369)) selection = (chain 'F' and (resid 2 through 241 or resid 250 through 259 or resid 261 throug \ h 368 or (resid 369 and (name N or name CA or name C or name O or name CB or nam \ e CG or name OD1 or name ND2)))) selection = chain 'G' } 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: 30.340 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.990 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 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 : 0.002 0.034 19784 Z= 0.120 Angle : 0.457 7.362 26822 Z= 0.275 Chirality : 0.041 0.242 3047 Planarity : 0.003 0.048 3531 Dihedral : 16.065 89.203 7072 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.10 % Allowed : 16.31 % Favored : 83.59 % 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: 0.94 (0.17), residues: 2549 helix: 1.73 (0.21), residues: 632 sheet: 0.59 (0.19), residues: 676 loop : 0.17 (0.18), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 161 TYR 0.022 0.001 TYR F 318 PHE 0.008 0.001 PHE F 254 TRP 0.007 0.001 TRP B 15 HIS 0.002 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00211 (19784) covalent geometry : angle 0.45660 (26822) hydrogen bonds : bond 0.13360 ( 787) hydrogen bonds : angle 5.29504 ( 2232) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 274 time to evaluate : 0.727 Fit side-chains REVERT: C 62 ARG cc_start: 0.8286 (ptt90) cc_final: 0.8050 (ptt-90) REVERT: C 65 ASN cc_start: 0.8370 (t0) cc_final: 0.8030 (t0) REVERT: E 80 ASP cc_start: 0.8032 (p0) cc_final: 0.7798 (p0) REVERT: F 49 LYS cc_start: 0.8610 (mttt) cc_final: 0.8338 (mttm) REVERT: G 87 ARG cc_start: 0.6908 (ttt180) cc_final: 0.6392 (ttt90) REVERT: G 99 ILE cc_start: 0.8660 (pt) cc_final: 0.8401 (pt) REVERT: G 212 ASP cc_start: 0.7982 (t0) cc_final: 0.7687 (t70) outliers start: 2 outliers final: 2 residues processed: 274 average time/residue: 0.1661 time to fit residues: 67.7628 Evaluate side-chains 254 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 252 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain G residue 21 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 247 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.102914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.088060 restraints weight = 23106.788| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 1.09 r_work: 0.2680 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 19784 Z= 0.296 Angle : 0.584 6.706 26822 Z= 0.315 Chirality : 0.047 0.152 3047 Planarity : 0.004 0.053 3531 Dihedral : 5.207 85.851 2784 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.76 % Allowed : 15.50 % Favored : 81.74 % 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: 0.37 (0.16), residues: 2549 helix: 0.98 (0.20), residues: 636 sheet: 0.20 (0.19), residues: 679 loop : 0.01 (0.18), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 161 TYR 0.015 0.002 TYR E 318 PHE 0.014 0.002 PHE G 312 TRP 0.016 0.002 TRP E 305 HIS 0.007 0.002 HIS G 227 Details of bonding type rmsd covalent geometry : bond 0.00720 (19784) covalent geometry : angle 0.58390 (26822) hydrogen bonds : bond 0.05222 ( 787) hydrogen bonds : angle 4.86518 ( 2232) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 245 time to evaluate : 0.763 Fit side-chains REVERT: A 78 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.6603 (mt-10) REVERT: A 255 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8540 (mt-10) REVERT: A 285 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.6719 (mm-30) REVERT: B 78 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7954 (mt-10) REVERT: B 129 ASP cc_start: 0.7978 (m-30) cc_final: 0.7747 (m-30) REVERT: C 45 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7116 (mt-10) REVERT: C 62 ARG cc_start: 0.8254 (ptt90) cc_final: 0.8017 (ptt-90) REVERT: C 75 GLU cc_start: 0.5074 (mp0) cc_final: 0.4523 (tt0) REVERT: C 94 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8391 (mtm180) REVERT: D 78 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.6406 (mt-10) REVERT: E 75 GLU cc_start: 0.4653 (mp0) cc_final: 0.2915 (tt0) REVERT: F 49 LYS cc_start: 0.8736 (mttt) cc_final: 0.8452 (mmtt) REVERT: F 180 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7022 (mp10) REVERT: F 255 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7945 (pt0) REVERT: G 106 ARG cc_start: 0.6797 (tpt90) cc_final: 0.5075 (mtt180) REVERT: G 206 LYS cc_start: 0.5614 (ttpt) cc_final: 0.5348 (ttpt) outliers start: 55 outliers final: 37 residues processed: 284 average time/residue: 0.1736 time to fit residues: 72.3860 Evaluate side-chains 270 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 226 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 189 ASN Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain F residue 37 GLU Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 215 ASN Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 170 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 107 optimal weight: 6.9990 chunk 196 optimal weight: 0.3980 chunk 171 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 111 optimal weight: 9.9990 chunk 181 optimal weight: 0.9980 chunk 230 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 195 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 21 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.105625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.090887 restraints weight = 23025.695| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 1.09 r_work: 0.2725 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19784 Z= 0.139 Angle : 0.450 5.358 26822 Z= 0.249 Chirality : 0.042 0.136 3047 Planarity : 0.003 0.050 3531 Dihedral : 4.336 21.534 2778 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.26 % Allowed : 16.36 % 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: 0.57 (0.17), residues: 2549 helix: 1.27 (0.20), residues: 636 sheet: 0.25 (0.19), residues: 677 loop : 0.11 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 116 TYR 0.009 0.001 TYR E 318 PHE 0.010 0.001 PHE G 312 TRP 0.009 0.001 TRP E 305 HIS 0.003 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00324 (19784) covalent geometry : angle 0.44992 (26822) hydrogen bonds : bond 0.04007 ( 787) hydrogen bonds : angle 4.44248 ( 2232) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 242 time to evaluate : 0.773 Fit side-chains REVERT: A 78 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.6636 (mt-10) REVERT: A 285 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.6924 (mm-30) REVERT: B 129 ASP cc_start: 0.7949 (m-30) cc_final: 0.7742 (m-30) REVERT: C 62 ARG cc_start: 0.8275 (ptt90) cc_final: 0.8067 (ptt-90) REVERT: C 75 GLU cc_start: 0.4940 (mp0) cc_final: 0.4539 (tt0) REVERT: C 312 PHE cc_start: 0.7928 (m-80) cc_final: 0.7613 (m-80) REVERT: E 75 GLU cc_start: 0.4641 (mp0) cc_final: 0.3009 (tt0) REVERT: E 234 ASP cc_start: 0.7533 (m-30) cc_final: 0.7210 (m-30) REVERT: E 295 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7244 (mm-40) REVERT: F 49 LYS cc_start: 0.8768 (mttt) cc_final: 0.8444 (mmtt) REVERT: F 255 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7913 (pt0) REVERT: G 79 GLU cc_start: 0.7963 (tt0) cc_final: 0.7688 (tt0) REVERT: G 106 ARG cc_start: 0.6802 (tpt90) cc_final: 0.5049 (mtt180) outliers start: 45 outliers final: 25 residues processed: 275 average time/residue: 0.1685 time to fit residues: 68.1554 Evaluate side-chains 256 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 228 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 295 GLN Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 215 ASN Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 320 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 221 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 chunk 202 optimal weight: 10.0000 chunk 162 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 149 optimal weight: 0.2980 chunk 99 optimal weight: 10.0000 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.103746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.088881 restraints weight = 23116.298| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 1.09 r_work: 0.2686 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2565 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 19784 Z= 0.212 Angle : 0.503 6.028 26822 Z= 0.275 Chirality : 0.044 0.144 3047 Planarity : 0.004 0.052 3531 Dihedral : 4.509 23.305 2778 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.61 % Allowed : 16.61 % Favored : 80.78 % 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: 0.43 (0.17), residues: 2549 helix: 1.05 (0.20), residues: 636 sheet: 0.17 (0.19), residues: 677 loop : 0.08 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 94 TYR 0.012 0.001 TYR E 318 PHE 0.012 0.001 PHE G 312 TRP 0.011 0.002 TRP E 305 HIS 0.004 0.001 HIS G 227 Details of bonding type rmsd covalent geometry : bond 0.00511 (19784) covalent geometry : angle 0.50348 (26822) hydrogen bonds : bond 0.04504 ( 787) hydrogen bonds : angle 4.54395 ( 2232) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 232 time to evaluate : 0.703 Fit side-chains REVERT: A 78 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7569 (mp0) REVERT: A 101 GLU cc_start: 0.8008 (tp30) cc_final: 0.7789 (tp30) REVERT: A 177 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.8107 (m-30) REVERT: A 285 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.6879 (mm-30) REVERT: B 78 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7940 (mt-10) REVERT: B 129 ASP cc_start: 0.7962 (m-30) cc_final: 0.7726 (m-30) REVERT: C 45 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7139 (mt-10) REVERT: C 62 ARG cc_start: 0.8313 (ptt90) cc_final: 0.8096 (ptt-90) REVERT: C 75 GLU cc_start: 0.5098 (mp0) cc_final: 0.4485 (tt0) REVERT: C 312 PHE cc_start: 0.8167 (m-80) cc_final: 0.7915 (m-80) REVERT: D 78 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.6317 (mt-10) REVERT: E 75 GLU cc_start: 0.5092 (mp0) cc_final: 0.3071 (tt0) REVERT: E 295 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7131 (mm-40) REVERT: F 49 LYS cc_start: 0.8786 (mttt) cc_final: 0.8463 (mmtt) REVERT: F 180 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7222 (mp10) REVERT: F 255 GLU cc_start: 0.8256 (mt-10) cc_final: 0.8020 (pt0) REVERT: G 79 GLU cc_start: 0.8019 (tt0) cc_final: 0.7734 (tt0) REVERT: G 106 ARG cc_start: 0.6783 (tpt90) cc_final: 0.5112 (mtt180) outliers start: 52 outliers final: 40 residues processed: 273 average time/residue: 0.1711 time to fit residues: 69.2597 Evaluate side-chains 272 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 224 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 189 ASN Chi-restraints excluded: chain E residue 203 CYS Chi-restraints excluded: chain E residue 295 GLN Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 215 ASN Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 236 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 158 optimal weight: 9.9990 chunk 206 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 234 optimal weight: 20.0000 chunk 30 optimal weight: 8.9990 chunk 204 optimal weight: 0.1980 chunk 60 optimal weight: 8.9990 chunk 193 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 182 optimal weight: 0.2980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.104925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.090208 restraints weight = 22994.449| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 1.09 r_work: 0.2709 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19784 Z= 0.155 Angle : 0.458 5.242 26822 Z= 0.253 Chirality : 0.043 0.140 3047 Planarity : 0.003 0.050 3531 Dihedral : 4.371 21.775 2778 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.01 % Allowed : 16.66 % Favored : 80.33 % 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: 0.52 (0.17), residues: 2549 helix: 1.21 (0.20), residues: 636 sheet: 0.17 (0.19), residues: 677 loop : 0.12 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 142 TYR 0.010 0.001 TYR E 318 PHE 0.011 0.001 PHE G 312 TRP 0.008 0.001 TRP E 305 HIS 0.003 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00365 (19784) covalent geometry : angle 0.45840 (26822) hydrogen bonds : bond 0.04063 ( 787) hydrogen bonds : angle 4.38846 ( 2232) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 235 time to evaluate : 0.654 Fit side-chains REVERT: A 78 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7481 (mp0) REVERT: A 101 GLU cc_start: 0.7976 (tp30) cc_final: 0.7720 (tp30) REVERT: A 177 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.8047 (m-30) REVERT: A 285 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.6917 (mm-30) REVERT: B 129 ASP cc_start: 0.7892 (m-30) cc_final: 0.7637 (m-30) REVERT: C 62 ARG cc_start: 0.8300 (ptt90) cc_final: 0.8075 (ptt-90) REVERT: C 75 GLU cc_start: 0.5210 (mp0) cc_final: 0.4634 (tt0) REVERT: C 312 PHE cc_start: 0.8016 (m-80) cc_final: 0.7750 (m-80) REVERT: D 78 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.6560 (mt-10) REVERT: E 75 GLU cc_start: 0.5007 (mp0) cc_final: 0.3048 (tt0) REVERT: E 295 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7294 (mm-40) REVERT: F 49 LYS cc_start: 0.8770 (mttt) cc_final: 0.8455 (mmtt) REVERT: F 180 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7111 (mp10) REVERT: F 255 GLU cc_start: 0.8263 (mt-10) cc_final: 0.8020 (pt0) REVERT: G 79 GLU cc_start: 0.7945 (tt0) cc_final: 0.7669 (tt0) REVERT: G 106 ARG cc_start: 0.6710 (tpt90) cc_final: 0.5055 (mtt180) REVERT: G 206 LYS cc_start: 0.5812 (tttt) cc_final: 0.5117 (tmtt) outliers start: 60 outliers final: 40 residues processed: 279 average time/residue: 0.1525 time to fit residues: 63.1611 Evaluate side-chains 272 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 226 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 189 ASN Chi-restraints excluded: chain E residue 203 CYS Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 295 GLN Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain F residue 37 GLU Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 215 ASN Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 236 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 18 optimal weight: 0.8980 chunk 198 optimal weight: 10.0000 chunk 177 optimal weight: 0.0270 chunk 55 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 210 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 173 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 overall best weight: 2.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.104872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.090415 restraints weight = 22919.836| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 1.04 r_work: 0.2717 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 19784 Z= 0.158 Angle : 0.462 5.501 26822 Z= 0.254 Chirality : 0.043 0.140 3047 Planarity : 0.004 0.050 3531 Dihedral : 4.354 21.772 2778 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.01 % Allowed : 16.96 % Favored : 80.03 % 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: 0.56 (0.17), residues: 2549 helix: 1.29 (0.20), residues: 630 sheet: 0.16 (0.19), residues: 677 loop : 0.15 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 142 TYR 0.010 0.001 TYR E 318 PHE 0.014 0.001 PHE G 312 TRP 0.008 0.001 TRP E 305 HIS 0.003 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00375 (19784) covalent geometry : angle 0.46158 (26822) hydrogen bonds : bond 0.04074 ( 787) hydrogen bonds : angle 4.36090 ( 2232) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 231 time to evaluate : 0.595 Fit side-chains REVERT: A 78 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7460 (mp0) REVERT: A 101 GLU cc_start: 0.7941 (tp30) cc_final: 0.7737 (tp30) REVERT: A 285 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.6863 (mm-30) REVERT: C 45 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7121 (mt-10) REVERT: C 62 ARG cc_start: 0.8311 (ptt90) cc_final: 0.8082 (ptt-90) REVERT: C 75 GLU cc_start: 0.5132 (mp0) cc_final: 0.4560 (tt0) REVERT: C 312 PHE cc_start: 0.8119 (m-80) cc_final: 0.7843 (m-80) REVERT: D 78 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.6579 (mt-10) REVERT: E 75 GLU cc_start: 0.5034 (mp0) cc_final: 0.3059 (tt0) REVERT: E 295 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7178 (mm-40) REVERT: F 49 LYS cc_start: 0.8754 (mttt) cc_final: 0.8444 (mmtt) REVERT: F 180 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7124 (mp10) REVERT: F 255 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7956 (pt0) REVERT: G 79 GLU cc_start: 0.8025 (tt0) cc_final: 0.7707 (tt0) REVERT: G 106 ARG cc_start: 0.6657 (tpt170) cc_final: 0.5029 (mtt180) REVERT: G 206 LYS cc_start: 0.5781 (tttt) cc_final: 0.5113 (tmtt) outliers start: 60 outliers final: 46 residues processed: 277 average time/residue: 0.1410 time to fit residues: 58.2215 Evaluate side-chains 282 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 230 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 189 ASN Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 295 GLN Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain F residue 37 GLU Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 215 ASN Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain G residue 170 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 109 optimal weight: 0.9990 chunk 205 optimal weight: 5.9990 chunk 203 optimal weight: 0.9990 chunk 123 optimal weight: 10.0000 chunk 38 optimal weight: 0.0570 chunk 88 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 144 optimal weight: 0.0470 chunk 162 optimal weight: 9.9990 chunk 245 optimal weight: 2.9990 overall best weight: 1.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.108458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.093898 restraints weight = 22880.847| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 1.08 r_work: 0.2774 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 19784 Z= 0.087 Angle : 0.405 4.961 26822 Z= 0.226 Chirality : 0.041 0.131 3047 Planarity : 0.003 0.048 3531 Dihedral : 3.980 19.779 2778 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.06 % Allowed : 17.81 % Favored : 80.13 % 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: 0.80 (0.17), residues: 2549 helix: 1.69 (0.21), residues: 626 sheet: 0.18 (0.20), residues: 694 loop : 0.26 (0.19), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 142 TYR 0.008 0.001 TYR B 318 PHE 0.010 0.001 PHE G 312 TRP 0.007 0.001 TRP B 15 HIS 0.002 0.001 HIS C 346 Details of bonding type rmsd covalent geometry : bond 0.00186 (19784) covalent geometry : angle 0.40464 (26822) hydrogen bonds : bond 0.03334 ( 787) hydrogen bonds : angle 4.07344 ( 2232) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 240 time to evaluate : 0.857 Fit side-chains REVERT: A 285 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.6935 (mm-30) REVERT: B 80 ASP cc_start: 0.8705 (p0) cc_final: 0.8450 (p0) REVERT: C 62 ARG cc_start: 0.8263 (ptt90) cc_final: 0.8056 (ptt-90) REVERT: C 75 GLU cc_start: 0.5175 (mp0) cc_final: 0.4807 (tt0) REVERT: D 78 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.6626 (mp0) REVERT: E 75 GLU cc_start: 0.4786 (mp0) cc_final: 0.3013 (tt0) REVERT: E 94 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8221 (ptt180) REVERT: F 49 LYS cc_start: 0.8744 (mttt) cc_final: 0.8432 (mmtt) REVERT: F 180 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.6805 (mp10) REVERT: F 255 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7934 (pt0) REVERT: G 79 GLU cc_start: 0.7971 (tt0) cc_final: 0.7652 (tt0) REVERT: G 106 ARG cc_start: 0.6599 (tpt170) cc_final: 0.4995 (mtt180) REVERT: G 206 LYS cc_start: 0.5575 (tttt) cc_final: 0.5018 (tttt) REVERT: G 212 ASP cc_start: 0.8181 (t0) cc_final: 0.7966 (t70) outliers start: 41 outliers final: 28 residues processed: 271 average time/residue: 0.1782 time to fit residues: 71.0838 Evaluate side-chains 263 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 231 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain E residue 94 ARG Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain F residue 37 GLU Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 215 ASN Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 320 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 149 optimal weight: 0.9980 chunk 108 optimal weight: 10.0000 chunk 219 optimal weight: 8.9990 chunk 148 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 144 optimal weight: 0.7980 chunk 230 optimal weight: 0.4980 chunk 211 optimal weight: 0.3980 chunk 27 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 234 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.110149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.095685 restraints weight = 22769.525| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 1.10 r_work: 0.2804 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19784 Z= 0.081 Angle : 0.399 6.637 26822 Z= 0.222 Chirality : 0.041 0.157 3047 Planarity : 0.003 0.047 3531 Dihedral : 3.783 19.090 2778 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.86 % Allowed : 18.01 % Favored : 80.13 % 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: 0.95 (0.17), residues: 2549 helix: 1.85 (0.21), residues: 632 sheet: 0.29 (0.20), residues: 695 loop : 0.31 (0.19), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 94 TYR 0.008 0.001 TYR B 318 PHE 0.009 0.001 PHE G 312 TRP 0.006 0.001 TRP A 15 HIS 0.002 0.001 HIS E 346 Details of bonding type rmsd covalent geometry : bond 0.00170 (19784) covalent geometry : angle 0.39949 (26822) hydrogen bonds : bond 0.03183 ( 787) hydrogen bonds : angle 3.92178 ( 2232) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 250 time to evaluate : 0.813 Fit side-chains REVERT: A 285 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7015 (mm-30) REVERT: B 49 LYS cc_start: 0.8667 (mtmm) cc_final: 0.8357 (mtpt) REVERT: B 59 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8074 (tp) REVERT: B 80 ASP cc_start: 0.8689 (p0) cc_final: 0.8435 (p0) REVERT: B 146 ARG cc_start: 0.9187 (OUTLIER) cc_final: 0.7658 (ptt-90) REVERT: C 62 ARG cc_start: 0.8246 (ptt90) cc_final: 0.8035 (ptt-90) REVERT: C 65 ASN cc_start: 0.8286 (t0) cc_final: 0.7936 (t0) REVERT: C 75 GLU cc_start: 0.5140 (mp0) cc_final: 0.4753 (tt0) REVERT: C 81 MET cc_start: 0.8685 (ttp) cc_final: 0.8398 (ptt) REVERT: D 78 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.6795 (mt-10) REVERT: D 80 ASP cc_start: 0.7971 (p0) cc_final: 0.7402 (p0) REVERT: E 75 GLU cc_start: 0.4645 (mp0) cc_final: 0.3085 (tt0) REVERT: E 80 ASP cc_start: 0.8062 (p0) cc_final: 0.7788 (p0) REVERT: E 94 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8368 (ptm160) REVERT: F 49 LYS cc_start: 0.8732 (mttt) cc_final: 0.8424 (mmtt) REVERT: F 180 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.6950 (mp10) REVERT: F 255 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7896 (pt0) REVERT: G 79 GLU cc_start: 0.7975 (tt0) cc_final: 0.7635 (tt0) REVERT: G 106 ARG cc_start: 0.6545 (tpt170) cc_final: 0.4990 (mtt180) outliers start: 37 outliers final: 24 residues processed: 280 average time/residue: 0.1680 time to fit residues: 70.0786 Evaluate side-chains 268 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 238 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain E residue 94 ARG Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 215 ASN Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 320 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 209 optimal weight: 9.9990 chunk 201 optimal weight: 6.9990 chunk 191 optimal weight: 6.9990 chunk 233 optimal weight: 0.0980 chunk 96 optimal weight: 6.9990 chunk 131 optimal weight: 9.9990 chunk 188 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 overall best weight: 5.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 295 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.103329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.088781 restraints weight = 23110.590| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 1.04 r_work: 0.2690 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 19784 Z= 0.255 Angle : 0.537 6.397 26822 Z= 0.292 Chirality : 0.045 0.182 3047 Planarity : 0.004 0.070 3531 Dihedral : 4.488 22.584 2778 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.11 % Allowed : 17.86 % Favored : 80.03 % 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: 0.56 (0.17), residues: 2549 helix: 1.23 (0.20), residues: 630 sheet: 0.21 (0.20), residues: 671 loop : 0.15 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 94 TYR 0.013 0.002 TYR E 318 PHE 0.015 0.002 PHE G 312 TRP 0.009 0.002 TRP E 305 HIS 0.005 0.001 HIS G 227 Details of bonding type rmsd covalent geometry : bond 0.00617 (19784) covalent geometry : angle 0.53749 (26822) hydrogen bonds : bond 0.04717 ( 787) hydrogen bonds : angle 4.45557 ( 2232) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 231 time to evaluate : 0.798 Fit side-chains REVERT: A 285 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.6816 (mm-30) REVERT: C 45 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7110 (mt-10) REVERT: C 62 ARG cc_start: 0.8308 (ptt90) cc_final: 0.8046 (ptt-90) REVERT: C 75 GLU cc_start: 0.5345 (mp0) cc_final: 0.4613 (tt0) REVERT: D 78 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.6496 (mt-10) REVERT: E 75 GLU cc_start: 0.5230 (mp0) cc_final: 0.3109 (tt0) REVERT: E 80 ASP cc_start: 0.8175 (p0) cc_final: 0.7852 (p0) REVERT: E 94 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8263 (ptt180) REVERT: E 295 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7200 (mm-40) REVERT: F 49 LYS cc_start: 0.8746 (mttt) cc_final: 0.8435 (mmtt) REVERT: F 180 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7168 (mp10) REVERT: F 255 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7988 (pt0) REVERT: G 78 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7279 (mt-10) REVERT: G 79 GLU cc_start: 0.8010 (tt0) cc_final: 0.7705 (tt0) REVERT: G 104 GLU cc_start: 0.8337 (tt0) cc_final: 0.8123 (tp30) REVERT: G 106 ARG cc_start: 0.6690 (tpt170) cc_final: 0.5054 (mtt180) outliers start: 42 outliers final: 30 residues processed: 261 average time/residue: 0.1797 time to fit residues: 68.5705 Evaluate side-chains 264 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 227 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain E residue 94 ARG Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 295 GLN Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain F residue 37 GLU Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 215 ASN Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain G residue 78 GLU Chi-restraints excluded: chain G residue 170 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 203 optimal weight: 0.8980 chunk 156 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 210 optimal weight: 0.8980 chunk 103 optimal weight: 0.2980 chunk 237 optimal weight: 3.9990 chunk 226 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 194 optimal weight: 1.9990 chunk 249 optimal weight: 7.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.106989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.092373 restraints weight = 22850.115| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 1.08 r_work: 0.2749 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 19784 Z= 0.108 Angle : 0.430 6.202 26822 Z= 0.239 Chirality : 0.042 0.138 3047 Planarity : 0.003 0.047 3531 Dihedral : 4.126 20.183 2778 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.66 % Allowed : 18.46 % Favored : 79.88 % 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: 0.74 (0.17), residues: 2549 helix: 1.58 (0.20), residues: 626 sheet: 0.22 (0.20), residues: 681 loop : 0.21 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 142 TYR 0.010 0.001 TYR E 318 PHE 0.011 0.001 PHE G 312 TRP 0.006 0.001 TRP A 15 HIS 0.003 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00242 (19784) covalent geometry : angle 0.43035 (26822) hydrogen bonds : bond 0.03593 ( 787) hydrogen bonds : angle 4.14697 ( 2232) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 232 time to evaluate : 0.919 Fit side-chains REVERT: A 285 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.6970 (mm-30) REVERT: B 49 LYS cc_start: 0.8668 (mtmm) cc_final: 0.8349 (mtpt) REVERT: B 80 ASP cc_start: 0.8705 (p0) cc_final: 0.8459 (p0) REVERT: C 45 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7129 (mt-10) REVERT: C 62 ARG cc_start: 0.8269 (ptt90) cc_final: 0.8043 (ptt-90) REVERT: C 75 GLU cc_start: 0.5141 (mp0) cc_final: 0.4609 (tt0) REVERT: C 81 MET cc_start: 0.8847 (ttp) cc_final: 0.8571 (ptt) REVERT: C 312 PHE cc_start: 0.7943 (m-10) cc_final: 0.7696 (m-10) REVERT: D 78 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.6445 (mp0) REVERT: D 80 ASP cc_start: 0.7977 (p0) cc_final: 0.7376 (p0) REVERT: E 75 GLU cc_start: 0.4895 (mp0) cc_final: 0.3062 (tt0) REVERT: E 80 ASP cc_start: 0.8094 (p0) cc_final: 0.7804 (p0) REVERT: E 94 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8241 (ptt180) REVERT: E 295 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7305 (mm-40) REVERT: F 49 LYS cc_start: 0.8716 (mttt) cc_final: 0.8384 (mmtt) REVERT: F 180 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7006 (mp10) REVERT: F 255 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7891 (pt0) REVERT: G 79 GLU cc_start: 0.7917 (tt0) cc_final: 0.7628 (tt0) REVERT: G 106 ARG cc_start: 0.6584 (tpt170) cc_final: 0.4991 (mtt180) outliers start: 33 outliers final: 23 residues processed: 260 average time/residue: 0.1716 time to fit residues: 65.8899 Evaluate side-chains 258 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 229 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain E residue 94 ARG Chi-restraints excluded: chain E residue 295 GLN Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain F residue 37 GLU Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 215 ASN Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 320 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 200 optimal weight: 0.9990 chunk 101 optimal weight: 0.0010 chunk 237 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 203 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 115 optimal weight: 10.0000 chunk 246 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.108640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.094122 restraints weight = 22739.961| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 1.09 r_work: 0.2768 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19784 Z= 0.093 Angle : 0.414 7.278 26822 Z= 0.230 Chirality : 0.041 0.131 3047 Planarity : 0.003 0.047 3531 Dihedral : 3.930 19.772 2778 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.66 % Allowed : 18.62 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.17), residues: 2549 helix: 1.53 (0.20), residues: 654 sheet: 0.27 (0.20), residues: 670 loop : 0.29 (0.19), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 142 TYR 0.008 0.001 TYR B 318 PHE 0.010 0.001 PHE G 312 TRP 0.006 0.001 TRP A 15 HIS 0.003 0.001 HIS F 346 Details of bonding type rmsd covalent geometry : bond 0.00205 (19784) covalent geometry : angle 0.41381 (26822) hydrogen bonds : bond 0.03363 ( 787) hydrogen bonds : angle 3.99874 ( 2232) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6034.49 seconds wall clock time: 103 minutes 57.54 seconds (6237.54 seconds total)