Starting phenix.real_space_refine on Sun Aug 24 18:30:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f8q_28933/08_2025/8f8q_28933.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f8q_28933/08_2025/8f8q_28933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8f8q_28933/08_2025/8f8q_28933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f8q_28933/08_2025/8f8q_28933.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8f8q_28933/08_2025/8f8q_28933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f8q_28933/08_2025/8f8q_28933.map" } resolution = 2.79 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= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 143 5.16 5 C 13862 2.51 5 N 3737 2.21 5 O 4246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22006 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2893 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 2262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2262 Classifications: {'peptide': 278} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 267} Chain: "H" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2138 Classifications: {'peptide': 270} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 259} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.81, per 1000 atoms: 0.22 Number of scatterers: 22006 At special positions: 0 Unit cell: (81, 112.32, 258.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 143 16.00 P 12 15.00 Mg 6 11.99 O 4246 8.00 N 3737 7.00 C 13862 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: 1.68 Conformation dependent library (CDL) restraints added in 797.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5158 Finding SS restraints... Secondary structure from input PDB file: 134 helices and 41 sheets defined 46.3% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.655A pdb=" N GLU A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.989A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.679A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.692A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.677A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 337 through 347 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.586A pdb=" N MET B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.744A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.989A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.546A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.987A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.875A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 4.111A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.575A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.051A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.513A pdb=" N GLY C 146 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.670A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.846A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.761A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 302 through 306 removed outlier: 4.109A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 4.181A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.611A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.004A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.629A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.985A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.625A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 368 through 374 removed outlier: 4.184A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.914A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.685A pdb=" N ILE E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 194 through 196 No H-bonds generated for 'chain 'E' and resid 194 through 196' Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.815A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 289 through 296 Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 337 Processing helix chain 'E' and resid 338 through 348 Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'F' and resid 55 through 60 Processing helix chain 'F' and resid 61 through 63 No H-bonds generated for 'chain 'F' and resid 61 through 63' Processing helix chain 'F' and resid 78 through 92 Processing helix chain 'F' and resid 112 through 126 removed outlier: 4.071A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 removed outlier: 3.541A pdb=" N SER F 145 " --> pdb=" O SER F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 175 removed outlier: 3.766A pdb=" N ILE F 175 " --> pdb=" O PRO F 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 172 through 175' Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 202 through 217 removed outlier: 3.775A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS F 217 " --> pdb=" O LYS F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 231 Processing helix chain 'F' and resid 252 through 257 removed outlier: 3.631A pdb=" N CYS F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 262 Processing helix chain 'F' and resid 263 through 267 removed outlier: 3.603A pdb=" N ILE F 267 " --> pdb=" O PRO F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 286 through 296 removed outlier: 4.317A pdb=" N LYS F 291 " --> pdb=" O ILE F 287 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ASP F 292 " --> pdb=" O ASP F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 305 removed outlier: 3.598A pdb=" N THR F 304 " --> pdb=" O GLY F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 338 through 348 Processing helix chain 'F' and resid 350 through 355 removed outlier: 3.651A pdb=" N GLN F 353 " --> pdb=" O SER F 350 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 368 through 372 removed outlier: 3.533A pdb=" N HIS F 371 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 29 through 41 removed outlier: 3.763A pdb=" N ASN G 41 " --> pdb=" O ARG G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 48 removed outlier: 3.753A pdb=" N LEU G 46 " --> pdb=" O ASN G 42 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU G 48 " --> pdb=" O ASN G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 62 removed outlier: 3.822A pdb=" N ALA G 55 " --> pdb=" O ALA G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 136 removed outlier: 4.274A pdb=" N SER G 123 " --> pdb=" O SER G 119 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N CYS G 124 " --> pdb=" O TRP G 120 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA G 127 " --> pdb=" O SER G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 167 Processing helix chain 'G' and resid 220 through 249 removed outlier: 4.136A pdb=" N GLU G 238 " --> pdb=" O ASN G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 254 removed outlier: 3.526A pdb=" N THR G 253 " --> pdb=" O THR G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 279 Processing helix chain 'G' and resid 280 through 282 No H-bonds generated for 'chain 'G' and resid 280 through 282' Processing helix chain 'H' and resid 3 through 15 removed outlier: 3.867A pdb=" N ARG H 15 " --> pdb=" O ASP H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 27 Processing helix chain 'H' and resid 35 through 40 removed outlier: 3.578A pdb=" N LEU H 40 " --> pdb=" O CYS H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 112 removed outlier: 3.680A pdb=" N GLU H 99 " --> pdb=" O LYS H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 231 Processing helix chain 'H' and resid 231 through 244 removed outlier: 3.519A pdb=" N ARG H 244 " --> pdb=" O VAL H 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 256 removed outlier: 3.736A pdb=" N LYS H 254 " --> pdb=" O ASP H 251 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE H 255 " --> pdb=" O ASN H 252 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS H 256 " --> pdb=" O GLN H 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 251 through 256' Processing helix chain 'H' and resid 257 through 271 removed outlier: 4.318A pdb=" N GLU H 261 " --> pdb=" O GLN H 257 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.970A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ASN A 12 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 removed outlier: 6.377A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 176 through 178 removed outlier: 3.650A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.864A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.592A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.559A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.949A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 176 through 178 removed outlier: 6.533A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 176 through 178 removed outlier: 4.314A pdb=" N GLN E 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.805A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 176 through 178 removed outlier: 6.611A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 176 through 178 removed outlier: 3.654A pdb=" N GLN F 41 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 3.861A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ASN E 12 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.256A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AD4, first strand: chain 'F' and resid 29 through 32 removed outlier: 6.527A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD6, first strand: chain 'F' and resid 71 through 72 removed outlier: 3.503A pdb=" N ILE F 75 " --> pdb=" O GLU F 72 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AD8, first strand: chain 'F' and resid 169 through 170 removed outlier: 6.388A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AE1, first strand: chain 'G' and resid 63 through 65 removed outlier: 3.890A pdb=" N THR G 63 " --> pdb=" O ILE G 76 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 86 through 89 removed outlier: 3.597A pdb=" N ILE G 94 " --> pdb=" O ASP G 89 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LYS G 97 " --> pdb=" O ASP G 107 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ASP G 107 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ASP G 99 " --> pdb=" O ALA G 105 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ALA G 105 " --> pdb=" O ASP G 99 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 139 through 147 removed outlier: 4.445A pdb=" N THR G 180 " --> pdb=" O GLN G 187 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N GLN G 187 " --> pdb=" O THR G 180 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N HIS G 209 " --> pdb=" O THR H 186 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS H 145 " --> pdb=" O GLN H 178 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 48 through 52 removed outlier: 4.032A pdb=" N LYS H 48 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS H 57 " --> pdb=" O ASP H 52 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 66 through 67 1114 hydrogen bonds defined for protein. 2985 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: 3.75 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7146 1.34 - 1.46: 4159 1.46 - 1.58: 10905 1.58 - 1.69: 18 1.69 - 1.81: 248 Bond restraints: 22476 Sorted by residual: bond pdb=" CE1 HIC F 73 " pdb=" NE2 HIC F 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.60e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.50e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.29e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.23e+00 bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.18e+00 ... (remaining 22471 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 29800 1.94 - 3.88: 570 3.88 - 5.82: 83 5.82 - 7.76: 20 7.76 - 9.70: 5 Bond angle restraints: 30478 Sorted by residual: angle pdb=" C ASP H 247 " pdb=" N ALA H 248 " pdb=" CA ALA H 248 " ideal model delta sigma weight residual 121.31 128.47 -7.16 1.49e+00 4.50e-01 2.31e+01 angle pdb=" C GLY A 46 " pdb=" N MET A 47 " pdb=" CA MET A 47 " ideal model delta sigma weight residual 121.54 129.48 -7.94 1.91e+00 2.74e-01 1.73e+01 angle pdb=" C GLY D 46 " pdb=" N MET D 47 " pdb=" CA MET D 47 " ideal model delta sigma weight residual 121.54 129.30 -7.76 1.91e+00 2.74e-01 1.65e+01 angle pdb=" N ALA H 248 " pdb=" CA ALA H 248 " pdb=" C ALA H 248 " ideal model delta sigma weight residual 110.35 115.46 -5.11 1.40e+00 5.10e-01 1.33e+01 angle pdb=" C GLY B 46 " pdb=" N MET B 47 " pdb=" CA MET B 47 " ideal model delta sigma weight residual 122.61 128.25 -5.64 1.56e+00 4.11e-01 1.31e+01 ... (remaining 30473 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.20: 12707 23.20 - 46.41: 705 46.41 - 69.61: 117 69.61 - 92.82: 14 92.82 - 116.02: 6 Dihedral angle restraints: 13549 sinusoidal: 5506 harmonic: 8043 Sorted by residual: dihedral pdb=" CA PHE E 127 " pdb=" C PHE E 127 " pdb=" N ASN E 128 " pdb=" CA ASN E 128 " ideal model delta harmonic sigma weight residual -180.00 -150.42 -29.58 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 -176.02 116.02 1 2.00e+01 2.50e-03 3.45e+01 dihedral pdb=" O1B ADP F 401 " pdb=" O3A ADP F 401 " pdb=" PB ADP F 401 " pdb=" PA ADP F 401 " ideal model delta sinusoidal sigma weight residual -60.00 -175.12 115.12 1 2.00e+01 2.50e-03 3.42e+01 ... (remaining 13546 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1956 0.034 - 0.068: 902 0.068 - 0.102: 337 0.102 - 0.137: 144 0.137 - 0.171: 28 Chirality restraints: 3367 Sorted by residual: chirality pdb=" CA CYS B 257 " pdb=" N CYS B 257 " pdb=" C CYS B 257 " pdb=" CB CYS B 257 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.30e-01 chirality pdb=" CA CYS C 257 " pdb=" N CYS C 257 " pdb=" C CYS C 257 " pdb=" CB CYS C 257 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CA CYS E 257 " pdb=" N CYS E 257 " pdb=" C CYS E 257 " pdb=" CB CYS E 257 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.90e-01 ... (remaining 3364 not shown) Planarity restraints: 3918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 242 " 0.051 5.00e-02 4.00e+02 7.73e-02 9.56e+00 pdb=" N PRO E 243 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO E 243 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 243 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 163 " 0.037 5.00e-02 4.00e+02 5.68e-02 5.15e+00 pdb=" N PRO E 164 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO E 164 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 164 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 242 " -0.035 5.00e-02 4.00e+02 5.33e-02 4.54e+00 pdb=" N PRO A 243 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " -0.030 5.00e-02 4.00e+02 ... (remaining 3915 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 227 2.64 - 3.20: 17674 3.20 - 3.77: 33848 3.77 - 4.33: 48410 4.33 - 4.90: 80185 Nonbonded interactions: 180344 Sorted by model distance: nonbonded pdb=" O3B ADP E 401 " pdb="MG MG E 402 " model vdw 2.072 2.170 nonbonded pdb=" O3B ADP A 401 " pdb="MG MG A 402 " model vdw 2.077 2.170 nonbonded pdb=" O3B ADP D 401 " pdb="MG MG D 402 " model vdw 2.196 2.170 nonbonded pdb=" OH TYR G 198 " pdb=" OE1 GLU G 200 " model vdw 2.287 3.040 nonbonded pdb=" O GLN D 314 " pdb=" OG1 THR D 318 " model vdw 2.292 3.040 ... (remaining 180339 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 6 through 402) selection = (chain 'B' and resid 6 through 402) selection = (chain 'C' and resid 6 through 402) selection = (chain 'D' and resid 6 through 402) selection = (chain 'E' and resid 6 through 402) selection = chain 'F' } 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: 5.920 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.120 Find NCS groups from input model: 0.280 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:8.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 22476 Z= 0.184 Angle : 0.686 9.700 30478 Z= 0.364 Chirality : 0.049 0.171 3367 Planarity : 0.006 0.077 3918 Dihedral : 14.383 116.021 8391 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.93 % Allowed : 9.29 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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 aren not related in a simple way. whole: -0.96 (0.15), residues: 2744 helix: -1.31 (0.14), residues: 1094 sheet: 0.91 (0.21), residues: 589 loop : -0.58 (0.19), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 183 TYR 0.013 0.001 TYR H 59 PHE 0.018 0.002 PHE E 31 TRP 0.020 0.002 TRP G 173 HIS 0.005 0.001 HIS G 209 Details of bonding type rmsd covalent geometry : bond 0.00395 (22476) covalent geometry : angle 0.68576 (30478) hydrogen bonds : bond 0.15990 ( 1094) hydrogen bonds : angle 6.84110 ( 2985) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 704 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8727 (pt) cc_final: 0.8407 (mt) REVERT: A 44 MET cc_start: 0.7786 (mmm) cc_final: 0.7515 (mmm) REVERT: A 99 GLU cc_start: 0.7793 (pm20) cc_final: 0.7563 (mp0) REVERT: A 107 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7695 (tt0) REVERT: A 263 GLN cc_start: 0.8595 (mt0) cc_final: 0.8355 (mt0) REVERT: A 359 LYS cc_start: 0.8044 (tmtm) cc_final: 0.7499 (tmtm) REVERT: A 363 ASP cc_start: 0.7261 (m-30) cc_final: 0.6890 (m-30) REVERT: A 372 ARG cc_start: 0.7272 (mtm-85) cc_final: 0.7021 (mtm-85) REVERT: B 59 GLN cc_start: 0.8658 (tp-100) cc_final: 0.8443 (mm110) REVERT: B 99 GLU cc_start: 0.7887 (mp0) cc_final: 0.7429 (mp0) REVERT: B 299 MET cc_start: 0.8847 (mtm) cc_final: 0.8539 (mtm) REVERT: B 361 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7477 (mt-10) REVERT: C 91 TYR cc_start: 0.8851 (m-80) cc_final: 0.8529 (m-80) REVERT: C 128 ASN cc_start: 0.8202 (p0) cc_final: 0.7929 (p0) REVERT: C 143 TYR cc_start: 0.8691 (m-80) cc_final: 0.8450 (m-80) REVERT: C 222 ASP cc_start: 0.8195 (t0) cc_final: 0.7948 (t0) REVERT: C 263 GLN cc_start: 0.8812 (mt0) cc_final: 0.8585 (mt0) REVERT: C 286 ASP cc_start: 0.7808 (m-30) cc_final: 0.7603 (m-30) REVERT: C 297 ASN cc_start: 0.8565 (m110) cc_final: 0.8306 (m-40) REVERT: C 373 LYS cc_start: 0.8628 (mmmt) cc_final: 0.8143 (mmmm) REVERT: D 53 TYR cc_start: 0.8844 (m-80) cc_final: 0.8536 (m-80) REVERT: D 211 ASP cc_start: 0.8167 (t0) cc_final: 0.7965 (m-30) REVERT: D 242 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7984 (mp) REVERT: D 276 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7811 (mt-10) REVERT: D 334 GLU cc_start: 0.7617 (pm20) cc_final: 0.7406 (pm20) REVERT: D 359 LYS cc_start: 0.8262 (tptp) cc_final: 0.8048 (tmtm) REVERT: D 364 GLU cc_start: 0.7507 (tm-30) cc_final: 0.7112 (tm-30) REVERT: E 113 LYS cc_start: 0.8199 (mmmm) cc_final: 0.7986 (mtmm) REVERT: E 176 MET cc_start: 0.8578 (mtp) cc_final: 0.8334 (mtp) REVERT: E 224 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7713 (mm-30) REVERT: E 236 LEU cc_start: 0.8525 (mt) cc_final: 0.8271 (mp) REVERT: E 286 ASP cc_start: 0.7702 (t0) cc_final: 0.7414 (t0) REVERT: E 363 ASP cc_start: 0.7778 (m-30) cc_final: 0.7525 (m-30) REVERT: F 25 ASP cc_start: 0.7572 (p0) cc_final: 0.7306 (p0) REVERT: F 44 MET cc_start: 0.8279 (mmm) cc_final: 0.7944 (mtt) REVERT: F 84 LYS cc_start: 0.8699 (ttmm) cc_final: 0.8485 (ttmt) REVERT: F 229 THR cc_start: 0.8751 (p) cc_final: 0.8511 (t) REVERT: F 244 ASP cc_start: 0.8296 (p0) cc_final: 0.8085 (p0) REVERT: F 270 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7393 (mm-30) REVERT: F 325 MET cc_start: 0.8594 (tpp) cc_final: 0.8291 (tpp) REVERT: F 354 GLN cc_start: 0.7746 (pt0) cc_final: 0.7524 (pt0) REVERT: G 31 GLU cc_start: 0.5928 (OUTLIER) cc_final: 0.5597 (mm-30) REVERT: G 34 ASN cc_start: 0.6855 (t0) cc_final: 0.6469 (t0) REVERT: G 36 VAL cc_start: 0.8332 (m) cc_final: 0.8032 (p) REVERT: G 38 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8186 (tt) REVERT: G 58 ASN cc_start: 0.8171 (m-40) cc_final: 0.7943 (m110) REVERT: G 60 ASP cc_start: 0.7072 (m-30) cc_final: 0.6814 (m-30) REVERT: G 72 ASP cc_start: 0.7216 (t0) cc_final: 0.7009 (t0) REVERT: G 99 ASP cc_start: 0.7035 (t0) cc_final: 0.6540 (t0) REVERT: G 121 ARG cc_start: 0.6912 (OUTLIER) cc_final: 0.6683 (ttt-90) REVERT: G 134 ASP cc_start: 0.7538 (t70) cc_final: 0.7187 (t0) REVERT: G 189 VAL cc_start: 0.7347 (OUTLIER) cc_final: 0.7070 (t) REVERT: G 200 GLU cc_start: 0.7785 (tt0) cc_final: 0.7355 (tt0) REVERT: G 206 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8347 (tp) REVERT: G 233 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6849 (mt-10) REVERT: G 266 ARG cc_start: 0.8407 (mpt-90) cc_final: 0.8069 (mmt-90) REVERT: G 270 ASP cc_start: 0.8367 (t0) cc_final: 0.7909 (t70) REVERT: G 281 LYS cc_start: 0.7938 (mtpp) cc_final: 0.7711 (mtpp) REVERT: H 11 ASP cc_start: 0.7598 (t0) cc_final: 0.7074 (t0) REVERT: H 23 LYS cc_start: 0.8253 (tmmt) cc_final: 0.7804 (tmmt) REVERT: H 168 LYS cc_start: 0.8265 (tttm) cc_final: 0.8023 (tttp) REVERT: H 222 ASN cc_start: 0.8786 (m-40) cc_final: 0.8274 (m110) REVERT: H 270 GLN cc_start: 0.7597 (mt0) cc_final: 0.7396 (mt0) outliers start: 93 outliers final: 30 residues processed: 767 average time/residue: 0.5853 time to fit residues: 504.3631 Evaluate side-chains 685 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 648 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 121 ARG Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 252 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.0970 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 162 ASN A 225 ASN A 280 ASN B 162 ASN C 121 GLN C 137 GLN C 246 GLN C 353 GLN D 12 ASN D 115 ASN D 162 ASN E 297 ASN E 353 GLN F 12 ASN F 246 GLN G 162 GLN G 164 GLN G 203 ASN G 205 GLN G 240 GLN H 20 GLN H 229 ASN H 241 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.115248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.097598 restraints weight = 31040.261| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.69 r_work: 0.3064 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22476 Z= 0.152 Angle : 0.598 8.295 30478 Z= 0.297 Chirality : 0.045 0.176 3367 Planarity : 0.005 0.058 3918 Dihedral : 8.456 105.808 3163 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.71 % Allowed : 16.72 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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 aren not related in a simple way. whole: -0.08 (0.16), residues: 2744 helix: -0.09 (0.15), residues: 1124 sheet: 0.90 (0.21), residues: 566 loop : -0.37 (0.19), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 210 TYR 0.015 0.001 TYR E 143 PHE 0.013 0.001 PHE G 168 TRP 0.019 0.002 TRP H 148 HIS 0.007 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00352 (22476) covalent geometry : angle 0.59839 (30478) hydrogen bonds : bond 0.03929 ( 1094) hydrogen bonds : angle 4.99181 ( 2985) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 683 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8764 (pt) cc_final: 0.8383 (mt) REVERT: A 78 ASN cc_start: 0.8238 (t0) cc_final: 0.8028 (m-40) REVERT: A 99 GLU cc_start: 0.8089 (pm20) cc_final: 0.7731 (mp0) REVERT: A 314 GLN cc_start: 0.8307 (tt0) cc_final: 0.7579 (tt0) REVERT: A 363 ASP cc_start: 0.7492 (m-30) cc_final: 0.7173 (m-30) REVERT: B 99 GLU cc_start: 0.8026 (mp0) cc_final: 0.7704 (mp0) REVERT: B 361 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7604 (mt-10) REVERT: B 372 ARG cc_start: 0.7466 (mtm-85) cc_final: 0.7197 (mtm-85) REVERT: C 68 LYS cc_start: 0.8776 (mmtp) cc_final: 0.8502 (mttm) REVERT: C 128 ASN cc_start: 0.8181 (p0) cc_final: 0.7844 (p0) REVERT: C 143 TYR cc_start: 0.8734 (m-80) cc_final: 0.8533 (m-80) REVERT: C 238 LYS cc_start: 0.8493 (mmtm) cc_final: 0.8288 (mmtm) REVERT: C 246 GLN cc_start: 0.8840 (mt0) cc_final: 0.8617 (mt0) REVERT: C 286 ASP cc_start: 0.7858 (m-30) cc_final: 0.7644 (m-30) REVERT: C 297 ASN cc_start: 0.8547 (m110) cc_final: 0.8135 (m-40) REVERT: C 373 LYS cc_start: 0.8561 (mmmt) cc_final: 0.8338 (mmmt) REVERT: D 334 GLU cc_start: 0.7633 (pm20) cc_final: 0.7391 (pm20) REVERT: D 364 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7478 (tm-30) REVERT: E 50 LYS cc_start: 0.8081 (ptpp) cc_final: 0.7818 (mtpt) REVERT: E 61 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8227 (ptmt) REVERT: E 224 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7820 (mm-30) REVERT: E 286 ASP cc_start: 0.7700 (t0) cc_final: 0.7428 (t0) REVERT: E 363 ASP cc_start: 0.7846 (m-30) cc_final: 0.7602 (m-30) REVERT: F 44 MET cc_start: 0.8403 (mmm) cc_final: 0.8061 (mtt) REVERT: F 206 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7963 (ttt180) REVERT: F 229 THR cc_start: 0.8654 (p) cc_final: 0.8440 (t) REVERT: F 354 GLN cc_start: 0.8244 (pt0) cc_final: 0.8023 (pt0) REVERT: G 34 ASN cc_start: 0.6862 (t0) cc_final: 0.6461 (t0) REVERT: G 36 VAL cc_start: 0.8207 (m) cc_final: 0.7970 (p) REVERT: G 58 ASN cc_start: 0.8143 (m-40) cc_final: 0.7881 (m110) REVERT: G 60 ASP cc_start: 0.7405 (m-30) cc_final: 0.7161 (m-30) REVERT: G 72 ASP cc_start: 0.7627 (t0) cc_final: 0.7382 (t0) REVERT: G 88 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7365 (pt) REVERT: G 99 ASP cc_start: 0.7391 (t0) cc_final: 0.6813 (t0) REVERT: G 121 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6817 (ttp-170) REVERT: G 134 ASP cc_start: 0.7739 (t70) cc_final: 0.7356 (t0) REVERT: G 189 VAL cc_start: 0.7401 (OUTLIER) cc_final: 0.7167 (t) REVERT: G 266 ARG cc_start: 0.8468 (mpt-90) cc_final: 0.8088 (mmt-90) REVERT: G 270 ASP cc_start: 0.8154 (t0) cc_final: 0.7678 (t70) REVERT: G 281 LYS cc_start: 0.7982 (mtpp) cc_final: 0.7778 (mtpp) REVERT: H 15 ARG cc_start: 0.8193 (ptp90) cc_final: 0.7808 (ptp90) REVERT: H 23 LYS cc_start: 0.8351 (ttmt) cc_final: 0.7970 (ttmt) REVERT: H 139 ASP cc_start: 0.7321 (t0) cc_final: 0.6933 (t0) REVERT: H 229 ASN cc_start: 0.8650 (t0) cc_final: 0.8430 (t0) REVERT: H 230 GLU cc_start: 0.8111 (mp0) cc_final: 0.7632 (mp0) REVERT: H 270 GLN cc_start: 0.7221 (mt0) cc_final: 0.6976 (mt0) outliers start: 88 outliers final: 39 residues processed: 718 average time/residue: 0.6098 time to fit residues: 489.5524 Evaluate side-chains 692 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 648 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 206 ARG Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 121 ARG Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 245 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 182 optimal weight: 0.4980 chunk 150 optimal weight: 0.9990 chunk 258 optimal weight: 0.7980 chunk 138 optimal weight: 0.5980 chunk 118 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 206 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 chunk 179 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN A 225 ASN A 280 ASN B 12 ASN B 92 ASN B 162 ASN C 121 GLN C 137 GLN C 263 GLN C 353 GLN D 12 ASN D 92 ASN D 115 ASN D 162 ASN E 297 ASN E 353 GLN F 12 ASN F 92 ASN F 246 GLN G 162 GLN G 164 GLN G 205 GLN G 240 GLN H 20 GLN H 222 ASN H 241 ASN ** H 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.113346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.095967 restraints weight = 31314.414| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.65 r_work: 0.3044 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22476 Z= 0.171 Angle : 0.602 9.210 30478 Z= 0.297 Chirality : 0.046 0.171 3367 Planarity : 0.004 0.055 3918 Dihedral : 7.893 104.099 3133 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.01 % Allowed : 18.19 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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 aren not related in a simple way. whole: 0.23 (0.16), residues: 2744 helix: 0.35 (0.16), residues: 1124 sheet: 0.85 (0.21), residues: 574 loop : -0.30 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 95 TYR 0.020 0.001 TYR E 143 PHE 0.013 0.002 PHE E 31 TRP 0.018 0.002 TRP H 148 HIS 0.007 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00407 (22476) covalent geometry : angle 0.60218 (30478) hydrogen bonds : bond 0.03847 ( 1094) hydrogen bonds : angle 4.79581 ( 2985) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 685 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8716 (pt) cc_final: 0.8329 (mt) REVERT: A 99 GLU cc_start: 0.8109 (pm20) cc_final: 0.7729 (mp0) REVERT: A 167 GLU cc_start: 0.8243 (mm-30) cc_final: 0.8003 (mm-30) REVERT: A 195 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7375 (tp30) REVERT: A 314 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7565 (tt0) REVERT: A 316 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7984 (mm-30) REVERT: A 363 ASP cc_start: 0.7477 (m-30) cc_final: 0.7177 (m-30) REVERT: B 99 GLU cc_start: 0.8001 (mp0) cc_final: 0.7679 (mp0) REVERT: B 153 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8520 (tp) REVERT: B 361 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7615 (mt-10) REVERT: C 68 LYS cc_start: 0.8767 (mmtp) cc_final: 0.8517 (mttm) REVERT: C 91 TYR cc_start: 0.8828 (m-80) cc_final: 0.8364 (m-80) REVERT: C 123 MET cc_start: 0.8721 (tpp) cc_final: 0.8445 (mmp) REVERT: C 128 ASN cc_start: 0.8212 (p0) cc_final: 0.7882 (p0) REVERT: C 184 ASP cc_start: 0.7810 (m-30) cc_final: 0.7606 (m-30) REVERT: C 201 VAL cc_start: 0.8274 (m) cc_final: 0.8053 (t) REVERT: C 246 GLN cc_start: 0.8890 (mt0) cc_final: 0.8653 (mt0) REVERT: C 286 ASP cc_start: 0.7912 (m-30) cc_final: 0.7696 (m-30) REVERT: C 297 ASN cc_start: 0.8524 (m110) cc_final: 0.8147 (m-40) REVERT: C 373 LYS cc_start: 0.8614 (mmmt) cc_final: 0.8400 (mmmt) REVERT: D 334 GLU cc_start: 0.7774 (pm20) cc_final: 0.7573 (pm20) REVERT: D 359 LYS cc_start: 0.8270 (ttpt) cc_final: 0.7922 (tttm) REVERT: D 364 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7492 (tm-30) REVERT: E 50 LYS cc_start: 0.8082 (ptpp) cc_final: 0.7800 (mtmt) REVERT: E 61 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8260 (ptmt) REVERT: E 211 ASP cc_start: 0.8399 (t0) cc_final: 0.8161 (t70) REVERT: E 286 ASP cc_start: 0.7720 (t0) cc_final: 0.7490 (t0) REVERT: E 363 ASP cc_start: 0.7847 (m-30) cc_final: 0.7630 (m-30) REVERT: F 44 MET cc_start: 0.8414 (mmm) cc_final: 0.8022 (mtt) REVERT: F 68 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8290 (mptt) REVERT: F 206 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7984 (ttt180) REVERT: G 34 ASN cc_start: 0.6859 (t0) cc_final: 0.6483 (t0) REVERT: G 36 VAL cc_start: 0.8290 (m) cc_final: 0.8049 (p) REVERT: G 54 PHE cc_start: 0.7590 (m-80) cc_final: 0.7382 (m-80) REVERT: G 58 ASN cc_start: 0.8189 (m-40) cc_final: 0.7845 (m110) REVERT: G 72 ASP cc_start: 0.7559 (t0) cc_final: 0.7320 (t0) REVERT: G 99 ASP cc_start: 0.7491 (t0) cc_final: 0.6939 (t0) REVERT: G 134 ASP cc_start: 0.7806 (t70) cc_final: 0.7422 (t0) REVERT: G 176 GLU cc_start: 0.7100 (tm-30) cc_final: 0.6840 (tm-30) REVERT: G 189 VAL cc_start: 0.7441 (OUTLIER) cc_final: 0.7179 (t) REVERT: G 270 ASP cc_start: 0.8195 (t0) cc_final: 0.7741 (t70) REVERT: H 13 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.8017 (ttp) REVERT: H 15 ARG cc_start: 0.8155 (ptp90) cc_final: 0.7903 (ptp90) REVERT: H 23 LYS cc_start: 0.8239 (ttmt) cc_final: 0.7953 (ttmt) REVERT: H 139 ASP cc_start: 0.7312 (t0) cc_final: 0.6917 (t0) REVERT: H 230 GLU cc_start: 0.8127 (mp0) cc_final: 0.7725 (mp0) REVERT: H 245 SER cc_start: 0.8286 (OUTLIER) cc_final: 0.8020 (p) REVERT: H 269 ARG cc_start: 0.7717 (tpp80) cc_final: 0.7269 (ttp80) REVERT: H 270 GLN cc_start: 0.7239 (mt0) cc_final: 0.6995 (mt0) outliers start: 95 outliers final: 52 residues processed: 721 average time/residue: 0.6130 time to fit residues: 493.7224 Evaluate side-chains 727 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 667 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 206 ARG Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain G residue 278 LYS Chi-restraints excluded: chain H residue 13 MET Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 245 SER Chi-restraints excluded: chain H residue 267 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 256 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 198 optimal weight: 0.9980 chunk 186 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 79 optimal weight: 0.3980 chunk 246 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 221 optimal weight: 2.9990 chunk 207 optimal weight: 0.5980 chunk 224 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN A 280 ASN B 12 ASN B 225 ASN C 121 GLN C 137 GLN C 353 GLN D 12 ASN E 297 ASN E 353 GLN F 92 ASN F 246 GLN G 162 GLN G 164 GLN G 205 GLN G 240 GLN G 272 ASN H 19 GLN H 20 GLN H 222 ASN H 229 ASN H 241 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.113833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.096126 restraints weight = 31276.081| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.69 r_work: 0.3035 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22476 Z= 0.179 Angle : 0.610 8.968 30478 Z= 0.300 Chirality : 0.046 0.168 3367 Planarity : 0.004 0.054 3918 Dihedral : 7.726 101.501 3127 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.52 % Allowed : 17.98 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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 aren not related in a simple way. whole: 0.33 (0.16), residues: 2744 helix: 0.51 (0.16), residues: 1125 sheet: 0.82 (0.21), residues: 574 loop : -0.29 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 95 TYR 0.024 0.001 TYR E 143 PHE 0.019 0.002 PHE G 163 TRP 0.015 0.002 TRP H 148 HIS 0.007 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00427 (22476) covalent geometry : angle 0.60978 (30478) hydrogen bonds : bond 0.03755 ( 1094) hydrogen bonds : angle 4.73062 ( 2985) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 674 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8727 (pt) cc_final: 0.8301 (mt) REVERT: A 99 GLU cc_start: 0.8104 (pm20) cc_final: 0.7714 (mp0) REVERT: A 167 GLU cc_start: 0.8278 (mm-30) cc_final: 0.8037 (mm-30) REVERT: A 195 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7376 (tp30) REVERT: A 314 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7523 (tt0) REVERT: A 316 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7977 (mm-30) REVERT: A 363 ASP cc_start: 0.7492 (m-30) cc_final: 0.7195 (m-30) REVERT: A 372 ARG cc_start: 0.7516 (mtm-85) cc_final: 0.7214 (mtm-85) REVERT: B 99 GLU cc_start: 0.8061 (mp0) cc_final: 0.7807 (mp0) REVERT: B 153 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8512 (tp) REVERT: B 355 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7956 (mtm) REVERT: B 361 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7582 (mt-10) REVERT: C 68 LYS cc_start: 0.8786 (mmtp) cc_final: 0.8546 (mttm) REVERT: C 91 TYR cc_start: 0.8851 (m-80) cc_final: 0.8523 (m-80) REVERT: C 128 ASN cc_start: 0.8234 (p0) cc_final: 0.7947 (p0) REVERT: C 184 ASP cc_start: 0.7833 (m-30) cc_final: 0.7631 (m-30) REVERT: C 201 VAL cc_start: 0.8259 (m) cc_final: 0.8041 (t) REVERT: C 222 ASP cc_start: 0.8202 (t70) cc_final: 0.7834 (t0) REVERT: C 246 GLN cc_start: 0.8896 (mt0) cc_final: 0.8651 (mt0) REVERT: C 286 ASP cc_start: 0.7964 (m-30) cc_final: 0.7740 (m-30) REVERT: C 297 ASN cc_start: 0.8556 (m110) cc_final: 0.8182 (m-40) REVERT: C 373 LYS cc_start: 0.8595 (mmmt) cc_final: 0.8388 (mmmt) REVERT: D 334 GLU cc_start: 0.7806 (pm20) cc_final: 0.7603 (pm20) REVERT: D 359 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7868 (tttm) REVERT: D 364 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7507 (tm-30) REVERT: E 25 ASP cc_start: 0.7819 (p0) cc_final: 0.7583 (p0) REVERT: E 50 LYS cc_start: 0.8107 (ptpp) cc_final: 0.7823 (mtmt) REVERT: E 61 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8282 (ptmt) REVERT: E 286 ASP cc_start: 0.7747 (t0) cc_final: 0.7545 (t0) REVERT: E 363 ASP cc_start: 0.7870 (m-30) cc_final: 0.7644 (m-30) REVERT: F 44 MET cc_start: 0.8415 (mmm) cc_final: 0.8147 (mtt) REVERT: F 68 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8310 (mptt) REVERT: F 325 MET cc_start: 0.8655 (tpp) cc_final: 0.8403 (tpp) REVERT: G 34 ASN cc_start: 0.6976 (t0) cc_final: 0.6605 (t0) REVERT: G 36 VAL cc_start: 0.8310 (m) cc_final: 0.8075 (p) REVERT: G 58 ASN cc_start: 0.8199 (m-40) cc_final: 0.7821 (m110) REVERT: G 72 ASP cc_start: 0.7557 (t0) cc_final: 0.7325 (t0) REVERT: G 99 ASP cc_start: 0.7501 (t0) cc_final: 0.6929 (t0) REVERT: G 134 ASP cc_start: 0.7828 (t70) cc_final: 0.7492 (t0) REVERT: G 162 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7463 (mm-40) REVERT: G 176 GLU cc_start: 0.7110 (tm-30) cc_final: 0.6797 (tm-30) REVERT: G 189 VAL cc_start: 0.7489 (OUTLIER) cc_final: 0.7221 (t) REVERT: G 270 ASP cc_start: 0.8236 (t0) cc_final: 0.7755 (t70) REVERT: H 11 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7422 (t70) REVERT: H 13 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.8021 (ttp) REVERT: H 23 LYS cc_start: 0.8231 (ttmt) cc_final: 0.7962 (ttmt) REVERT: H 47 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8085 (mm) REVERT: H 124 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7882 (pp) REVERT: H 139 ASP cc_start: 0.7356 (t0) cc_final: 0.6930 (t0) REVERT: H 229 ASN cc_start: 0.8642 (t0) cc_final: 0.8411 (t0) REVERT: H 230 GLU cc_start: 0.8135 (mp0) cc_final: 0.7743 (mp0) REVERT: H 245 SER cc_start: 0.8307 (p) cc_final: 0.8047 (p) REVERT: H 261 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7179 (mt-10) REVERT: H 269 ARG cc_start: 0.7769 (tpp80) cc_final: 0.7312 (ttp80) REVERT: H 270 GLN cc_start: 0.7301 (mt0) cc_final: 0.7029 (mt0) outliers start: 107 outliers final: 60 residues processed: 720 average time/residue: 0.6291 time to fit residues: 506.2955 Evaluate side-chains 742 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 670 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 359 LYS Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 162 GLN Chi-restraints excluded: chain G residue 166 LYS Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 13 MET Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 267 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 243 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 198 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 209 optimal weight: 0.7980 chunk 123 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN A 280 ASN B 12 ASN B 225 ASN C 121 GLN C 137 GLN C 353 GLN D 12 ASN E 297 ASN E 353 GLN F 92 ASN F 246 GLN G 162 GLN G 164 GLN G 205 GLN G 240 GLN H 19 GLN H 20 GLN H 222 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.112716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.095418 restraints weight = 31117.742| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.64 r_work: 0.3038 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 22476 Z= 0.195 Angle : 0.621 9.100 30478 Z= 0.307 Chirality : 0.047 0.170 3367 Planarity : 0.005 0.058 3918 Dihedral : 7.731 100.972 3126 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.60 % Allowed : 18.49 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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 aren not related in a simple way. whole: 0.41 (0.16), residues: 2744 helix: 0.56 (0.16), residues: 1123 sheet: 0.84 (0.21), residues: 574 loop : -0.23 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 95 TYR 0.030 0.001 TYR E 143 PHE 0.039 0.002 PHE G 163 TRP 0.015 0.002 TRP G 173 HIS 0.007 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00469 (22476) covalent geometry : angle 0.62089 (30478) hydrogen bonds : bond 0.03849 ( 1094) hydrogen bonds : angle 4.73063 ( 2985) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 674 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8730 (pt) cc_final: 0.8328 (mt) REVERT: A 92 ASN cc_start: 0.8590 (m-40) cc_final: 0.8387 (m110) REVERT: A 167 GLU cc_start: 0.8274 (mm-30) cc_final: 0.8031 (mm-30) REVERT: A 195 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7409 (tp30) REVERT: A 316 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7971 (mm-30) REVERT: A 363 ASP cc_start: 0.7489 (m-30) cc_final: 0.7198 (m-30) REVERT: A 372 ARG cc_start: 0.7487 (mtm-85) cc_final: 0.7201 (mtm-85) REVERT: B 99 GLU cc_start: 0.8064 (mp0) cc_final: 0.7807 (mp0) REVERT: B 153 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8519 (tp) REVERT: B 355 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7942 (mtm) REVERT: B 361 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7576 (mt-10) REVERT: C 68 LYS cc_start: 0.8769 (mmtp) cc_final: 0.8535 (mttm) REVERT: C 91 TYR cc_start: 0.8847 (m-80) cc_final: 0.8512 (m-80) REVERT: C 123 MET cc_start: 0.8734 (tpp) cc_final: 0.8445 (mmp) REVERT: C 128 ASN cc_start: 0.8244 (p0) cc_final: 0.7952 (p0) REVERT: C 201 VAL cc_start: 0.8286 (m) cc_final: 0.8071 (t) REVERT: C 222 ASP cc_start: 0.8201 (t70) cc_final: 0.7853 (t0) REVERT: C 246 GLN cc_start: 0.8897 (mt0) cc_final: 0.8639 (mt0) REVERT: C 269 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8505 (mtm) REVERT: C 286 ASP cc_start: 0.7945 (m-30) cc_final: 0.7708 (m-30) REVERT: C 297 ASN cc_start: 0.8565 (m110) cc_final: 0.8171 (m-40) REVERT: D 83 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: D 334 GLU cc_start: 0.7819 (pm20) cc_final: 0.7600 (pm20) REVERT: D 359 LYS cc_start: 0.8258 (ttpt) cc_final: 0.7959 (tmtm) REVERT: D 364 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7537 (tm-30) REVERT: E 50 LYS cc_start: 0.8120 (ptpp) cc_final: 0.7845 (mtmt) REVERT: E 61 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8279 (ptmt) REVERT: E 363 ASP cc_start: 0.7859 (m-30) cc_final: 0.7633 (m-30) REVERT: F 44 MET cc_start: 0.8422 (mmm) cc_final: 0.8156 (mtt) REVERT: F 68 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8297 (mptt) REVERT: F 205 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7834 (mt-10) REVERT: G 34 ASN cc_start: 0.7013 (t0) cc_final: 0.6641 (t0) REVERT: G 36 VAL cc_start: 0.8319 (m) cc_final: 0.8093 (p) REVERT: G 58 ASN cc_start: 0.8214 (m-40) cc_final: 0.7824 (m110) REVERT: G 72 ASP cc_start: 0.7558 (t0) cc_final: 0.7337 (t0) REVERT: G 99 ASP cc_start: 0.7474 (t0) cc_final: 0.6913 (t0) REVERT: G 134 ASP cc_start: 0.7855 (t70) cc_final: 0.7555 (t0) REVERT: G 176 GLU cc_start: 0.7114 (tm-30) cc_final: 0.6797 (tm-30) REVERT: G 189 VAL cc_start: 0.7518 (OUTLIER) cc_final: 0.7259 (t) REVERT: G 270 ASP cc_start: 0.8229 (t0) cc_final: 0.7806 (t70) REVERT: H 11 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7421 (t70) REVERT: H 13 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.8077 (ttp) REVERT: H 23 LYS cc_start: 0.8246 (ttmt) cc_final: 0.8002 (ttmt) REVERT: H 47 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8082 (mm) REVERT: H 139 ASP cc_start: 0.7342 (t0) cc_final: 0.6934 (t0) REVERT: H 230 GLU cc_start: 0.8115 (mp0) cc_final: 0.7738 (mp0) REVERT: H 245 SER cc_start: 0.8299 (p) cc_final: 0.8064 (p) REVERT: H 261 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7176 (mt-10) REVERT: H 269 ARG cc_start: 0.7758 (tpp80) cc_final: 0.7281 (ttp80) outliers start: 109 outliers final: 67 residues processed: 722 average time/residue: 0.6434 time to fit residues: 518.6795 Evaluate side-chains 742 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 665 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 369 ILE Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 73 GLN Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 13 MET Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 155 GLU Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 267 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 51 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 207 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 256 optimal weight: 1.9990 chunk 211 optimal weight: 0.3980 chunk 151 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 88 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN A 280 ASN B 12 ASN B 225 ASN C 121 GLN C 137 GLN C 353 GLN D 12 ASN E 297 ASN E 353 GLN F 92 ASN F 246 GLN G 162 GLN G 164 GLN G 205 GLN G 240 GLN H 19 GLN H 20 GLN H 222 ASN H 229 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.110225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.092706 restraints weight = 31216.551| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.68 r_work: 0.3044 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22476 Z= 0.153 Angle : 0.604 8.207 30478 Z= 0.296 Chirality : 0.045 0.169 3367 Planarity : 0.004 0.065 3918 Dihedral : 7.585 99.272 3126 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.31 % Allowed : 19.21 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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 aren not related in a simple way. whole: 0.40 (0.16), residues: 2744 helix: 0.54 (0.16), residues: 1158 sheet: 0.86 (0.21), residues: 572 loop : -0.24 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 95 TYR 0.029 0.001 TYR E 143 PHE 0.028 0.001 PHE G 163 TRP 0.013 0.002 TRP G 173 HIS 0.006 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00366 (22476) covalent geometry : angle 0.60414 (30478) hydrogen bonds : bond 0.03527 ( 1094) hydrogen bonds : angle 4.66594 ( 2985) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 668 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8733 (pt) cc_final: 0.8333 (mt) REVERT: A 99 GLU cc_start: 0.8113 (pm20) cc_final: 0.7706 (mp0) REVERT: A 167 GLU cc_start: 0.8295 (mm-30) cc_final: 0.8045 (mm-30) REVERT: A 195 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7398 (tp30) REVERT: A 314 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7499 (tt0) REVERT: A 316 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7960 (mm-30) REVERT: A 363 ASP cc_start: 0.7484 (m-30) cc_final: 0.7198 (m-30) REVERT: A 372 ARG cc_start: 0.7509 (mtm-85) cc_final: 0.7214 (mtm-85) REVERT: B 99 GLU cc_start: 0.8075 (mp0) cc_final: 0.7812 (mp0) REVERT: B 153 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8520 (tp) REVERT: B 355 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7938 (mtm) REVERT: B 361 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7549 (mt-10) REVERT: C 68 LYS cc_start: 0.8787 (mmtp) cc_final: 0.8558 (mttm) REVERT: C 91 TYR cc_start: 0.8844 (m-80) cc_final: 0.8407 (m-80) REVERT: C 123 MET cc_start: 0.8719 (tpp) cc_final: 0.8499 (tpt) REVERT: C 128 ASN cc_start: 0.8243 (p0) cc_final: 0.7977 (p0) REVERT: C 201 VAL cc_start: 0.8271 (m) cc_final: 0.8055 (t) REVERT: C 222 ASP cc_start: 0.8196 (t70) cc_final: 0.7826 (t0) REVERT: C 246 GLN cc_start: 0.8888 (mt0) cc_final: 0.8639 (mt0) REVERT: C 286 ASP cc_start: 0.7974 (m-30) cc_final: 0.7721 (m-30) REVERT: C 297 ASN cc_start: 0.8560 (m110) cc_final: 0.8147 (m-40) REVERT: D 83 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7358 (mp0) REVERT: D 359 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7915 (tmtm) REVERT: D 364 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7529 (tm-30) REVERT: E 50 LYS cc_start: 0.8106 (ptpp) cc_final: 0.7843 (mtmt) REVERT: E 61 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8277 (ptmt) REVERT: E 363 ASP cc_start: 0.7855 (m-30) cc_final: 0.7615 (m-30) REVERT: F 68 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8317 (mptt) REVERT: F 205 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7824 (mt-10) REVERT: G 34 ASN cc_start: 0.6949 (t0) cc_final: 0.6580 (t0) REVERT: G 36 VAL cc_start: 0.8288 (m) cc_final: 0.8078 (p) REVERT: G 58 ASN cc_start: 0.8191 (m-40) cc_final: 0.7772 (m110) REVERT: G 59 MET cc_start: 0.7797 (mtt) cc_final: 0.7341 (mpp) REVERT: G 72 ASP cc_start: 0.7570 (t0) cc_final: 0.7351 (t0) REVERT: G 99 ASP cc_start: 0.7492 (t0) cc_final: 0.6898 (t0) REVERT: G 134 ASP cc_start: 0.7843 (t70) cc_final: 0.7546 (t0) REVERT: G 162 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.7240 (tm-30) REVERT: G 176 GLU cc_start: 0.7115 (tm-30) cc_final: 0.6816 (tm-30) REVERT: G 189 VAL cc_start: 0.7480 (OUTLIER) cc_final: 0.7220 (t) REVERT: G 270 ASP cc_start: 0.8241 (t0) cc_final: 0.7792 (t70) REVERT: H 11 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7049 (t70) REVERT: H 13 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.8086 (ttp) REVERT: H 15 ARG cc_start: 0.8194 (ptp90) cc_final: 0.7182 (ptp90) REVERT: H 23 LYS cc_start: 0.8179 (ttmt) cc_final: 0.7961 (ttmt) REVERT: H 31 LEU cc_start: 0.7417 (mm) cc_final: 0.7128 (mp) REVERT: H 133 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8411 (mp) REVERT: H 139 ASP cc_start: 0.7311 (t0) cc_final: 0.6902 (t0) REVERT: H 230 GLU cc_start: 0.8133 (mp0) cc_final: 0.7745 (mp0) REVERT: H 245 SER cc_start: 0.8314 (OUTLIER) cc_final: 0.8051 (p) REVERT: H 261 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7156 (mt-10) REVERT: H 269 ARG cc_start: 0.7770 (tpp80) cc_final: 0.7406 (ttp80) outliers start: 102 outliers final: 66 residues processed: 713 average time/residue: 0.6738 time to fit residues: 536.1638 Evaluate side-chains 736 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 657 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 359 LYS Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 369 ILE Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 162 GLN Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 13 MET Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 245 SER Chi-restraints excluded: chain H residue 267 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 41 optimal weight: 0.9980 chunk 245 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 228 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 198 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 chunk 268 optimal weight: 0.9980 chunk 256 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 225 ASN A 280 ASN B 12 ASN B 111 ASN B 225 ASN C 121 GLN C 137 GLN C 353 GLN C 371 HIS D 12 ASN D 92 ASN E 115 ASN E 297 ASN E 353 GLN F 92 ASN F 246 GLN G 164 GLN G 205 GLN G 240 GLN H 19 GLN H 20 GLN H 222 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.112235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.094856 restraints weight = 31256.624| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.68 r_work: 0.3028 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 22476 Z= 0.231 Angle : 0.651 9.553 30478 Z= 0.322 Chirality : 0.048 0.214 3367 Planarity : 0.005 0.061 3918 Dihedral : 7.784 102.294 3126 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.60 % Allowed : 19.46 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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 aren not related in a simple way. whole: 0.37 (0.16), residues: 2744 helix: 0.54 (0.16), residues: 1129 sheet: 0.80 (0.21), residues: 572 loop : -0.25 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 95 TYR 0.034 0.002 TYR E 143 PHE 0.028 0.002 PHE G 163 TRP 0.015 0.002 TRP H 148 HIS 0.008 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00558 (22476) covalent geometry : angle 0.65084 (30478) hydrogen bonds : bond 0.04070 ( 1094) hydrogen bonds : angle 4.76738 ( 2985) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 666 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7597 (mp0) REVERT: A 148 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8451 (m) REVERT: A 167 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8050 (mm-30) REVERT: A 195 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7112 (tp30) REVERT: A 305 MET cc_start: 0.8940 (mmt) cc_final: 0.8731 (mmt) REVERT: A 316 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7990 (mm-30) REVERT: A 363 ASP cc_start: 0.7502 (m-30) cc_final: 0.7227 (m-30) REVERT: A 364 GLU cc_start: 0.7499 (tm-30) cc_final: 0.7243 (tm-30) REVERT: A 372 ARG cc_start: 0.7506 (mtm-85) cc_final: 0.7217 (mtm-85) REVERT: B 99 GLU cc_start: 0.8100 (mp0) cc_final: 0.7835 (mp0) REVERT: B 153 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8544 (tp) REVERT: B 355 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7949 (mtm) REVERT: C 68 LYS cc_start: 0.8807 (mmtp) cc_final: 0.8574 (mttm) REVERT: C 91 TYR cc_start: 0.8852 (m-80) cc_final: 0.8428 (m-80) REVERT: C 128 ASN cc_start: 0.8285 (p0) cc_final: 0.8047 (p0) REVERT: C 201 VAL cc_start: 0.8278 (m) cc_final: 0.8076 (t) REVERT: C 222 ASP cc_start: 0.8192 (t70) cc_final: 0.7824 (t0) REVERT: C 225 ASN cc_start: 0.8407 (m-40) cc_final: 0.7977 (m110) REVERT: C 286 ASP cc_start: 0.8021 (m-30) cc_final: 0.7796 (m-30) REVERT: C 297 ASN cc_start: 0.8621 (m110) cc_final: 0.8213 (m-40) REVERT: D 83 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7410 (mp0) REVERT: D 359 LYS cc_start: 0.8222 (ttpt) cc_final: 0.7923 (tmtm) REVERT: D 364 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7540 (tm-30) REVERT: E 50 LYS cc_start: 0.8167 (ptpp) cc_final: 0.7888 (mtmt) REVERT: E 61 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8257 (ptmt) REVERT: E 115 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.8225 (t0) REVERT: E 363 ASP cc_start: 0.7848 (m-30) cc_final: 0.7624 (m-30) REVERT: F 68 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8334 (mptt) REVERT: F 205 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7880 (mt-10) REVERT: G 34 ASN cc_start: 0.7133 (t0) cc_final: 0.6762 (t0) REVERT: G 36 VAL cc_start: 0.8309 (m) cc_final: 0.8107 (p) REVERT: G 58 ASN cc_start: 0.8209 (m-40) cc_final: 0.7765 (m110) REVERT: G 72 ASP cc_start: 0.7597 (t0) cc_final: 0.7373 (t0) REVERT: G 99 ASP cc_start: 0.7477 (t0) cc_final: 0.6863 (t0) REVERT: G 134 ASP cc_start: 0.7847 (t70) cc_final: 0.7583 (t0) REVERT: G 162 GLN cc_start: 0.7721 (mm-40) cc_final: 0.7256 (tm-30) REVERT: G 176 GLU cc_start: 0.7146 (tm-30) cc_final: 0.6760 (tm-30) REVERT: G 189 VAL cc_start: 0.7533 (OUTLIER) cc_final: 0.7274 (t) REVERT: G 270 ASP cc_start: 0.8255 (t0) cc_final: 0.7781 (t70) REVERT: H 11 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7411 (t70) REVERT: H 13 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8138 (ttp) REVERT: H 31 LEU cc_start: 0.7464 (mm) cc_final: 0.7159 (mp) REVERT: H 139 ASP cc_start: 0.7307 (t0) cc_final: 0.6890 (t0) REVERT: H 230 GLU cc_start: 0.8078 (mp0) cc_final: 0.7727 (mp0) REVERT: H 269 ARG cc_start: 0.7858 (tpp80) cc_final: 0.7463 (ttp80) REVERT: H 270 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7256 (mt0) outliers start: 109 outliers final: 68 residues processed: 709 average time/residue: 0.6472 time to fit residues: 511.9685 Evaluate side-chains 749 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 669 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 369 ILE Chi-restraints excluded: chain G residue 73 GLN Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 13 MET Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain H residue 155 GLU Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 245 SER Chi-restraints excluded: chain H residue 267 THR Chi-restraints excluded: chain H residue 270 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 243 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 245 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 218 optimal weight: 0.9980 chunk 82 optimal weight: 0.2980 chunk 197 optimal weight: 2.9990 chunk 274 optimal weight: 3.9990 chunk 46 optimal weight: 0.3980 chunk 28 optimal weight: 0.8980 chunk 258 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 225 ASN A 280 ASN B 225 ASN C 121 GLN C 137 GLN C 246 GLN C 353 GLN D 12 ASN E 297 ASN E 353 GLN F 92 ASN F 246 GLN F 353 GLN G 164 GLN G 195 GLN G 205 GLN G 240 GLN H 19 GLN H 20 GLN H 222 ASN H 229 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.112650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.095504 restraints weight = 31071.611| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.63 r_work: 0.3043 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22476 Z= 0.185 Angle : 0.631 8.831 30478 Z= 0.311 Chirality : 0.047 0.217 3367 Planarity : 0.005 0.064 3918 Dihedral : 7.681 100.440 3126 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.31 % Allowed : 20.18 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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 aren not related in a simple way. whole: 0.42 (0.16), residues: 2744 helix: 0.60 (0.16), residues: 1129 sheet: 0.80 (0.21), residues: 572 loop : -0.23 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 95 TYR 0.030 0.001 TYR E 143 PHE 0.027 0.002 PHE G 163 TRP 0.014 0.002 TRP D 356 HIS 0.007 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00445 (22476) covalent geometry : angle 0.63079 (30478) hydrogen bonds : bond 0.03768 ( 1094) hydrogen bonds : angle 4.71615 ( 2985) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 664 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: A 147 ARG cc_start: 0.8705 (ptp90) cc_final: 0.8165 (ptp90) REVERT: A 148 THR cc_start: 0.8699 (OUTLIER) cc_final: 0.8444 (m) REVERT: A 167 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8040 (mm-30) REVERT: A 195 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7509 (tp30) REVERT: A 215 LYS cc_start: 0.8657 (mttm) cc_final: 0.8242 (mttm) REVERT: A 316 GLU cc_start: 0.8232 (mm-30) cc_final: 0.8003 (mm-30) REVERT: A 363 ASP cc_start: 0.7501 (m-30) cc_final: 0.7221 (m-30) REVERT: A 364 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7237 (tm-30) REVERT: A 372 ARG cc_start: 0.7495 (mtm-85) cc_final: 0.7223 (mtm-85) REVERT: B 153 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8529 (tp) REVERT: B 355 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7925 (mtm) REVERT: C 68 LYS cc_start: 0.8768 (mmtp) cc_final: 0.8538 (mttm) REVERT: C 123 MET cc_start: 0.8680 (tpp) cc_final: 0.8361 (mmp) REVERT: C 128 ASN cc_start: 0.8279 (p0) cc_final: 0.8023 (p0) REVERT: C 201 VAL cc_start: 0.8276 (OUTLIER) cc_final: 0.8062 (t) REVERT: C 222 ASP cc_start: 0.8178 (t70) cc_final: 0.7925 (t0) REVERT: C 225 ASN cc_start: 0.8434 (m-40) cc_final: 0.8100 (m-40) REVERT: C 286 ASP cc_start: 0.7971 (m-30) cc_final: 0.7762 (m-30) REVERT: C 297 ASN cc_start: 0.8555 (m110) cc_final: 0.8159 (m-40) REVERT: D 83 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7421 (mp0) REVERT: D 286 ASP cc_start: 0.8062 (m-30) cc_final: 0.7852 (m-30) REVERT: D 359 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7956 (tmtm) REVERT: D 364 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7539 (tm-30) REVERT: E 50 LYS cc_start: 0.8133 (ptpp) cc_final: 0.7866 (mtmt) REVERT: E 61 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8265 (ptmt) REVERT: E 363 ASP cc_start: 0.7815 (m-30) cc_final: 0.7574 (m-30) REVERT: F 68 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8326 (mptt) REVERT: F 107 GLU cc_start: 0.7374 (tp30) cc_final: 0.7123 (tp30) REVERT: F 116 ARG cc_start: 0.8356 (mtp85) cc_final: 0.8151 (mtm180) REVERT: F 205 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7817 (mt-10) REVERT: G 34 ASN cc_start: 0.7124 (t0) cc_final: 0.6770 (t0) REVERT: G 58 ASN cc_start: 0.8214 (m-40) cc_final: 0.7750 (m110) REVERT: G 59 MET cc_start: 0.7748 (mtt) cc_final: 0.7492 (mpp) REVERT: G 72 ASP cc_start: 0.7525 (t0) cc_final: 0.7305 (t0) REVERT: G 99 ASP cc_start: 0.7448 (t0) cc_final: 0.6868 (t0) REVERT: G 134 ASP cc_start: 0.7829 (t70) cc_final: 0.7586 (t0) REVERT: G 162 GLN cc_start: 0.7649 (mm-40) cc_final: 0.7324 (tm-30) REVERT: G 176 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6788 (tm-30) REVERT: G 189 VAL cc_start: 0.7505 (OUTLIER) cc_final: 0.7255 (t) REVERT: G 236 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7167 (mt-10) REVERT: G 270 ASP cc_start: 0.8232 (t0) cc_final: 0.7797 (t70) REVERT: H 11 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7023 (t70) REVERT: H 13 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8140 (ttp) REVERT: H 15 ARG cc_start: 0.8240 (ptp90) cc_final: 0.7218 (ptp90) REVERT: H 31 LEU cc_start: 0.7413 (mm) cc_final: 0.7093 (mp) REVERT: H 139 ASP cc_start: 0.7291 (t0) cc_final: 0.6909 (t0) REVERT: H 230 GLU cc_start: 0.8077 (mp0) cc_final: 0.7732 (mp0) REVERT: H 269 ARG cc_start: 0.7815 (tpp80) cc_final: 0.7420 (ttp80) outliers start: 102 outliers final: 63 residues processed: 708 average time/residue: 0.6107 time to fit residues: 482.7136 Evaluate side-chains 736 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 661 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 359 LYS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain G residue 73 GLN Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain G residue 278 LYS Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 13 MET Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 245 SER Chi-restraints excluded: chain H residue 267 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 213 optimal weight: 0.2980 chunk 182 optimal weight: 0.9990 chunk 264 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 204 optimal weight: 0.8980 chunk 190 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 238 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 280 ASN B 225 ASN C 121 GLN C 137 GLN C 246 GLN C 353 GLN D 12 ASN E 297 ASN E 353 GLN F 92 ASN F 246 GLN G 162 GLN G 164 GLN G 195 GLN G 205 GLN G 240 GLN H 19 GLN H 222 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.112707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.095540 restraints weight = 31154.545| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.63 r_work: 0.3044 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22476 Z= 0.179 Angle : 0.639 8.610 30478 Z= 0.315 Chirality : 0.047 0.202 3367 Planarity : 0.005 0.066 3918 Dihedral : 7.638 99.537 3126 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.63 % Allowed : 21.32 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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 aren not related in a simple way. whole: 0.44 (0.16), residues: 2744 helix: 0.63 (0.16), residues: 1129 sheet: 0.81 (0.21), residues: 572 loop : -0.22 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 95 TYR 0.031 0.001 TYR E 143 PHE 0.024 0.002 PHE G 163 TRP 0.013 0.002 TRP D 356 HIS 0.007 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00430 (22476) covalent geometry : angle 0.63862 (30478) hydrogen bonds : bond 0.03720 ( 1094) hydrogen bonds : angle 4.69754 ( 2985) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 659 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: A 147 ARG cc_start: 0.8697 (ptp90) cc_final: 0.8157 (ptp90) REVERT: A 148 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8447 (m) REVERT: A 167 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8038 (mm-30) REVERT: A 195 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7585 (tp30) REVERT: A 215 LYS cc_start: 0.8647 (mttm) cc_final: 0.8228 (mttm) REVERT: A 316 GLU cc_start: 0.8235 (mm-30) cc_final: 0.8007 (mm-30) REVERT: A 363 ASP cc_start: 0.7520 (m-30) cc_final: 0.7257 (m-30) REVERT: A 364 GLU cc_start: 0.7499 (tm-30) cc_final: 0.7240 (tm-30) REVERT: A 372 ARG cc_start: 0.7510 (mtm-85) cc_final: 0.7259 (mtm-85) REVERT: B 99 GLU cc_start: 0.8058 (mp0) cc_final: 0.7778 (mp0) REVERT: B 153 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8523 (tp) REVERT: B 355 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7909 (mtm) REVERT: B 362 TYR cc_start: 0.8379 (t80) cc_final: 0.8164 (t80) REVERT: C 68 LYS cc_start: 0.8765 (mmtp) cc_final: 0.8535 (mttm) REVERT: C 123 MET cc_start: 0.8691 (tpp) cc_final: 0.8334 (mmp) REVERT: C 128 ASN cc_start: 0.8275 (p0) cc_final: 0.8011 (p0) REVERT: C 201 VAL cc_start: 0.8287 (OUTLIER) cc_final: 0.8074 (t) REVERT: C 222 ASP cc_start: 0.8184 (t70) cc_final: 0.7923 (t0) REVERT: C 225 ASN cc_start: 0.8371 (m-40) cc_final: 0.8038 (m-40) REVERT: C 286 ASP cc_start: 0.7989 (m-30) cc_final: 0.7766 (m-30) REVERT: C 297 ASN cc_start: 0.8558 (m110) cc_final: 0.8164 (m-40) REVERT: D 83 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7411 (mp0) REVERT: D 359 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7963 (tmtm) REVERT: D 364 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7548 (tm-30) REVERT: E 50 LYS cc_start: 0.8074 (ptpp) cc_final: 0.7803 (mtmt) REVERT: E 61 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8252 (ptmt) REVERT: E 363 ASP cc_start: 0.7804 (m-30) cc_final: 0.7568 (m-30) REVERT: F 68 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8331 (mptt) REVERT: F 107 GLU cc_start: 0.7371 (tp30) cc_final: 0.7087 (tp30) REVERT: F 116 ARG cc_start: 0.8363 (mtp85) cc_final: 0.8159 (mtm180) REVERT: F 119 MET cc_start: 0.8084 (mtm) cc_final: 0.7874 (mtp) REVERT: F 205 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7811 (mt-10) REVERT: G 34 ASN cc_start: 0.7139 (t0) cc_final: 0.6790 (t0) REVERT: G 38 LEU cc_start: 0.8532 (tt) cc_final: 0.8239 (tt) REVERT: G 58 ASN cc_start: 0.8215 (m-40) cc_final: 0.7728 (m110) REVERT: G 59 MET cc_start: 0.7745 (mtt) cc_final: 0.7526 (mpp) REVERT: G 72 ASP cc_start: 0.7538 (t0) cc_final: 0.7321 (t0) REVERT: G 99 ASP cc_start: 0.7443 (t0) cc_final: 0.6853 (t0) REVERT: G 134 ASP cc_start: 0.7841 (t70) cc_final: 0.7583 (t0) REVERT: G 162 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.7282 (tm-30) REVERT: G 172 ARG cc_start: 0.8108 (tpp-160) cc_final: 0.7839 (tpp80) REVERT: G 176 GLU cc_start: 0.7138 (tm-30) cc_final: 0.6799 (tm-30) REVERT: G 189 VAL cc_start: 0.7518 (OUTLIER) cc_final: 0.7257 (t) REVERT: G 236 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7171 (mt-10) REVERT: G 270 ASP cc_start: 0.8227 (t0) cc_final: 0.7774 (t70) REVERT: H 11 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7223 (t70) REVERT: H 13 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.8144 (ttp) REVERT: H 15 ARG cc_start: 0.8230 (ptp90) cc_final: 0.7414 (ptp90) REVERT: H 31 LEU cc_start: 0.7388 (mm) cc_final: 0.7052 (mp) REVERT: H 139 ASP cc_start: 0.7288 (t0) cc_final: 0.6862 (t0) REVERT: H 230 GLU cc_start: 0.8080 (mp0) cc_final: 0.7711 (mp0) REVERT: H 237 LYS cc_start: 0.8531 (tttm) cc_final: 0.8309 (tttp) REVERT: H 261 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7182 (mt-10) REVERT: H 269 ARG cc_start: 0.7812 (tpp80) cc_final: 0.7417 (ttp80) outliers start: 86 outliers final: 63 residues processed: 703 average time/residue: 0.6105 time to fit residues: 479.3952 Evaluate side-chains 736 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 660 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 359 LYS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain G residue 73 GLN Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 162 GLN Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain G residue 278 LYS Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 13 MET Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 245 SER Chi-restraints excluded: chain H residue 267 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 249 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 202 optimal weight: 2.9990 chunk 165 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 232 optimal weight: 0.0010 chunk 37 optimal weight: 3.9990 chunk 88 optimal weight: 0.2980 chunk 21 optimal weight: 0.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 280 ASN B 225 ASN C 121 GLN C 137 GLN C 246 GLN C 353 GLN D 12 ASN E 297 ASN E 353 GLN F 246 GLN G 195 GLN G 205 GLN G 240 GLN H 19 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.110268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.092912 restraints weight = 31286.568| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.67 r_work: 0.3046 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22476 Z= 0.154 Angle : 0.635 8.811 30478 Z= 0.312 Chirality : 0.046 0.205 3367 Planarity : 0.005 0.097 3918 Dihedral : 7.500 98.440 3124 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.55 % Allowed : 21.65 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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 aren not related in a simple way. whole: 0.38 (0.16), residues: 2744 helix: 0.55 (0.16), residues: 1164 sheet: 0.81 (0.21), residues: 572 loop : -0.26 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 95 TYR 0.030 0.001 TYR E 143 PHE 0.020 0.001 PHE G 163 TRP 0.014 0.002 TRP D 356 HIS 0.006 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00369 (22476) covalent geometry : angle 0.63516 (30478) hydrogen bonds : bond 0.03528 ( 1094) hydrogen bonds : angle 4.65966 ( 2985) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 661 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: A 147 ARG cc_start: 0.8691 (ptp90) cc_final: 0.8151 (ptp90) REVERT: A 148 THR cc_start: 0.8676 (OUTLIER) cc_final: 0.8416 (m) REVERT: A 167 GLU cc_start: 0.8284 (mm-30) cc_final: 0.8050 (mm-30) REVERT: A 195 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7530 (tp30) REVERT: A 215 LYS cc_start: 0.8626 (mttm) cc_final: 0.8271 (mttm) REVERT: A 316 GLU cc_start: 0.8238 (mm-30) cc_final: 0.8009 (mm-30) REVERT: A 363 ASP cc_start: 0.7528 (m-30) cc_final: 0.7250 (m-30) REVERT: A 364 GLU cc_start: 0.7496 (tm-30) cc_final: 0.7232 (tm-30) REVERT: A 372 ARG cc_start: 0.7516 (mtm-85) cc_final: 0.7251 (mtm-85) REVERT: B 99 GLU cc_start: 0.8065 (mp0) cc_final: 0.7790 (mp0) REVERT: B 153 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8506 (tp) REVERT: B 355 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7923 (mtm) REVERT: C 68 LYS cc_start: 0.8773 (mmtp) cc_final: 0.8542 (mttm) REVERT: C 123 MET cc_start: 0.8684 (tpp) cc_final: 0.8320 (mmp) REVERT: C 128 ASN cc_start: 0.8270 (p0) cc_final: 0.8002 (p0) REVERT: C 201 VAL cc_start: 0.8281 (OUTLIER) cc_final: 0.8061 (t) REVERT: C 222 ASP cc_start: 0.8212 (t70) cc_final: 0.7876 (t0) REVERT: C 286 ASP cc_start: 0.7994 (m-30) cc_final: 0.7770 (m-30) REVERT: C 297 ASN cc_start: 0.8560 (m110) cc_final: 0.8158 (m-40) REVERT: D 286 ASP cc_start: 0.8085 (m-30) cc_final: 0.7868 (m-30) REVERT: D 359 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7925 (tmtm) REVERT: D 364 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7542 (tm-30) REVERT: E 50 LYS cc_start: 0.8081 (ptpp) cc_final: 0.7809 (mtmt) REVERT: E 61 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8261 (ptmt) REVERT: E 363 ASP cc_start: 0.7819 (m-30) cc_final: 0.7557 (m-30) REVERT: F 68 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8330 (mptt) REVERT: F 107 GLU cc_start: 0.7378 (tp30) cc_final: 0.7082 (tp30) REVERT: F 119 MET cc_start: 0.8103 (mtm) cc_final: 0.7886 (mtp) REVERT: F 205 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7816 (mt-10) REVERT: G 34 ASN cc_start: 0.7155 (t0) cc_final: 0.6781 (t0) REVERT: G 38 LEU cc_start: 0.8491 (tt) cc_final: 0.8196 (tt) REVERT: G 59 MET cc_start: 0.7774 (mtt) cc_final: 0.7538 (mpp) REVERT: G 72 ASP cc_start: 0.7525 (t0) cc_final: 0.7304 (t0) REVERT: G 99 ASP cc_start: 0.7452 (t0) cc_final: 0.6853 (t0) REVERT: G 134 ASP cc_start: 0.7840 (t70) cc_final: 0.7570 (t0) REVERT: G 172 ARG cc_start: 0.8079 (tpp-160) cc_final: 0.7834 (tpp80) REVERT: G 176 GLU cc_start: 0.7150 (tm-30) cc_final: 0.6834 (tm-30) REVERT: G 189 VAL cc_start: 0.7484 (OUTLIER) cc_final: 0.7229 (t) REVERT: G 236 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7164 (mt-10) REVERT: G 270 ASP cc_start: 0.8250 (t0) cc_final: 0.7748 (t70) REVERT: H 11 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7170 (t70) REVERT: H 13 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.8169 (ttp) REVERT: H 15 ARG cc_start: 0.8186 (ptp90) cc_final: 0.7374 (ptp90) REVERT: H 139 ASP cc_start: 0.7257 (t0) cc_final: 0.6813 (t0) REVERT: H 230 GLU cc_start: 0.8089 (mp0) cc_final: 0.7688 (mp0) REVERT: H 237 LYS cc_start: 0.8497 (tttm) cc_final: 0.8274 (tttp) REVERT: H 261 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7167 (mt-10) REVERT: H 269 ARG cc_start: 0.7820 (tpp80) cc_final: 0.7415 (ttp80) outliers start: 84 outliers final: 60 residues processed: 703 average time/residue: 0.6282 time to fit residues: 492.7516 Evaluate side-chains 728 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 657 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 359 LYS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain G residue 278 LYS Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 13 MET Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 245 SER Chi-restraints excluded: chain H residue 267 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 187 optimal weight: 0.0870 chunk 135 optimal weight: 0.9990 chunk 203 optimal weight: 0.1980 chunk 58 optimal weight: 0.0980 chunk 40 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 232 optimal weight: 0.3980 chunk 170 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 124 optimal weight: 0.5980 overall best weight: 0.2758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN B 225 ASN C 121 GLN C 137 GLN C 246 GLN C 353 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 ASN E 353 GLN F 92 ASN F 246 GLN G 58 ASN G 195 GLN G 205 GLN G 240 GLN H 19 GLN H 222 ASN H 229 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.114436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.097279 restraints weight = 31124.611| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.63 r_work: 0.3079 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22476 Z= 0.113 Angle : 0.617 12.540 30478 Z= 0.299 Chirality : 0.045 0.248 3367 Planarity : 0.005 0.108 3918 Dihedral : 7.137 93.390 3124 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.66 % Allowed : 22.84 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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 aren not related in a simple way. whole: 0.59 (0.16), residues: 2744 helix: 0.76 (0.16), residues: 1153 sheet: 0.84 (0.21), residues: 575 loop : -0.16 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 95 TYR 0.036 0.001 TYR E 166 PHE 0.022 0.001 PHE G 163 TRP 0.014 0.002 TRP D 356 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00263 (22476) covalent geometry : angle 0.61697 (30478) hydrogen bonds : bond 0.03059 ( 1094) hydrogen bonds : angle 4.52342 ( 2985) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9285.33 seconds wall clock time: 158 minutes 5.24 seconds (9485.24 seconds total)