Starting phenix.real_space_refine on Thu Jun 19 04:03:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f8q_28933/06_2025/8f8q_28933.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f8q_28933/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8f8q_28933/06_2025/8f8q_28933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f8q_28933/06_2025/8f8q_28933.map" model { file = "/net/cci-nas-00/data/ceres_data/8f8q_28933/06_2025/8f8q_28933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f8q_28933/06_2025/8f8q_28933.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.67, per 1000 atoms: 0.62 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: 5.56 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 3.34 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: 8.35 Time building geometry restraints manager: 6.19 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 375 or resid 401 through 402)) selection = (chain 'B' and (resid 6 through 375 or resid 401 through 402)) selection = (chain 'C' and (resid 6 through 375 or resid 401 through 402)) selection = (chain 'D' and (resid 6 through 375 or resid 401 through 402)) selection = (chain 'E' and (resid 6 through 375 or resid 401 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: 6.200 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: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 51.220 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.850 ------------------------------------------------------------------------------- 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 : 3.55 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.020 0.002 TRP G 173 HIS 0.005 0.001 HIS G 209 PHE 0.018 0.002 PHE E 31 TYR 0.013 0.001 TYR H 59 ARG 0.004 0.001 ARG A 183 Details of bonding type rmsd hydrogen bonds : bond 0.15990 ( 1094) hydrogen bonds : angle 6.84110 ( 2985) covalent geometry : bond 0.00395 (22476) covalent geometry : angle 0.68576 (30478) *********************** 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 : 2.439 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: 0.7305 (p0) REVERT: F 44 MET cc_start: 0.8279 (mmm) cc_final: 0.7945 (mtt) REVERT: F 84 LYS cc_start: 0.8699 (ttmm) cc_final: 0.8486 (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: 0.7523 (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: 0.6813 (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 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: 1.5428 time to fit residues: 1326.6405 Evaluate side-chains 684 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 648 time to evaluate : 2.620 ------------------------------------------------------------------------------- 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 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 233 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 116 optimal weight: 0.0970 chunk 71 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 216 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 250 optimal weight: 3.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- 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 111 ASN B 162 ASN C 121 GLN C 137 GLN C 246 GLN C 353 GLN C 371 HIS 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: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.113649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.096046 restraints weight = 30937.200| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.67 r_work: 0.3032 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 22476 Z= 0.249 Angle : 0.661 9.792 30478 Z= 0.331 Chirality : 0.049 0.192 3367 Planarity : 0.006 0.148 3918 Dihedral : 8.704 111.208 3159 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.88 % Allowed : 16.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.16), residues: 2744 helix: -0.14 (0.15), residues: 1119 sheet: 0.77 (0.21), residues: 572 loop : -0.47 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP H 148 HIS 0.010 0.002 HIS B 161 PHE 0.016 0.002 PHE E 31 TYR 0.016 0.002 TYR H 59 ARG 0.009 0.001 ARG F 28 Details of bonding type rmsd hydrogen bonds : bond 0.04614 ( 1094) hydrogen bonds : angle 5.06936 ( 2985) covalent geometry : bond 0.00594 (22476) covalent geometry : angle 0.66117 (30478) *********************** 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 768 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 676 time to evaluate : 2.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8743 (pt) cc_final: 0.8384 (mt) REVERT: A 99 GLU cc_start: 0.8116 (pm20) cc_final: 0.7722 (mp0) REVERT: A 314 GLN cc_start: 0.8357 (tt0) cc_final: 0.7615 (tt0) REVERT: A 338 SER cc_start: 0.8151 (m) cc_final: 0.7931 (m) REVERT: A 363 ASP cc_start: 0.7509 (m-30) cc_final: 0.7237 (m-30) REVERT: B 99 GLU cc_start: 0.8048 (mp0) cc_final: 0.7749 (mp0) REVERT: B 299 MET cc_start: 0.8819 (mtm) cc_final: 0.8609 (mtm) REVERT: B 361 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7596 (mt-10) REVERT: B 372 ARG cc_start: 0.7498 (mtm-85) cc_final: 0.7238 (mtm-85) REVERT: C 68 LYS cc_start: 0.8750 (mmtp) cc_final: 0.8497 (mttm) REVERT: C 128 ASN cc_start: 0.8256 (p0) cc_final: 0.7978 (p0) REVERT: C 201 VAL cc_start: 0.8324 (m) cc_final: 0.8078 (t) REVERT: C 222 ASP cc_start: 0.8210 (t0) cc_final: 0.7929 (t0) REVERT: C 286 ASP cc_start: 0.7947 (m-30) cc_final: 0.7721 (m-30) REVERT: C 297 ASN cc_start: 0.8592 (m110) cc_final: 0.8165 (m-40) REVERT: C 373 LYS cc_start: 0.8576 (mmmt) cc_final: 0.8354 (mmmt) REVERT: D 334 GLU cc_start: 0.7767 (pm20) cc_final: 0.7539 (pm20) REVERT: D 364 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7499 (tm-30) REVERT: E 50 LYS cc_start: 0.8114 (ptpp) cc_final: 0.7846 (mtpt) REVERT: E 61 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8219 (ptmt) REVERT: E 286 ASP cc_start: 0.7767 (t0) cc_final: 0.7502 (t0) REVERT: E 363 ASP cc_start: 0.7854 (m-30) cc_final: 0.7578 (m-30) REVERT: F 44 MET cc_start: 0.8429 (mmm) cc_final: 0.8068 (mtt) REVERT: F 125 GLU cc_start: 0.7761 (mp0) cc_final: 0.7373 (mp0) REVERT: F 206 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7996 (ttt180) REVERT: F 229 THR cc_start: 0.8648 (p) cc_final: 0.8446 (t) REVERT: F 354 GLN cc_start: 0.8309 (pt0) cc_final: 0.8006 (pt0) REVERT: G 34 ASN cc_start: 0.6998 (t0) cc_final: 0.6606 (t0) REVERT: G 36 VAL cc_start: 0.8247 (m) cc_final: 0.8022 (p) REVERT: G 58 ASN cc_start: 0.8198 (m-40) cc_final: 0.7900 (m110) REVERT: G 60 ASP cc_start: 0.7444 (m-30) cc_final: 0.7214 (m-30) REVERT: G 99 ASP cc_start: 0.7438 (t0) cc_final: 0.6847 (t0) REVERT: G 134 ASP cc_start: 0.7778 (t70) cc_final: 0.7384 (t0) REVERT: G 162 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7504 (mm-40) REVERT: G 176 GLU cc_start: 0.7150 (tm-30) cc_final: 0.6832 (tm-30) REVERT: G 189 VAL cc_start: 0.7477 (OUTLIER) cc_final: 0.7213 (t) REVERT: G 268 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.7983 (mmmm) REVERT: G 270 ASP cc_start: 0.8197 (t0) cc_final: 0.7703 (t70) REVERT: G 281 LYS cc_start: 0.8067 (mtpp) cc_final: 0.7852 (mtpp) REVERT: H 15 ARG cc_start: 0.8257 (ptp90) cc_final: 0.7879 (ptp90) REVERT: H 23 LYS cc_start: 0.8309 (ttmt) cc_final: 0.7947 (ttmt) REVERT: H 139 ASP cc_start: 0.7343 (t0) cc_final: 0.6940 (t0) REVERT: H 168 LYS cc_start: 0.8460 (tttm) cc_final: 0.8205 (tttp) REVERT: H 222 ASN cc_start: 0.8688 (m-40) cc_final: 0.8471 (m110) REVERT: H 229 ASN cc_start: 0.8694 (t0) cc_final: 0.8477 (t0) REVERT: H 230 GLU cc_start: 0.8098 (mp0) cc_final: 0.7706 (mp0) outliers start: 92 outliers final: 52 residues processed: 717 average time/residue: 1.5333 time to fit residues: 1229.3855 Evaluate side-chains 704 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 647 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 137 GLN 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 C residue 368 SER 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 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 8 LEU 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 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 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 G residue 268 LYS Chi-restraints excluded: chain G residue 283 MET Chi-restraints excluded: chain H residue 47 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 245 SER Chi-restraints excluded: chain H residue 267 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 82 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 187 optimal weight: 0.7980 chunk 120 optimal weight: 0.2980 chunk 190 optimal weight: 0.1980 chunk 118 optimal weight: 0.9990 chunk 19 optimal weight: 0.0980 chunk 174 optimal weight: 0.0870 chunk 186 optimal weight: 0.9980 chunk 189 optimal weight: 0.0010 chunk 149 optimal weight: 0.5980 overall best weight: 0.1364 ------------------------------------------------------------------------------- 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 92 ASN B 111 ASN C 115 ASN C 121 GLN C 137 GLN C 246 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 205 GLN G 240 GLN H 20 GLN H 241 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.112594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.094939 restraints weight = 30981.363| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.69 r_work: 0.3082 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22476 Z= 0.096 Angle : 0.555 7.740 30478 Z= 0.270 Chirality : 0.043 0.168 3367 Planarity : 0.004 0.095 3918 Dihedral : 7.541 99.703 3130 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.55 % Allowed : 18.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.16), residues: 2744 helix: 0.48 (0.16), residues: 1119 sheet: 0.85 (0.21), residues: 571 loop : -0.18 (0.19), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 173 HIS 0.005 0.001 HIS G 161 PHE 0.013 0.001 PHE G 29 TYR 0.018 0.001 TYR E 143 ARG 0.006 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03038 ( 1094) hydrogen bonds : angle 4.65193 ( 2985) covalent geometry : bond 0.00208 (22476) covalent geometry : angle 0.55462 (30478) *********************** 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 751 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 667 time to evaluate : 2.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8742 (pt) cc_final: 0.8349 (mt) REVERT: A 99 GLU cc_start: 0.8134 (pm20) cc_final: 0.7746 (mp0) REVERT: A 167 GLU cc_start: 0.8281 (mm-30) cc_final: 0.8029 (mm-30) REVERT: A 195 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7320 (tp30) REVERT: A 314 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7434 (tt0) REVERT: A 316 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7961 (mm-30) REVERT: A 338 SER cc_start: 0.8210 (m) cc_final: 0.7981 (m) REVERT: A 363 ASP cc_start: 0.7406 (m-30) cc_final: 0.7091 (m-30) REVERT: B 72 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7640 (mt-10) REVERT: B 99 GLU cc_start: 0.8022 (mp0) cc_final: 0.7754 (mp0) REVERT: B 153 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8463 (tp) REVERT: B 355 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7958 (mtm) REVERT: B 361 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7597 (mt-10) REVERT: C 68 LYS cc_start: 0.8800 (mmtp) cc_final: 0.8537 (mttm) REVERT: C 91 TYR cc_start: 0.8817 (m-80) cc_final: 0.8377 (m-80) REVERT: C 123 MET cc_start: 0.8713 (tpp) cc_final: 0.8412 (mmp) REVERT: C 128 ASN cc_start: 0.8161 (p0) cc_final: 0.7833 (p0) REVERT: C 286 ASP cc_start: 0.7908 (m-30) cc_final: 0.7675 (m-30) REVERT: C 297 ASN cc_start: 0.8504 (m110) cc_final: 0.8115 (m-40) REVERT: C 373 LYS cc_start: 0.8590 (mmmt) cc_final: 0.8380 (mmmt) REVERT: D 276 GLU cc_start: 0.8263 (mt-10) cc_final: 0.8056 (mt-10) REVERT: D 325 MET cc_start: 0.8284 (mmp) cc_final: 0.8046 (mmt) REVERT: D 359 LYS cc_start: 0.8266 (ttpt) cc_final: 0.7905 (tttm) REVERT: D 364 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7488 (tm-30) REVERT: E 25 ASP cc_start: 0.7780 (p0) cc_final: 0.7555 (p0) REVERT: E 50 LYS cc_start: 0.8077 (ptpp) cc_final: 0.7797 (mtmt) REVERT: E 115 ASN cc_start: 0.8244 (t0) cc_final: 0.8022 (t0) REVERT: E 211 ASP cc_start: 0.8439 (t0) cc_final: 0.8206 (t70) REVERT: E 286 ASP cc_start: 0.7615 (t0) cc_final: 0.7394 (t0) REVERT: E 363 ASP cc_start: 0.7847 (m-30) cc_final: 0.7632 (m-30) REVERT: F 206 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7903 (ttt180) REVERT: F 229 THR cc_start: 0.8626 (p) cc_final: 0.8415 (t) REVERT: F 252 ASN cc_start: 0.8555 (p0) cc_final: 0.8293 (p0) REVERT: F 269 MET cc_start: 0.8401 (mtt) cc_final: 0.8114 (ttt) REVERT: G 34 ASN cc_start: 0.6846 (t0) cc_final: 0.6438 (t0) REVERT: G 36 VAL cc_start: 0.8253 (m) cc_final: 0.8012 (p) REVERT: G 58 ASN cc_start: 0.8093 (m-40) cc_final: 0.7765 (m110) REVERT: G 60 ASP cc_start: 0.7355 (m-30) cc_final: 0.7154 (m-30) REVERT: G 99 ASP cc_start: 0.7435 (t0) cc_final: 0.6901 (t0) REVERT: G 134 ASP cc_start: 0.7800 (t70) cc_final: 0.7453 (t0) REVERT: G 189 VAL cc_start: 0.7381 (OUTLIER) cc_final: 0.7142 (t) REVERT: G 266 ARG cc_start: 0.8417 (mpt-90) cc_final: 0.8129 (mmt-90) REVERT: G 270 ASP cc_start: 0.8198 (t0) cc_final: 0.7690 (t70) REVERT: G 281 LYS cc_start: 0.7988 (mtpp) cc_final: 0.7744 (mtpp) REVERT: H 11 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7474 (t70) REVERT: H 47 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8150 (mm) REVERT: H 133 LEU cc_start: 0.8672 (mt) cc_final: 0.8451 (mp) REVERT: H 139 ASP cc_start: 0.7293 (t0) cc_final: 0.6926 (t0) REVERT: H 230 GLU cc_start: 0.8120 (mp0) cc_final: 0.7686 (mp0) REVERT: H 245 SER cc_start: 0.8280 (p) cc_final: 0.8009 (p) REVERT: H 261 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7162 (mt-10) REVERT: H 269 ARG cc_start: 0.7742 (tpp80) cc_final: 0.7274 (ttp80) outliers start: 84 outliers final: 34 residues processed: 702 average time/residue: 1.5757 time to fit residues: 1233.7003 Evaluate side-chains 695 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 654 time to evaluate : 2.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 148 THR 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 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 326 LYS 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 96 VAL Chi-restraints excluded: chain C residue 104 LEU 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 242 LEU 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 351 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 159 VAL 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 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 283 MET Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 216 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 172 optimal weight: 1.9990 chunk 229 optimal weight: 1.9990 chunk 268 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 210 optimal weight: 0.9990 chunk 158 optimal weight: 0.0000 chunk 165 optimal weight: 0.8980 chunk 272 optimal weight: 0.9990 chunk 273 optimal weight: 0.0570 overall best weight: 0.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 225 ASN A 280 ASN B 12 ASN B 225 ASN C 121 GLN C 137 GLN C 162 ASN C 246 GLN C 353 GLN D 12 ASN E 297 ASN E 353 GLN F 92 ASN F 246 GLN G 195 GLN G 240 GLN G 272 ASN H 20 GLN H 180 ASN H 222 ASN H 229 ASN H 241 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.110495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.092938 restraints weight = 31514.652| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.69 r_work: 0.3042 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22476 Z= 0.157 Angle : 0.591 7.574 30478 Z= 0.289 Chirality : 0.045 0.161 3367 Planarity : 0.004 0.098 3918 Dihedral : 7.506 97.211 3126 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.93 % Allowed : 19.12 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.16), residues: 2744 helix: 0.65 (0.16), residues: 1119 sheet: 0.86 (0.21), residues: 574 loop : -0.19 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 148 HIS 0.007 0.001 HIS C 161 PHE 0.012 0.001 PHE E 31 TYR 0.026 0.001 TYR E 143 ARG 0.008 0.001 ARG D 206 Details of bonding type rmsd hydrogen bonds : bond 0.03532 ( 1094) hydrogen bonds : angle 4.62378 ( 2985) covalent geometry : bond 0.00374 (22476) covalent geometry : angle 0.59137 (30478) *********************** 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 767 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 674 time to evaluate : 2.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8743 (pt) cc_final: 0.8351 (mt) REVERT: A 99 GLU cc_start: 0.8105 (pm20) cc_final: 0.7723 (mp0) REVERT: A 167 GLU cc_start: 0.8267 (mm-30) cc_final: 0.8019 (mm-30) REVERT: A 195 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7350 (tp30) REVERT: A 210 ARG cc_start: 0.8138 (ttp80) cc_final: 0.7931 (ttp80) REVERT: A 280 ASN cc_start: 0.8808 (m-40) cc_final: 0.8451 (m-40) REVERT: A 314 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7479 (tt0) REVERT: A 316 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7980 (mm-30) REVERT: A 363 ASP cc_start: 0.7466 (m-30) cc_final: 0.7168 (m-30) REVERT: A 372 ARG cc_start: 0.7520 (mtm-85) cc_final: 0.7231 (mtm-85) REVERT: B 99 GLU cc_start: 0.8061 (mp0) cc_final: 0.7785 (mp0) REVERT: B 153 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8509 (tp) REVERT: B 355 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7968 (mtm) REVERT: B 361 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7595 (mt-10) REVERT: C 68 LYS cc_start: 0.8807 (mmtp) cc_final: 0.8568 (mttm) REVERT: C 128 ASN cc_start: 0.8188 (p0) cc_final: 0.7863 (p0) REVERT: C 201 VAL cc_start: 0.8268 (m) cc_final: 0.8058 (t) REVERT: C 286 ASP cc_start: 0.7930 (m-30) cc_final: 0.7689 (m-30) REVERT: C 297 ASN cc_start: 0.8551 (m110) cc_final: 0.8151 (m-40) REVERT: C 373 LYS cc_start: 0.8603 (mmmt) cc_final: 0.8399 (mmmt) REVERT: D 83 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7173 (mp0) REVERT: D 359 LYS cc_start: 0.8242 (ttpt) cc_final: 0.7912 (tmtm) REVERT: D 364 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7534 (tm-30) REVERT: E 50 LYS cc_start: 0.8114 (ptpp) cc_final: 0.7847 (mtmt) REVERT: E 61 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8270 (ptmt) REVERT: E 286 ASP cc_start: 0.7731 (t0) cc_final: 0.7500 (t0) REVERT: E 363 ASP cc_start: 0.7846 (m-30) cc_final: 0.7602 (m-30) REVERT: F 68 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8289 (mptt) REVERT: F 84 LYS cc_start: 0.8753 (ttmm) cc_final: 0.8506 (ttmm) REVERT: F 119 MET cc_start: 0.8198 (ttm) cc_final: 0.7993 (ttm) REVERT: F 206 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7928 (ttt180) REVERT: F 269 MET cc_start: 0.8413 (mtt) cc_final: 0.8177 (ttt) REVERT: G 34 ASN cc_start: 0.6972 (t0) cc_final: 0.6574 (t0) REVERT: G 36 VAL cc_start: 0.8302 (m) cc_final: 0.8064 (p) REVERT: G 54 PHE cc_start: 0.7557 (m-80) cc_final: 0.7340 (m-80) REVERT: G 58 ASN cc_start: 0.8193 (m-40) cc_final: 0.7841 (m110) REVERT: G 99 ASP cc_start: 0.7483 (t0) cc_final: 0.6926 (t0) REVERT: G 134 ASP cc_start: 0.7831 (t70) cc_final: 0.7508 (t0) REVERT: G 189 VAL cc_start: 0.7472 (OUTLIER) cc_final: 0.7228 (t) REVERT: G 266 ARG cc_start: 0.8512 (mpt-90) cc_final: 0.8193 (mmt-90) REVERT: G 270 ASP cc_start: 0.8214 (t0) cc_final: 0.7740 (t70) REVERT: G 281 LYS cc_start: 0.7951 (mtpp) cc_final: 0.7738 (mtpp) REVERT: H 11 ASP cc_start: 0.7862 (t0) cc_final: 0.7463 (t70) REVERT: H 47 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8083 (mm) REVERT: H 124 LEU cc_start: 0.8017 (pp) cc_final: 0.7808 (pp) REVERT: H 139 ASP cc_start: 0.7335 (t0) cc_final: 0.6913 (t0) REVERT: H 230 GLU cc_start: 0.8130 (mp0) cc_final: 0.7724 (mp0) REVERT: H 245 SER cc_start: 0.8296 (p) cc_final: 0.8029 (p) REVERT: H 269 ARG cc_start: 0.7743 (tpp80) cc_final: 0.7393 (ttp80) REVERT: H 270 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7348 (mt0) outliers start: 93 outliers final: 52 residues processed: 715 average time/residue: 1.7639 time to fit residues: 1415.2181 Evaluate side-chains 718 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 656 time to evaluate : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 122 ILE 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 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 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 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 D residue 83 GLU Chi-restraints excluded: chain D residue 94 LEU 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 47 MET Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 99 GLU 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 206 ARG Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 283 MET 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 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 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 145 LYS 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 270 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 204 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 192 optimal weight: 0.5980 chunk 12 optimal weight: 0.0020 chunk 103 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 213 optimal weight: 0.5980 chunk 79 optimal weight: 0.0570 chunk 271 optimal weight: 1.9990 overall best weight: 0.4508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 115 ASN A 225 ASN B 12 ASN C 121 GLN C 137 GLN C 353 GLN D 12 ASN E 297 ASN F 92 ASN F 246 GLN G 195 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.113308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.096013 restraints weight = 31352.364| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.65 r_work: 0.3060 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22476 Z= 0.133 Angle : 0.584 7.155 30478 Z= 0.286 Chirality : 0.044 0.162 3367 Planarity : 0.004 0.118 3918 Dihedral : 7.392 96.986 3125 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.14 % Allowed : 19.21 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.16), residues: 2744 helix: 0.62 (0.16), residues: 1152 sheet: 0.86 (0.21), residues: 574 loop : -0.17 (0.20), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 148 HIS 0.006 0.001 HIS B 161 PHE 0.024 0.001 PHE G 163 TYR 0.029 0.001 TYR E 143 ARG 0.010 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03324 ( 1094) hydrogen bonds : angle 4.57076 ( 2985) covalent geometry : bond 0.00315 (22476) covalent geometry : angle 0.58433 (30478) *********************** 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 765 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 667 time to evaluate : 2.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8735 (pt) cc_final: 0.8341 (mt) REVERT: A 99 GLU cc_start: 0.8075 (pm20) cc_final: 0.7699 (mp0) REVERT: A 167 GLU cc_start: 0.8266 (mm-30) cc_final: 0.8027 (mm-30) REVERT: A 195 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7356 (tp30) REVERT: A 280 ASN cc_start: 0.8811 (m-40) cc_final: 0.8448 (m-40) REVERT: A 314 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7486 (tt0) REVERT: A 316 GLU cc_start: 0.8226 (mm-30) cc_final: 0.8000 (mm-30) REVERT: A 363 ASP cc_start: 0.7456 (m-30) cc_final: 0.7167 (m-30) REVERT: A 372 ARG cc_start: 0.7502 (mtm-85) cc_final: 0.7226 (mtm-85) REVERT: B 99 GLU cc_start: 0.8036 (mp0) cc_final: 0.7776 (mp0) REVERT: B 153 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8491 (tp) REVERT: B 355 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7960 (mtm) REVERT: B 361 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7625 (mt-10) REVERT: C 68 LYS cc_start: 0.8813 (mmtp) cc_final: 0.8585 (mttm) REVERT: C 128 ASN cc_start: 0.8184 (p0) cc_final: 0.7855 (p0) REVERT: C 201 VAL cc_start: 0.8259 (m) cc_final: 0.8042 (t) REVERT: C 222 ASP cc_start: 0.8178 (t70) cc_final: 0.7836 (t0) REVERT: C 286 ASP cc_start: 0.7908 (m-30) cc_final: 0.7662 (m-30) REVERT: C 297 ASN cc_start: 0.8519 (m110) cc_final: 0.8145 (m-40) REVERT: D 83 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7323 (mp0) REVERT: D 359 LYS cc_start: 0.8256 (ttpt) cc_final: 0.7935 (tmtm) REVERT: D 364 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7535 (tm-30) REVERT: E 50 LYS cc_start: 0.8097 (ptpp) cc_final: 0.7821 (mtmt) REVERT: E 61 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8267 (ptmt) REVERT: E 363 ASP cc_start: 0.7823 (m-30) cc_final: 0.7595 (m-30) REVERT: F 68 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8313 (mptt) REVERT: F 252 ASN cc_start: 0.8601 (p0) cc_final: 0.8316 (p0) REVERT: F 269 MET cc_start: 0.8403 (mtt) cc_final: 0.8185 (ttt) REVERT: F 325 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8376 (tpp) REVERT: G 34 ASN cc_start: 0.6969 (t0) cc_final: 0.6590 (t0) REVERT: G 58 ASN cc_start: 0.8195 (m-40) cc_final: 0.7833 (m110) REVERT: G 99 ASP cc_start: 0.7472 (t0) cc_final: 0.6927 (t0) REVERT: G 134 ASP cc_start: 0.7833 (t70) cc_final: 0.7523 (t0) REVERT: G 189 VAL cc_start: 0.7469 (OUTLIER) cc_final: 0.7223 (t) REVERT: G 266 ARG cc_start: 0.8503 (mpt-90) cc_final: 0.8157 (mmt-90) REVERT: G 270 ASP cc_start: 0.8205 (t0) cc_final: 0.7718 (t70) REVERT: G 281 LYS cc_start: 0.7935 (mtpp) cc_final: 0.7730 (mtpp) REVERT: H 11 ASP cc_start: 0.7797 (t0) cc_final: 0.7420 (t70) REVERT: H 31 LEU cc_start: 0.7330 (mm) cc_final: 0.7008 (mp) REVERT: H 47 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8102 (mm) REVERT: H 124 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7830 (pp) REVERT: H 139 ASP cc_start: 0.7332 (t0) cc_final: 0.6904 (t0) REVERT: H 229 ASN cc_start: 0.8593 (OUTLIER) cc_final: 0.8383 (t0) REVERT: H 230 GLU cc_start: 0.8125 (mp0) cc_final: 0.7727 (mp0) REVERT: H 245 SER cc_start: 0.8286 (p) cc_final: 0.8025 (p) REVERT: H 269 ARG cc_start: 0.7733 (tpp80) cc_final: 0.7392 (ttp80) REVERT: H 270 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.7333 (mt0) outliers start: 98 outliers final: 58 residues processed: 706 average time/residue: 1.5658 time to fit residues: 1232.7599 Evaluate side-chains 722 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 652 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE 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 260 THR Chi-restraints excluded: chain A residue 276 GLU 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 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 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 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 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 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 178 LEU Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 216 LEU 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 283 MET Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 325 MET 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 166 LYS Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 214 ASP 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 124 LEU Chi-restraints excluded: chain H residue 145 LYS 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 229 ASN Chi-restraints excluded: chain H residue 267 THR Chi-restraints excluded: chain H residue 270 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 140 optimal weight: 1.9990 chunk 233 optimal weight: 0.7980 chunk 266 optimal weight: 0.7980 chunk 194 optimal weight: 0.9990 chunk 168 optimal weight: 0.9990 chunk 206 optimal weight: 0.8980 chunk 274 optimal weight: 4.9990 chunk 137 optimal weight: 0.4980 chunk 138 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 225 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 195 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.109837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.092325 restraints weight = 31165.808| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.68 r_work: 0.3033 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 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 : 0.005 0.050 22476 Z= 0.191 Angle : 0.621 7.763 30478 Z= 0.305 Chirality : 0.047 0.194 3367 Planarity : 0.005 0.123 3918 Dihedral : 7.542 99.470 3125 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.35 % Allowed : 19.50 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.16), residues: 2744 helix: 0.59 (0.16), residues: 1153 sheet: 0.87 (0.21), residues: 572 loop : -0.19 (0.20), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 148 HIS 0.008 0.001 HIS B 161 PHE 0.041 0.002 PHE G 163 TYR 0.028 0.001 TYR E 166 ARG 0.017 0.001 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03763 ( 1094) hydrogen bonds : angle 4.64913 ( 2985) covalent geometry : bond 0.00460 (22476) covalent geometry : angle 0.62092 (30478) *********************** 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 768 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 665 time to evaluate : 2.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8723 (pt) cc_final: 0.8336 (mt) REVERT: A 99 GLU cc_start: 0.8088 (pm20) cc_final: 0.7710 (mp0) REVERT: A 167 GLU cc_start: 0.8292 (mm-30) cc_final: 0.8044 (mm-30) REVERT: A 195 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7362 (tp30) REVERT: A 280 ASN cc_start: 0.8823 (m-40) cc_final: 0.8496 (m110) REVERT: A 314 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7499 (tt0) REVERT: A 316 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7964 (mm-30) REVERT: A 363 ASP cc_start: 0.7487 (m-30) cc_final: 0.7208 (m-30) REVERT: A 372 ARG cc_start: 0.7504 (mtm-85) cc_final: 0.7208 (mtm-85) REVERT: B 99 GLU cc_start: 0.8068 (mp0) cc_final: 0.7797 (mp0) REVERT: B 153 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8532 (tp) REVERT: B 283 MET cc_start: 0.8820 (mmp) cc_final: 0.8613 (mmm) REVERT: B 355 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7952 (mtm) REVERT: B 361 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7554 (mt-10) REVERT: C 68 LYS cc_start: 0.8789 (mmtp) cc_final: 0.8564 (mttm) REVERT: C 123 MET cc_start: 0.8683 (tpp) cc_final: 0.8297 (mmp) REVERT: C 128 ASN cc_start: 0.8233 (p0) cc_final: 0.7919 (p0) REVERT: C 222 ASP cc_start: 0.8175 (t70) cc_final: 0.7822 (t0) REVERT: C 286 ASP cc_start: 0.7981 (m-30) cc_final: 0.7751 (m-30) REVERT: C 297 ASN cc_start: 0.8587 (m110) cc_final: 0.8182 (m-40) REVERT: D 83 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7374 (mp0) REVERT: D 359 LYS cc_start: 0.8254 (ttpt) cc_final: 0.7915 (tmtm) REVERT: D 364 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7545 (tm-30) REVERT: E 50 LYS cc_start: 0.8117 (ptpp) cc_final: 0.7838 (mtmt) REVERT: E 61 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8256 (ptmt) REVERT: E 363 ASP cc_start: 0.7858 (m-30) cc_final: 0.7618 (m-30) REVERT: F 68 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8339 (mptt) REVERT: F 215 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8125 (mppt) REVERT: F 269 MET cc_start: 0.8429 (mtt) cc_final: 0.8193 (ttt) REVERT: F 325 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8409 (tpp) REVERT: G 34 ASN cc_start: 0.6999 (t0) cc_final: 0.6616 (t0) REVERT: G 58 ASN cc_start: 0.8205 (m-40) cc_final: 0.7790 (m110) REVERT: G 59 MET cc_start: 0.7816 (mtt) cc_final: 0.7353 (mpp) REVERT: G 96 PHE cc_start: 0.8084 (p90) cc_final: 0.7880 (p90) REVERT: G 99 ASP cc_start: 0.7478 (t0) cc_final: 0.6895 (t0) REVERT: G 134 ASP cc_start: 0.7861 (t70) cc_final: 0.7576 (t0) REVERT: G 162 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7415 (mm-40) REVERT: G 176 GLU cc_start: 0.7111 (tm-30) cc_final: 0.6820 (tm-30) REVERT: G 189 VAL cc_start: 0.7499 (OUTLIER) cc_final: 0.7234 (t) REVERT: G 266 ARG cc_start: 0.8533 (mpt-90) cc_final: 0.8191 (mmt-90) REVERT: G 270 ASP cc_start: 0.8228 (t0) cc_final: 0.7741 (t70) REVERT: H 11 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7423 (t70) REVERT: H 48 LYS cc_start: 0.7933 (mmmt) cc_final: 0.7725 (mmmt) REVERT: H 139 ASP cc_start: 0.7340 (t0) cc_final: 0.6915 (t0) REVERT: H 187 MET cc_start: 0.8320 (mtp) cc_final: 0.8012 (ttt) REVERT: H 230 GLU cc_start: 0.7941 (mp0) cc_final: 0.7558 (mp0) REVERT: H 245 SER cc_start: 0.8306 (p) cc_final: 0.8045 (p) REVERT: H 269 ARG cc_start: 0.7795 (tpp80) cc_final: 0.7414 (ttp80) REVERT: H 270 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7267 (mt0) outliers start: 103 outliers final: 64 residues processed: 710 average time/residue: 1.5954 time to fit residues: 1263.2439 Evaluate side-chains 726 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 651 time to evaluate : 2.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 122 ILE 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 260 THR Chi-restraints excluded: chain A residue 276 GLU 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 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 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 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 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 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 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 191 LYS Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 283 MET Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 325 MET 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 94 ILE Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 148 ILE 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 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 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 Chi-restraints excluded: chain H residue 270 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 242 optimal weight: 2.9990 chunk 153 optimal weight: 0.3980 chunk 163 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 219 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 215 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 115 ASN A 225 ASN B 12 ASN B 225 ASN C 121 GLN C 137 GLN D 12 ASN E 297 ASN E 353 GLN F 92 ASN F 246 GLN G 195 GLN G 205 GLN G 240 GLN H 19 GLN H 20 GLN H 222 ASN H 241 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.110220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.092784 restraints weight = 31245.929| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.68 r_work: 0.3045 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22476 Z= 0.168 Angle : 0.616 8.063 30478 Z= 0.302 Chirality : 0.046 0.235 3367 Planarity : 0.005 0.117 3918 Dihedral : 7.506 99.038 3125 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.76 % Allowed : 20.60 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.16), residues: 2744 helix: 0.64 (0.16), residues: 1152 sheet: 0.84 (0.21), residues: 572 loop : -0.18 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 173 HIS 0.007 0.001 HIS B 161 PHE 0.033 0.001 PHE G 163 TYR 0.029 0.001 TYR E 166 ARG 0.011 0.001 ARG A 206 Details of bonding type rmsd hydrogen bonds : bond 0.03614 ( 1094) hydrogen bonds : angle 4.63049 ( 2985) covalent geometry : bond 0.00404 (22476) covalent geometry : angle 0.61592 (30478) *********************** 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 742 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 653 time to evaluate : 2.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8728 (pt) cc_final: 0.8332 (mt) REVERT: A 99 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7716 (mp0) REVERT: A 363 ASP cc_start: 0.7490 (m-30) cc_final: 0.7228 (m-30) REVERT: A 364 GLU cc_start: 0.7434 (tm-30) cc_final: 0.7173 (tm-30) REVERT: A 372 ARG cc_start: 0.7516 (mtm-85) cc_final: 0.7230 (mtm-85) REVERT: B 99 GLU cc_start: 0.8068 (mp0) cc_final: 0.7849 (mp0) REVERT: B 153 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8508 (tp) REVERT: B 283 MET cc_start: 0.8823 (mmp) cc_final: 0.8619 (mmm) REVERT: B 355 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7944 (mtm) REVERT: B 361 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7539 (mt-10) REVERT: C 68 LYS cc_start: 0.8784 (mmtp) cc_final: 0.8557 (mttm) REVERT: C 128 ASN cc_start: 0.8240 (p0) cc_final: 0.7951 (p0) REVERT: C 222 ASP cc_start: 0.8171 (t70) cc_final: 0.7830 (t0) REVERT: C 286 ASP cc_start: 0.7981 (m-30) cc_final: 0.7755 (m-30) REVERT: C 297 ASN cc_start: 0.8582 (m110) cc_final: 0.8179 (m-40) REVERT: C 353 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.8014 (mp10) REVERT: D 83 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7390 (mp0) REVERT: D 107 GLU cc_start: 0.7631 (tt0) cc_final: 0.7415 (tm-30) REVERT: D 359 LYS cc_start: 0.8259 (ttpt) cc_final: 0.7918 (tmtm) REVERT: D 364 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7547 (tm-30) REVERT: E 50 LYS cc_start: 0.8117 (ptpp) cc_final: 0.7849 (mtmt) REVERT: E 61 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8282 (ptmt) REVERT: E 363 ASP cc_start: 0.7853 (m-30) cc_final: 0.7604 (m-30) REVERT: F 44 MET cc_start: 0.8597 (mmt) cc_final: 0.8347 (mmm) REVERT: F 68 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8332 (mptt) REVERT: F 269 MET cc_start: 0.8412 (mtt) cc_final: 0.8172 (ttt) REVERT: F 325 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8428 (tpp) REVERT: G 34 ASN cc_start: 0.6988 (t0) cc_final: 0.6603 (t0) REVERT: G 36 VAL cc_start: 0.8236 (m) cc_final: 0.8023 (p) REVERT: G 58 ASN cc_start: 0.8190 (m-40) cc_final: 0.7796 (m110) REVERT: G 96 PHE cc_start: 0.8073 (p90) cc_final: 0.7853 (p90) REVERT: G 99 ASP cc_start: 0.7480 (t0) cc_final: 0.6882 (t0) REVERT: G 134 ASP cc_start: 0.7846 (t70) cc_final: 0.7566 (t0) REVERT: G 176 GLU cc_start: 0.7121 (tm-30) cc_final: 0.6821 (tm-30) REVERT: G 189 VAL cc_start: 0.7479 (OUTLIER) cc_final: 0.7224 (t) REVERT: G 266 ARG cc_start: 0.8500 (mpt-90) cc_final: 0.8157 (mmt-90) REVERT: G 270 ASP cc_start: 0.8238 (t0) cc_final: 0.7731 (t70) REVERT: H 11 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.6970 (t70) REVERT: H 15 ARG cc_start: 0.8201 (ptp90) cc_final: 0.7301 (ptp90) REVERT: H 47 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8111 (mm) REVERT: H 48 LYS cc_start: 0.7934 (mmmt) cc_final: 0.7729 (mmmt) REVERT: H 139 ASP cc_start: 0.7315 (t0) cc_final: 0.6900 (t0) REVERT: H 230 GLU cc_start: 0.7988 (mp0) cc_final: 0.7559 (mp0) REVERT: H 245 SER cc_start: 0.8304 (p) cc_final: 0.8039 (p) REVERT: H 269 ARG cc_start: 0.7820 (tpp80) cc_final: 0.7426 (ttp80) REVERT: H 270 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7263 (mt0) outliers start: 89 outliers final: 60 residues processed: 693 average time/residue: 1.5689 time to fit residues: 1215.5977 Evaluate side-chains 719 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 647 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LYS 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 28 ARG 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 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 353 GLN 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 D residue 276 GLU 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 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 283 MET Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 325 MET 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 94 ILE Chi-restraints excluded: chain G residue 117 LEU 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 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 145 LYS 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 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 70 optimal weight: 1.9990 chunk 223 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 262 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 238 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 21 optimal weight: 0.0470 chunk 224 optimal weight: 0.7980 chunk 192 optimal weight: 0.9980 chunk 9 optimal weight: 0.2980 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 115 ASN A 225 ASN A 280 ASN B 12 ASN B 101 HIS B 225 ASN C 121 GLN C 137 GLN D 12 ASN E 297 ASN E 353 GLN F 92 ASN F 246 GLN G 195 GLN G 205 GLN G 240 GLN H 19 GLN H 20 GLN H 222 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.112786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.095663 restraints weight = 31344.743| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.64 r_work: 0.3048 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22476 Z= 0.167 Angle : 0.626 9.200 30478 Z= 0.305 Chirality : 0.046 0.233 3367 Planarity : 0.005 0.086 3918 Dihedral : 7.478 98.639 3125 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.01 % Allowed : 20.56 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.16), residues: 2744 helix: 0.65 (0.16), residues: 1153 sheet: 0.83 (0.21), residues: 572 loop : -0.17 (0.20), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 148 HIS 0.007 0.001 HIS B 161 PHE 0.030 0.001 PHE G 163 TYR 0.028 0.001 TYR E 166 ARG 0.020 0.001 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03595 ( 1094) hydrogen bonds : angle 4.63028 ( 2985) covalent geometry : bond 0.00401 (22476) covalent geometry : angle 0.62595 (30478) *********************** 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 745 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 650 time to evaluate : 2.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8723 (pt) cc_final: 0.8325 (mt) REVERT: A 99 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7691 (mp0) REVERT: A 147 ARG cc_start: 0.8707 (ptp90) cc_final: 0.8219 (ptp90) REVERT: A 280 ASN cc_start: 0.8820 (m-40) cc_final: 0.8470 (m-40) REVERT: A 363 ASP cc_start: 0.7466 (m-30) cc_final: 0.7198 (m-30) REVERT: A 364 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7192 (tm-30) REVERT: A 372 ARG cc_start: 0.7497 (mtm-85) cc_final: 0.7246 (mtm-85) REVERT: B 99 GLU cc_start: 0.8049 (mp0) cc_final: 0.7842 (mp0) REVERT: B 153 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8507 (tp) REVERT: B 355 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.7941 (mtm) REVERT: C 68 LYS cc_start: 0.8785 (mmtp) cc_final: 0.8541 (mttm) REVERT: C 128 ASN cc_start: 0.8251 (p0) cc_final: 0.7962 (p0) REVERT: C 222 ASP cc_start: 0.8149 (t70) cc_final: 0.7818 (t0) REVERT: C 286 ASP cc_start: 0.7967 (m-30) cc_final: 0.7724 (m-30) REVERT: C 297 ASN cc_start: 0.8561 (m110) cc_final: 0.8172 (m-40) REVERT: C 353 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.8018 (mp10) REVERT: D 83 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7395 (mp0) REVERT: D 359 LYS cc_start: 0.8255 (ttpt) cc_final: 0.7948 (tmtm) REVERT: D 364 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7549 (tm-30) REVERT: E 50 LYS cc_start: 0.8096 (ptpp) cc_final: 0.7822 (mtmt) REVERT: E 61 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8285 (ptmt) REVERT: E 363 ASP cc_start: 0.7794 (m-30) cc_final: 0.7552 (m-30) REVERT: F 44 MET cc_start: 0.8583 (mmt) cc_final: 0.8347 (mmm) REVERT: F 68 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8330 (mptt) REVERT: F 215 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8134 (mppt) REVERT: F 269 MET cc_start: 0.8387 (mtt) cc_final: 0.8149 (ttt) REVERT: F 325 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8349 (tpp) REVERT: G 34 ASN cc_start: 0.6993 (t0) cc_final: 0.6641 (t0) REVERT: G 36 VAL cc_start: 0.8306 (m) cc_final: 0.8081 (p) REVERT: G 58 ASN cc_start: 0.8204 (m-40) cc_final: 0.7775 (m110) REVERT: G 59 MET cc_start: 0.7687 (mtt) cc_final: 0.7438 (mpp) REVERT: G 96 PHE cc_start: 0.8078 (p90) cc_final: 0.7846 (p90) REVERT: G 99 ASP cc_start: 0.7464 (t0) cc_final: 0.6905 (t0) REVERT: G 134 ASP cc_start: 0.7848 (t70) cc_final: 0.7585 (t0) REVERT: G 176 GLU cc_start: 0.7102 (tm-30) cc_final: 0.6829 (tm-30) REVERT: G 189 VAL cc_start: 0.7501 (OUTLIER) cc_final: 0.7236 (t) REVERT: G 266 ARG cc_start: 0.8519 (mpt-90) cc_final: 0.8164 (mmt-90) REVERT: G 270 ASP cc_start: 0.8225 (t0) cc_final: 0.7739 (t70) REVERT: H 11 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.7262 (t0) REVERT: H 47 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8123 (mm) REVERT: H 48 LYS cc_start: 0.7964 (mmmt) cc_final: 0.7746 (mmmt) REVERT: H 139 ASP cc_start: 0.7317 (t0) cc_final: 0.6913 (t0) REVERT: H 230 GLU cc_start: 0.7980 (mp0) cc_final: 0.7553 (mp0) REVERT: H 245 SER cc_start: 0.8305 (p) cc_final: 0.8054 (p) REVERT: H 269 ARG cc_start: 0.7779 (tpp80) cc_final: 0.7391 (ttp80) REVERT: H 270 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.7334 (mt0) outliers start: 95 outliers final: 66 residues processed: 689 average time/residue: 1.5281 time to fit residues: 1177.0751 Evaluate side-chains 724 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 645 time to evaluate : 2.442 ------------------------------------------------------------------------------- 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 99 GLU Chi-restraints excluded: chain A residue 115 ASN 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 28 ARG 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 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 353 GLN 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 D residue 276 GLU Chi-restraints excluded: chain D residue 338 SER 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 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 215 LYS Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 283 MET Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 313 MET Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 325 MET 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 94 ILE Chi-restraints excluded: chain G residue 117 LEU 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 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 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 267 THR Chi-restraints excluded: chain H residue 270 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 114 optimal weight: 0.9990 chunk 172 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 210 optimal weight: 0.7980 chunk 225 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 216 optimal weight: 0.9980 chunk 254 optimal weight: 0.7980 chunk 221 optimal weight: 0.0970 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 115 ASN A 225 ASN B 12 ASN B 225 ASN C 121 GLN C 137 GLN D 12 ASN E 297 ASN E 353 GLN F 92 ASN F 246 GLN G 195 GLN G 205 GLN G 240 GLN H 19 GLN H 20 GLN H 222 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.112357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.095264 restraints weight = 31261.912| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.63 r_work: 0.3047 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1905 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= 0.182 Angle : 0.642 11.668 30478 Z= 0.315 Chirality : 0.047 0.221 3367 Planarity : 0.005 0.066 3918 Dihedral : 7.503 98.894 3125 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.63 % Allowed : 21.23 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.16), residues: 2744 helix: 0.63 (0.16), residues: 1153 sheet: 0.81 (0.21), residues: 572 loop : -0.19 (0.20), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 173 HIS 0.007 0.001 HIS B 161 PHE 0.028 0.002 PHE G 163 TYR 0.034 0.001 TYR E 166 ARG 0.011 0.001 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03709 ( 1094) hydrogen bonds : angle 4.66754 ( 2985) covalent geometry : bond 0.00438 (22476) covalent geometry : angle 0.64174 (30478) *********************** 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 738 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 652 time to evaluate : 4.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8726 (pt) cc_final: 0.8342 (mt) REVERT: A 99 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7655 (mp0) REVERT: A 147 ARG cc_start: 0.8720 (ptp90) cc_final: 0.8219 (ptp90) REVERT: A 314 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7551 (tt0) REVERT: A 363 ASP cc_start: 0.7482 (m-30) cc_final: 0.7217 (m-30) REVERT: A 364 GLU cc_start: 0.7479 (tm-30) cc_final: 0.7215 (tm-30) REVERT: A 372 ARG cc_start: 0.7504 (mtm-85) cc_final: 0.7250 (mtm-85) REVERT: B 99 GLU cc_start: 0.8047 (mp0) cc_final: 0.7844 (mp0) REVERT: B 153 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8525 (tp) REVERT: B 283 MET cc_start: 0.8806 (mmp) cc_final: 0.8580 (mmm) REVERT: B 355 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7939 (mtm) REVERT: C 68 LYS cc_start: 0.8776 (mmtp) cc_final: 0.8538 (mttm) REVERT: C 128 ASN cc_start: 0.8263 (p0) cc_final: 0.8006 (p0) REVERT: C 222 ASP cc_start: 0.8172 (t70) cc_final: 0.7859 (t0) REVERT: C 286 ASP cc_start: 0.7965 (m-30) cc_final: 0.7727 (m-30) REVERT: C 297 ASN cc_start: 0.8565 (m110) cc_final: 0.8168 (m-40) REVERT: C 353 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.8013 (mp10) REVERT: D 83 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: D 359 LYS cc_start: 0.8257 (ttpt) cc_final: 0.7956 (tmtm) REVERT: D 364 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7546 (tm-30) REVERT: E 50 LYS cc_start: 0.8084 (ptpp) cc_final: 0.7813 (mtmt) REVERT: E 61 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8263 (ptmt) REVERT: E 269 MET cc_start: 0.8815 (mtm) cc_final: 0.8596 (mtm) REVERT: E 363 ASP cc_start: 0.7803 (m-30) cc_final: 0.7562 (m-30) REVERT: F 68 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8325 (mptt) REVERT: F 215 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8140 (mppt) REVERT: F 269 MET cc_start: 0.8391 (mtt) cc_final: 0.8146 (ttt) REVERT: F 325 MET cc_start: 0.8602 (tpp) cc_final: 0.8346 (tpp) REVERT: G 34 ASN cc_start: 0.7123 (t0) cc_final: 0.6762 (t0) REVERT: G 36 VAL cc_start: 0.8284 (m) cc_final: 0.8067 (p) REVERT: G 38 LEU cc_start: 0.8486 (tt) cc_final: 0.8176 (tt) REVERT: G 96 PHE cc_start: 0.8086 (p90) cc_final: 0.7857 (p90) REVERT: G 99 ASP cc_start: 0.7443 (t0) cc_final: 0.6884 (t0) REVERT: G 134 ASP cc_start: 0.7851 (t70) cc_final: 0.7581 (t0) REVERT: G 176 GLU cc_start: 0.7117 (tm-30) cc_final: 0.6847 (tm-30) REVERT: G 189 VAL cc_start: 0.7518 (OUTLIER) cc_final: 0.7253 (t) REVERT: G 266 ARG cc_start: 0.8513 (mpt-90) cc_final: 0.8157 (mmt-90) REVERT: G 270 ASP cc_start: 0.8230 (t0) cc_final: 0.7748 (t70) REVERT: H 11 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7034 (t70) REVERT: H 15 ARG cc_start: 0.8204 (ptp90) cc_final: 0.7364 (ptp90) REVERT: H 48 LYS cc_start: 0.7981 (mmmt) cc_final: 0.7762 (mmmt) REVERT: H 139 ASP cc_start: 0.7281 (t0) cc_final: 0.6858 (t0) REVERT: H 230 GLU cc_start: 0.7982 (mp0) cc_final: 0.7557 (mp0) REVERT: H 245 SER cc_start: 0.8308 (p) cc_final: 0.8056 (p) REVERT: H 269 ARG cc_start: 0.7765 (tpp80) cc_final: 0.7384 (ttp80) REVERT: H 270 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.7310 (mt0) outliers start: 86 outliers final: 63 residues processed: 690 average time/residue: 1.8830 time to fit residues: 1448.1639 Evaluate side-chains 731 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 656 time to evaluate : 2.195 ------------------------------------------------------------------------------- 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 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 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 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 353 GLN Chi-restraints excluded: chain C residue 368 SER 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 D residue 276 GLU Chi-restraints excluded: chain D residue 338 SER 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 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 215 LYS Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 283 MET Chi-restraints excluded: chain F residue 313 MET 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 H residue 11 ASP 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 145 LYS 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 246 ILE Chi-restraints excluded: chain H residue 267 THR Chi-restraints excluded: chain H residue 270 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 212 optimal weight: 0.2980 chunk 239 optimal weight: 0.2980 chunk 83 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 182 optimal weight: 0.9990 chunk 154 optimal weight: 0.9980 chunk 257 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN B 12 ASN B 225 ASN C 121 GLN C 137 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 ASN E 353 GLN F 92 ASN F 246 GLN F 353 GLN G 58 ASN G 195 GLN G 205 GLN G 240 GLN H 19 GLN H 20 GLN H 222 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.112756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.095645 restraints weight = 31199.435| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.62 r_work: 0.3053 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1939 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= 0.160 Angle : 0.635 8.928 30478 Z= 0.312 Chirality : 0.046 0.233 3367 Planarity : 0.005 0.095 3918 Dihedral : 7.383 98.084 3123 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.80 % Allowed : 21.57 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.16), residues: 2744 helix: 0.67 (0.16), residues: 1152 sheet: 0.83 (0.21), residues: 572 loop : -0.16 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 173 HIS 0.006 0.001 HIS B 161 PHE 0.027 0.001 PHE G 163 TYR 0.035 0.001 TYR E 166 ARG 0.021 0.001 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03550 ( 1094) hydrogen bonds : angle 4.63431 ( 2985) covalent geometry : bond 0.00385 (22476) covalent geometry : angle 0.63535 (30478) ********************** 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 741 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 651 time to evaluate : 2.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8723 (pt) cc_final: 0.8318 (mt) REVERT: A 99 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: A 147 ARG cc_start: 0.8719 (ptp90) cc_final: 0.8213 (ptp90) REVERT: A 280 ASN cc_start: 0.8815 (m-40) cc_final: 0.8450 (m-40) REVERT: A 305 MET cc_start: 0.8901 (mmt) cc_final: 0.8675 (mmt) REVERT: A 314 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7531 (tt0) REVERT: A 363 ASP cc_start: 0.7465 (m-30) cc_final: 0.7209 (m-30) REVERT: A 364 GLU cc_start: 0.7481 (tm-30) cc_final: 0.7207 (tm-30) REVERT: A 372 ARG cc_start: 0.7504 (mtm-85) cc_final: 0.7249 (mtm-85) REVERT: B 99 GLU cc_start: 0.8043 (mp0) cc_final: 0.7697 (mp0) REVERT: B 153 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8503 (tp) REVERT: B 355 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7921 (mtm) REVERT: C 68 LYS cc_start: 0.8791 (mmtp) cc_final: 0.8555 (mttm) REVERT: C 128 ASN cc_start: 0.8270 (p0) cc_final: 0.8002 (p0) REVERT: C 222 ASP cc_start: 0.8174 (t70) cc_final: 0.7858 (t0) REVERT: C 286 ASP cc_start: 0.7969 (m-30) cc_final: 0.7729 (m-30) REVERT: C 297 ASN cc_start: 0.8551 (m110) cc_final: 0.8164 (m-40) REVERT: C 353 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.8022 (mp10) REVERT: D 83 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: D 286 ASP cc_start: 0.8029 (m-30) cc_final: 0.7825 (m-30) REVERT: D 359 LYS cc_start: 0.8254 (ttpt) cc_final: 0.7960 (tmtm) REVERT: D 364 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7544 (tm-30) REVERT: E 50 LYS cc_start: 0.8076 (ptpp) cc_final: 0.7804 (mtmt) REVERT: E 61 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8273 (ptmt) REVERT: E 167 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7498 (mp0) REVERT: E 269 MET cc_start: 0.8812 (mtm) cc_final: 0.8574 (mtm) REVERT: E 363 ASP cc_start: 0.7795 (m-30) cc_final: 0.7540 (m-30) REVERT: F 68 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8335 (mptt) REVERT: F 215 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8139 (mppt) REVERT: F 269 MET cc_start: 0.8367 (mtt) cc_final: 0.8119 (ttt) REVERT: G 34 ASN cc_start: 0.7109 (t0) cc_final: 0.6736 (t0) REVERT: G 36 VAL cc_start: 0.8287 (m) cc_final: 0.8075 (p) REVERT: G 96 PHE cc_start: 0.8105 (p90) cc_final: 0.7874 (p90) REVERT: G 99 ASP cc_start: 0.7449 (t0) cc_final: 0.6886 (t0) REVERT: G 134 ASP cc_start: 0.7847 (t70) cc_final: 0.7594 (t0) REVERT: G 162 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7355 (mm-40) REVERT: G 176 GLU cc_start: 0.7121 (tm-30) cc_final: 0.6849 (tm-30) REVERT: G 189 VAL cc_start: 0.7509 (OUTLIER) cc_final: 0.7247 (t) REVERT: G 266 ARG cc_start: 0.8517 (mpt-90) cc_final: 0.8160 (mmt-90) REVERT: G 270 ASP cc_start: 0.8224 (t0) cc_final: 0.7763 (t70) REVERT: H 11 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7209 (t0) REVERT: H 48 LYS cc_start: 0.7978 (mmmt) cc_final: 0.7749 (mmmt) REVERT: H 139 ASP cc_start: 0.7296 (t0) cc_final: 0.6880 (t0) REVERT: H 230 GLU cc_start: 0.7987 (mp0) cc_final: 0.7560 (mp0) REVERT: H 245 SER cc_start: 0.8317 (OUTLIER) cc_final: 0.8069 (p) REVERT: H 261 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7175 (mt-10) REVERT: H 269 ARG cc_start: 0.7770 (tpp80) cc_final: 0.7380 (ttp80) REVERT: H 270 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7329 (mt0) outliers start: 90 outliers final: 63 residues processed: 690 average time/residue: 1.8606 time to fit residues: 1449.9663 Evaluate side-chains 734 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 658 time to evaluate : 2.940 ------------------------------------------------------------------------------- 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 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 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 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 244 ASP 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 353 GLN Chi-restraints excluded: chain C residue 368 SER 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 D residue 276 GLU Chi-restraints excluded: chain D residue 338 SER 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 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 215 LYS Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 283 MET Chi-restraints excluded: chain F residue 313 MET 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 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 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 246 ILE Chi-restraints excluded: chain H residue 267 THR Chi-restraints excluded: chain H residue 270 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 205 optimal weight: 0.7980 chunk 234 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 245 optimal weight: 0.9990 chunk 269 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 169 optimal weight: 0.6980 chunk 215 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 219 optimal weight: 1.9990 chunk 88 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN B 225 ASN C 121 GLN C 137 GLN D 12 ASN D 92 ASN E 297 ASN E 353 GLN F 246 GLN G 56 GLN G 58 ASN G 195 GLN G 205 GLN G 240 GLN H 19 GLN H 20 GLN H 222 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.112502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.095383 restraints weight = 31363.334| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.63 r_work: 0.3046 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1955 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= 0.165 Angle : 0.645 8.818 30478 Z= 0.316 Chirality : 0.046 0.229 3367 Planarity : 0.004 0.069 3918 Dihedral : 7.361 98.142 3123 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.46 % Allowed : 22.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.16), residues: 2744 helix: 0.68 (0.16), residues: 1152 sheet: 0.82 (0.21), residues: 572 loop : -0.16 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 173 HIS 0.006 0.001 HIS B 161 PHE 0.025 0.001 PHE G 163 TYR 0.037 0.001 TYR E 166 ARG 0.012 0.001 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03575 ( 1094) hydrogen bonds : angle 4.64039 ( 2985) covalent geometry : bond 0.00396 (22476) covalent geometry : angle 0.64508 (30478) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23711.15 seconds wall clock time: 409 minutes 42.50 seconds (24582.50 seconds total)