Starting phenix.real_space_refine on Tue Aug 26 13:04:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yg7_33810/08_2025/7yg7_33810.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yg7_33810/08_2025/7yg7_33810.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yg7_33810/08_2025/7yg7_33810.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yg7_33810/08_2025/7yg7_33810.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yg7_33810/08_2025/7yg7_33810.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yg7_33810/08_2025/7yg7_33810.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 98 5.49 5 S 187 5.16 5 C 23925 2.51 5 N 6281 2.21 5 O 7544 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38035 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3278 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 18, 'TRANS': 395} Chain: "B" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3278 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 18, 'TRANS': 395} Chain: "C" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3278 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 18, 'TRANS': 395} Chain: "D" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3278 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 18, 'TRANS': 395} Chain: "E" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3278 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 18, 'TRANS': 395} Chain: "F" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3278 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 18, 'TRANS': 395} Chain: "G" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3278 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 18, 'TRANS': 395} Chain: "H" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3278 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 18, 'TRANS': 395} Chain: "I" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3278 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 18, 'TRANS': 395} Chain: "J" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3278 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 18, 'TRANS': 395} Chain: "K" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3278 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 18, 'TRANS': 395} Chain: "U" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 1977 Classifications: {'RNA': 99} Modifications used: {'5*END': 1, 'rna2p_pyr': 13, 'rna3p_pyr': 86} Link IDs: {'rna2p': 13, 'rna3p': 85} Time building chain proxies: 8.91, per 1000 atoms: 0.23 Number of scatterers: 38035 At special positions: 0 Unit cell: (189.06, 189.06, 100.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 187 16.00 P 98 15.00 O 7544 8.00 N 6281 7.00 C 23925 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: 3.27 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 953.7 nanoseconds 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8514 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 11 sheets defined 46.9% alpha, 1.2% beta 0 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 4.23 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 127 through 130 removed outlier: 3.842A pdb=" N ALA A 130 " --> pdb=" O GLU A 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 127 through 130' Processing helix chain 'A' and resid 131 through 144 removed outlier: 3.611A pdb=" N ARG A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 162 removed outlier: 3.843A pdb=" N MET A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 186 through 203 removed outlier: 3.501A pdb=" N HIS A 202 " --> pdb=" O MET A 198 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 203 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 213 removed outlier: 3.533A pdb=" N ALA A 209 " --> pdb=" O SER A 206 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR A 210 " --> pdb=" O ILE A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 219 Processing helix chain 'A' and resid 223 through 237 removed outlier: 3.974A pdb=" N ALA A 227 " --> pdb=" O CYS A 223 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR A 236 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 246 Processing helix chain 'A' and resid 249 through 260 Processing helix chain 'A' and resid 299 through 306 Processing helix chain 'A' and resid 310 through 314 removed outlier: 3.581A pdb=" N ALA A 314 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 339 removed outlier: 3.734A pdb=" N ILE A 325 " --> pdb=" O ASP A 321 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 339 " --> pdb=" O ALA A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 382 removed outlier: 3.548A pdb=" N TRP A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 382 " --> pdb=" O TRP A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 399 Processing helix chain 'A' and resid 408 through 417 Processing helix chain 'B' and resid 45 through 55 Processing helix chain 'B' and resid 63 through 76 Processing helix chain 'B' and resid 127 through 130 removed outlier: 3.842A pdb=" N ALA B 130 " --> pdb=" O GLU B 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 127 through 130' Processing helix chain 'B' and resid 131 through 144 removed outlier: 3.610A pdb=" N ARG B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 162 removed outlier: 3.843A pdb=" N MET B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 186 through 203 removed outlier: 3.501A pdb=" N HIS B 202 " --> pdb=" O MET B 198 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE B 203 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 213 removed outlier: 3.533A pdb=" N ALA B 209 " --> pdb=" O SER B 206 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR B 210 " --> pdb=" O ILE B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 219 Processing helix chain 'B' and resid 223 through 237 removed outlier: 3.974A pdb=" N ALA B 227 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR B 236 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY B 237 " --> pdb=" O VAL B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 246 Processing helix chain 'B' and resid 249 through 260 Processing helix chain 'B' and resid 299 through 306 Processing helix chain 'B' and resid 310 through 314 removed outlier: 3.581A pdb=" N ALA B 314 " --> pdb=" O ALA B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 339 removed outlier: 3.734A pdb=" N ILE B 325 " --> pdb=" O ASP B 321 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER B 339 " --> pdb=" O ALA B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 382 removed outlier: 3.548A pdb=" N TRP B 375 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 382 " --> pdb=" O TRP B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 399 Processing helix chain 'B' and resid 408 through 417 Processing helix chain 'C' and resid 45 through 55 Processing helix chain 'C' and resid 63 through 76 Processing helix chain 'C' and resid 127 through 130 removed outlier: 3.842A pdb=" N ALA C 130 " --> pdb=" O GLU C 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 127 through 130' Processing helix chain 'C' and resid 131 through 144 removed outlier: 3.611A pdb=" N ARG C 141 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 162 removed outlier: 3.843A pdb=" N MET C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 186 through 203 removed outlier: 3.502A pdb=" N HIS C 202 " --> pdb=" O MET C 198 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE C 203 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.533A pdb=" N ALA C 209 " --> pdb=" O SER C 206 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR C 210 " --> pdb=" O ILE C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 219 Processing helix chain 'C' and resid 223 through 237 removed outlier: 3.974A pdb=" N ALA C 227 " --> pdb=" O CYS C 223 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR C 236 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY C 237 " --> pdb=" O VAL C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 246 Processing helix chain 'C' and resid 249 through 260 Processing helix chain 'C' and resid 299 through 306 Processing helix chain 'C' and resid 310 through 314 removed outlier: 3.581A pdb=" N ALA C 314 " --> pdb=" O ALA C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 339 removed outlier: 3.734A pdb=" N ILE C 325 " --> pdb=" O ASP C 321 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER C 339 " --> pdb=" O ALA C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 382 removed outlier: 3.547A pdb=" N TRP C 375 " --> pdb=" O SER C 371 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL C 382 " --> pdb=" O TRP C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 399 Processing helix chain 'C' and resid 408 through 417 Processing helix chain 'D' and resid 45 through 55 Processing helix chain 'D' and resid 63 through 76 Processing helix chain 'D' and resid 127 through 130 removed outlier: 3.842A pdb=" N ALA D 130 " --> pdb=" O GLU D 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 127 through 130' Processing helix chain 'D' and resid 131 through 144 removed outlier: 3.611A pdb=" N ARG D 141 " --> pdb=" O LEU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 162 removed outlier: 3.843A pdb=" N MET D 155 " --> pdb=" O ARG D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 185 Processing helix chain 'D' and resid 186 through 203 removed outlier: 3.501A pdb=" N HIS D 202 " --> pdb=" O MET D 198 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE D 203 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 213 removed outlier: 3.533A pdb=" N ALA D 209 " --> pdb=" O SER D 206 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR D 210 " --> pdb=" O ILE D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 219 Processing helix chain 'D' and resid 223 through 237 removed outlier: 3.975A pdb=" N ALA D 227 " --> pdb=" O CYS D 223 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR D 236 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY D 237 " --> pdb=" O VAL D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 246 Processing helix chain 'D' and resid 249 through 260 Processing helix chain 'D' and resid 299 through 306 Processing helix chain 'D' and resid 310 through 314 removed outlier: 3.581A pdb=" N ALA D 314 " --> pdb=" O ALA D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 339 removed outlier: 3.735A pdb=" N ILE D 325 " --> pdb=" O ASP D 321 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER D 339 " --> pdb=" O ALA D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 382 removed outlier: 3.548A pdb=" N TRP D 375 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL D 382 " --> pdb=" O TRP D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 399 Processing helix chain 'D' and resid 408 through 417 Processing helix chain 'E' and resid 45 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 127 through 130 removed outlier: 3.842A pdb=" N ALA E 130 " --> pdb=" O GLU E 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 127 through 130' Processing helix chain 'E' and resid 131 through 144 removed outlier: 3.610A pdb=" N ARG E 141 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 162 removed outlier: 3.844A pdb=" N MET E 155 " --> pdb=" O ARG E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 185 Processing helix chain 'E' and resid 186 through 203 removed outlier: 3.502A pdb=" N HIS E 202 " --> pdb=" O MET E 198 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE E 203 " --> pdb=" O PHE E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 213 removed outlier: 3.533A pdb=" N ALA E 209 " --> pdb=" O SER E 206 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR E 210 " --> pdb=" O ILE E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 219 Processing helix chain 'E' and resid 223 through 237 removed outlier: 3.975A pdb=" N ALA E 227 " --> pdb=" O CYS E 223 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR E 236 " --> pdb=" O VAL E 232 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY E 237 " --> pdb=" O VAL E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 246 Processing helix chain 'E' and resid 249 through 260 Processing helix chain 'E' and resid 299 through 306 Processing helix chain 'E' and resid 310 through 314 removed outlier: 3.581A pdb=" N ALA E 314 " --> pdb=" O ALA E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 339 removed outlier: 3.734A pdb=" N ILE E 325 " --> pdb=" O ASP E 321 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER E 339 " --> pdb=" O ALA E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 371 through 382 removed outlier: 3.549A pdb=" N TRP E 375 " --> pdb=" O SER E 371 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL E 382 " --> pdb=" O TRP E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 399 Processing helix chain 'E' and resid 408 through 417 Processing helix chain 'F' and resid 45 through 55 Processing helix chain 'F' and resid 63 through 76 Processing helix chain 'F' and resid 127 through 130 removed outlier: 3.842A pdb=" N ALA F 130 " --> pdb=" O GLU F 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 127 through 130' Processing helix chain 'F' and resid 131 through 144 removed outlier: 3.610A pdb=" N ARG F 141 " --> pdb=" O LEU F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 162 removed outlier: 3.843A pdb=" N MET F 155 " --> pdb=" O ARG F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 185 Processing helix chain 'F' and resid 186 through 203 removed outlier: 3.501A pdb=" N HIS F 202 " --> pdb=" O MET F 198 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE F 203 " --> pdb=" O PHE F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 213 removed outlier: 3.533A pdb=" N ALA F 209 " --> pdb=" O SER F 206 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR F 210 " --> pdb=" O ILE F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 219 Processing helix chain 'F' and resid 223 through 237 removed outlier: 3.974A pdb=" N ALA F 227 " --> pdb=" O CYS F 223 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR F 236 " --> pdb=" O VAL F 232 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY F 237 " --> pdb=" O VAL F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 246 Processing helix chain 'F' and resid 249 through 260 Processing helix chain 'F' and resid 299 through 306 Processing helix chain 'F' and resid 310 through 314 removed outlier: 3.581A pdb=" N ALA F 314 " --> pdb=" O ALA F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 339 removed outlier: 3.734A pdb=" N ILE F 325 " --> pdb=" O ASP F 321 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER F 339 " --> pdb=" O ALA F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 382 removed outlier: 3.549A pdb=" N TRP F 375 " --> pdb=" O SER F 371 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL F 382 " --> pdb=" O TRP F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 399 Processing helix chain 'F' and resid 408 through 417 Processing helix chain 'G' and resid 45 through 55 Processing helix chain 'G' and resid 63 through 76 Processing helix chain 'G' and resid 127 through 130 removed outlier: 3.842A pdb=" N ALA G 130 " --> pdb=" O GLU G 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 127 through 130' Processing helix chain 'G' and resid 131 through 144 removed outlier: 3.612A pdb=" N ARG G 141 " --> pdb=" O LEU G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 162 removed outlier: 3.843A pdb=" N MET G 155 " --> pdb=" O ARG G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 185 Processing helix chain 'G' and resid 186 through 203 removed outlier: 3.501A pdb=" N HIS G 202 " --> pdb=" O MET G 198 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE G 203 " --> pdb=" O PHE G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 213 removed outlier: 3.533A pdb=" N ALA G 209 " --> pdb=" O SER G 206 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR G 210 " --> pdb=" O ILE G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 219 Processing helix chain 'G' and resid 223 through 237 removed outlier: 3.974A pdb=" N ALA G 227 " --> pdb=" O CYS G 223 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR G 236 " --> pdb=" O VAL G 232 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY G 237 " --> pdb=" O VAL G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 246 Processing helix chain 'G' and resid 249 through 260 Processing helix chain 'G' and resid 299 through 306 Processing helix chain 'G' and resid 310 through 314 removed outlier: 3.581A pdb=" N ALA G 314 " --> pdb=" O ALA G 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 339 removed outlier: 3.735A pdb=" N ILE G 325 " --> pdb=" O ASP G 321 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER G 339 " --> pdb=" O ALA G 335 " (cutoff:3.500A) Processing helix chain 'G' and resid 371 through 382 removed outlier: 3.548A pdb=" N TRP G 375 " --> pdb=" O SER G 371 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL G 382 " --> pdb=" O TRP G 378 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 399 Processing helix chain 'G' and resid 408 through 417 Processing helix chain 'H' and resid 45 through 55 Processing helix chain 'H' and resid 63 through 76 Processing helix chain 'H' and resid 127 through 130 removed outlier: 3.842A pdb=" N ALA H 130 " --> pdb=" O GLU H 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 127 through 130' Processing helix chain 'H' and resid 131 through 144 removed outlier: 3.611A pdb=" N ARG H 141 " --> pdb=" O LEU H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 151 through 162 removed outlier: 3.844A pdb=" N MET H 155 " --> pdb=" O ARG H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 180 through 185 Processing helix chain 'H' and resid 186 through 203 removed outlier: 3.501A pdb=" N HIS H 202 " --> pdb=" O MET H 198 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE H 203 " --> pdb=" O PHE H 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 213 removed outlier: 3.533A pdb=" N ALA H 209 " --> pdb=" O SER H 206 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR H 210 " --> pdb=" O ILE H 207 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 219 Processing helix chain 'H' and resid 223 through 237 removed outlier: 3.974A pdb=" N ALA H 227 " --> pdb=" O CYS H 223 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR H 236 " --> pdb=" O VAL H 232 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY H 237 " --> pdb=" O VAL H 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 239 through 246 Processing helix chain 'H' and resid 249 through 260 Processing helix chain 'H' and resid 299 through 306 Processing helix chain 'H' and resid 310 through 314 removed outlier: 3.581A pdb=" N ALA H 314 " --> pdb=" O ALA H 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 321 through 339 removed outlier: 3.734A pdb=" N ILE H 325 " --> pdb=" O ASP H 321 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER H 339 " --> pdb=" O ALA H 335 " (cutoff:3.500A) Processing helix chain 'H' and resid 371 through 382 removed outlier: 3.548A pdb=" N TRP H 375 " --> pdb=" O SER H 371 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL H 382 " --> pdb=" O TRP H 378 " (cutoff:3.500A) Processing helix chain 'H' and resid 387 through 399 Processing helix chain 'H' and resid 408 through 417 Processing helix chain 'I' and resid 45 through 55 Processing helix chain 'I' and resid 63 through 76 Processing helix chain 'I' and resid 127 through 130 removed outlier: 3.842A pdb=" N ALA I 130 " --> pdb=" O GLU I 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 127 through 130' Processing helix chain 'I' and resid 131 through 144 removed outlier: 3.611A pdb=" N ARG I 141 " --> pdb=" O LEU I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 162 removed outlier: 3.844A pdb=" N MET I 155 " --> pdb=" O ARG I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 185 Processing helix chain 'I' and resid 186 through 203 removed outlier: 3.501A pdb=" N HIS I 202 " --> pdb=" O MET I 198 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE I 203 " --> pdb=" O PHE I 199 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.533A pdb=" N ALA I 209 " --> pdb=" O SER I 206 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR I 210 " --> pdb=" O ILE I 207 " (cutoff:3.500A) Processing helix chain 'I' and resid 215 through 219 Processing helix chain 'I' and resid 223 through 237 removed outlier: 3.975A pdb=" N ALA I 227 " --> pdb=" O CYS I 223 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR I 236 " --> pdb=" O VAL I 232 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY I 237 " --> pdb=" O VAL I 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 239 through 246 Processing helix chain 'I' and resid 249 through 260 Processing helix chain 'I' and resid 299 through 306 Processing helix chain 'I' and resid 310 through 314 removed outlier: 3.581A pdb=" N ALA I 314 " --> pdb=" O ALA I 311 " (cutoff:3.500A) Processing helix chain 'I' and resid 321 through 339 removed outlier: 3.734A pdb=" N ILE I 325 " --> pdb=" O ASP I 321 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER I 339 " --> pdb=" O ALA I 335 " (cutoff:3.500A) Processing helix chain 'I' and resid 371 through 382 removed outlier: 3.548A pdb=" N TRP I 375 " --> pdb=" O SER I 371 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL I 382 " --> pdb=" O TRP I 378 " (cutoff:3.500A) Processing helix chain 'I' and resid 387 through 399 Processing helix chain 'I' and resid 408 through 417 Processing helix chain 'J' and resid 45 through 55 Processing helix chain 'J' and resid 63 through 76 Processing helix chain 'J' and resid 127 through 130 removed outlier: 3.842A pdb=" N ALA J 130 " --> pdb=" O GLU J 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 127 through 130' Processing helix chain 'J' and resid 131 through 144 removed outlier: 3.611A pdb=" N ARG J 141 " --> pdb=" O LEU J 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 162 removed outlier: 3.843A pdb=" N MET J 155 " --> pdb=" O ARG J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 185 Processing helix chain 'J' and resid 186 through 203 removed outlier: 3.501A pdb=" N HIS J 202 " --> pdb=" O MET J 198 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE J 203 " --> pdb=" O PHE J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 213 removed outlier: 3.533A pdb=" N ALA J 209 " --> pdb=" O SER J 206 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR J 210 " --> pdb=" O ILE J 207 " (cutoff:3.500A) Processing helix chain 'J' and resid 215 through 219 Processing helix chain 'J' and resid 223 through 237 removed outlier: 3.975A pdb=" N ALA J 227 " --> pdb=" O CYS J 223 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR J 236 " --> pdb=" O VAL J 232 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY J 237 " --> pdb=" O VAL J 233 " (cutoff:3.500A) Processing helix chain 'J' and resid 239 through 246 Processing helix chain 'J' and resid 249 through 260 Processing helix chain 'J' and resid 299 through 306 Processing helix chain 'J' and resid 310 through 314 removed outlier: 3.581A pdb=" N ALA J 314 " --> pdb=" O ALA J 311 " (cutoff:3.500A) Processing helix chain 'J' and resid 321 through 339 removed outlier: 3.734A pdb=" N ILE J 325 " --> pdb=" O ASP J 321 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER J 339 " --> pdb=" O ALA J 335 " (cutoff:3.500A) Processing helix chain 'J' and resid 371 through 382 removed outlier: 3.549A pdb=" N TRP J 375 " --> pdb=" O SER J 371 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL J 382 " --> pdb=" O TRP J 378 " (cutoff:3.500A) Processing helix chain 'J' and resid 387 through 399 Processing helix chain 'J' and resid 408 through 417 Processing helix chain 'K' and resid 45 through 55 Processing helix chain 'K' and resid 63 through 76 Processing helix chain 'K' and resid 127 through 130 removed outlier: 3.842A pdb=" N ALA K 130 " --> pdb=" O GLU K 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 127 through 130' Processing helix chain 'K' and resid 131 through 144 removed outlier: 3.611A pdb=" N ARG K 141 " --> pdb=" O LEU K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 151 through 162 removed outlier: 3.843A pdb=" N MET K 155 " --> pdb=" O ARG K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 180 through 185 Processing helix chain 'K' and resid 186 through 203 removed outlier: 3.502A pdb=" N HIS K 202 " --> pdb=" O MET K 198 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE K 203 " --> pdb=" O PHE K 199 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 213 removed outlier: 3.532A pdb=" N ALA K 209 " --> pdb=" O SER K 206 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR K 210 " --> pdb=" O ILE K 207 " (cutoff:3.500A) Processing helix chain 'K' and resid 215 through 219 Processing helix chain 'K' and resid 223 through 237 removed outlier: 3.975A pdb=" N ALA K 227 " --> pdb=" O CYS K 223 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR K 236 " --> pdb=" O VAL K 232 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY K 237 " --> pdb=" O VAL K 233 " (cutoff:3.500A) Processing helix chain 'K' and resid 239 through 246 Processing helix chain 'K' and resid 249 through 260 Processing helix chain 'K' and resid 299 through 306 Processing helix chain 'K' and resid 310 through 314 removed outlier: 3.581A pdb=" N ALA K 314 " --> pdb=" O ALA K 311 " (cutoff:3.500A) Processing helix chain 'K' and resid 321 through 339 removed outlier: 3.735A pdb=" N ILE K 325 " --> pdb=" O ASP K 321 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER K 339 " --> pdb=" O ALA K 335 " (cutoff:3.500A) Processing helix chain 'K' and resid 371 through 382 removed outlier: 3.548A pdb=" N TRP K 375 " --> pdb=" O SER K 371 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL K 382 " --> pdb=" O TRP K 378 " (cutoff:3.500A) Processing helix chain 'K' and resid 387 through 399 Processing helix chain 'K' and resid 408 through 417 Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 88 removed outlier: 6.952A pdb=" N TRP A 86 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A 88 " --> pdb=" O HIS A 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 86 through 88 removed outlier: 6.952A pdb=" N TRP B 86 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B 88 " --> pdb=" O HIS B 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 86 through 88 removed outlier: 6.952A pdb=" N TRP C 86 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER C 88 " --> pdb=" O HIS C 91 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 86 through 88 removed outlier: 6.952A pdb=" N TRP D 86 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER D 88 " --> pdb=" O HIS D 91 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 86 through 88 removed outlier: 6.951A pdb=" N TRP E 86 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER E 88 " --> pdb=" O HIS E 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 86 through 88 removed outlier: 6.952A pdb=" N TRP F 86 " --> pdb=" O ILE F 93 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER F 88 " --> pdb=" O HIS F 91 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 86 through 88 removed outlier: 6.952A pdb=" N TRP G 86 " --> pdb=" O ILE G 93 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER G 88 " --> pdb=" O HIS G 91 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 86 through 88 removed outlier: 6.952A pdb=" N TRP H 86 " --> pdb=" O ILE H 93 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER H 88 " --> pdb=" O HIS H 91 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 86 through 88 removed outlier: 6.952A pdb=" N TRP I 86 " --> pdb=" O ILE I 93 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER I 88 " --> pdb=" O HIS I 91 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 86 through 88 removed outlier: 6.951A pdb=" N TRP J 86 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER J 88 " --> pdb=" O HIS J 91 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 86 through 88 removed outlier: 6.952A pdb=" N TRP K 86 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER K 88 " --> pdb=" O HIS K 91 " (cutoff:3.500A) 1254 hydrogen bonds defined for protein. 3432 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 6.64 Time building geometry restraints manager: 4.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7628 1.33 - 1.45: 9682 1.45 - 1.57: 21243 1.57 - 1.69: 196 1.69 - 1.81: 319 Bond restraints: 39068 Sorted by residual: bond pdb=" SD MET H 279 " pdb=" CE MET H 279 " ideal model delta sigma weight residual 1.791 1.743 0.048 2.50e-02 1.60e+03 3.65e+00 bond pdb=" SD MET F 279 " pdb=" CE MET F 279 " ideal model delta sigma weight residual 1.791 1.743 0.048 2.50e-02 1.60e+03 3.63e+00 bond pdb=" SD MET D 279 " pdb=" CE MET D 279 " ideal model delta sigma weight residual 1.791 1.744 0.047 2.50e-02 1.60e+03 3.56e+00 bond pdb=" SD MET I 279 " pdb=" CE MET I 279 " ideal model delta sigma weight residual 1.791 1.744 0.047 2.50e-02 1.60e+03 3.55e+00 bond pdb=" SD MET B 279 " pdb=" CE MET B 279 " ideal model delta sigma weight residual 1.791 1.744 0.047 2.50e-02 1.60e+03 3.54e+00 ... (remaining 39063 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 51953 2.07 - 4.14: 1145 4.14 - 6.21: 167 6.21 - 8.29: 55 8.29 - 10.36: 44 Bond angle restraints: 53364 Sorted by residual: angle pdb=" C ARG F 353 " pdb=" N LYS F 354 " pdb=" CA LYS F 354 " ideal model delta sigma weight residual 121.80 130.22 -8.42 2.44e+00 1.68e-01 1.19e+01 angle pdb=" C ARG C 353 " pdb=" N LYS C 354 " pdb=" CA LYS C 354 " ideal model delta sigma weight residual 121.80 130.21 -8.41 2.44e+00 1.68e-01 1.19e+01 angle pdb=" C ARG B 353 " pdb=" N LYS B 354 " pdb=" CA LYS B 354 " ideal model delta sigma weight residual 121.80 130.20 -8.40 2.44e+00 1.68e-01 1.18e+01 angle pdb=" C ARG I 353 " pdb=" N LYS I 354 " pdb=" CA LYS I 354 " ideal model delta sigma weight residual 121.80 130.20 -8.40 2.44e+00 1.68e-01 1.18e+01 angle pdb=" C ARG A 353 " pdb=" N LYS A 354 " pdb=" CA LYS A 354 " ideal model delta sigma weight residual 121.80 130.20 -8.40 2.44e+00 1.68e-01 1.18e+01 ... (remaining 53359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.72: 22475 34.72 - 69.44: 1157 69.44 - 104.16: 40 104.16 - 138.88: 4 138.88 - 173.60: 12 Dihedral angle restraints: 23688 sinusoidal: 10422 harmonic: 13266 Sorted by residual: dihedral pdb=" O4' U U 95 " pdb=" C1' U U 95 " pdb=" N1 U U 95 " pdb=" C2 U U 95 " ideal model delta sinusoidal sigma weight residual -160.00 13.60 -173.60 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' U U 97 " pdb=" C1' U U 97 " pdb=" N1 U U 97 " pdb=" C2 U U 97 " ideal model delta sinusoidal sigma weight residual 200.00 26.52 173.48 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' U U 5 " pdb=" C1' U U 5 " pdb=" N1 U U 5 " pdb=" C2 U U 5 " ideal model delta sinusoidal sigma weight residual -160.00 12.68 -172.68 1 1.50e+01 4.44e-03 8.50e+01 ... (remaining 23685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4079 0.045 - 0.090: 1497 0.090 - 0.135: 297 0.135 - 0.180: 48 0.180 - 0.224: 40 Chirality restraints: 5961 Sorted by residual: chirality pdb=" CG LEU D 132 " pdb=" CB LEU D 132 " pdb=" CD1 LEU D 132 " pdb=" CD2 LEU D 132 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CG LEU C 132 " pdb=" CB LEU C 132 " pdb=" CD1 LEU C 132 " pdb=" CD2 LEU C 132 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CG LEU F 132 " pdb=" CB LEU F 132 " pdb=" CD1 LEU F 132 " pdb=" CD2 LEU F 132 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 5958 not shown) Planarity restraints: 6479 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU K 16 " 0.070 5.00e-02 4.00e+02 1.05e-01 1.75e+01 pdb=" N PRO K 17 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO K 17 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO K 17 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G 16 " -0.070 5.00e-02 4.00e+02 1.05e-01 1.75e+01 pdb=" N PRO G 17 " 0.181 5.00e-02 4.00e+02 pdb=" CA PRO G 17 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO G 17 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 16 " 0.070 5.00e-02 4.00e+02 1.05e-01 1.75e+01 pdb=" N PRO B 17 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO B 17 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 17 " 0.056 5.00e-02 4.00e+02 ... (remaining 6476 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 396 2.63 - 3.20: 32506 3.20 - 3.77: 58402 3.77 - 4.33: 79342 4.33 - 4.90: 126441 Nonbonded interactions: 297087 Sorted by model distance: nonbonded pdb=" O2' U U 38 " pdb=" O5' U U 39 " model vdw 2.065 3.040 nonbonded pdb=" O2' U U 38 " pdb=" O4' U U 39 " model vdw 2.221 3.040 nonbonded pdb=" O2' U U 41 " pdb=" OP1 U U 43 " model vdw 2.235 3.040 nonbonded pdb=" N THR A 289 " pdb=" OP2 U U 76 " model vdw 2.293 3.120 nonbonded pdb=" OH TYR F 150 " pdb=" OP2 U U 26 " model vdw 2.304 3.040 ... (remaining 297082 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } 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 group one per residue 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: 0.210 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: 0.030 Extract box with map and model: 0.510 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 37.030 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 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 0.060 39068 Z= 0.210 Angle : 0.796 10.357 53364 Z= 0.415 Chirality : 0.050 0.224 5961 Planarity : 0.007 0.105 6479 Dihedral : 18.894 173.599 15174 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 1.00 % Allowed : 26.99 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.57 (0.11), residues: 4532 helix: -1.01 (0.10), residues: 2002 sheet: None (None), residues: 0 loop : -2.37 (0.11), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 37 TYR 0.054 0.003 TYR F 70 PHE 0.029 0.002 PHE B 180 TRP 0.020 0.002 TRP C 183 HIS 0.002 0.001 HIS G 177 Details of bonding type rmsd covalent geometry : bond 0.00446 (39068) covalent geometry : angle 0.79568 (53364) hydrogen bonds : bond 0.15541 ( 1254) hydrogen bonds : angle 5.09380 ( 3432) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 525 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 342 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8575 (mt) REVERT: A 368 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7568 (mmmt) REVERT: C 37 ARG cc_start: 0.6995 (mmt90) cc_final: 0.6600 (mtm-85) REVERT: C 260 MET cc_start: 0.8099 (mmt) cc_final: 0.7638 (mmm) REVERT: C 342 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8870 (mt) REVERT: D 342 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8338 (mt) REVERT: D 396 ARG cc_start: 0.8206 (ttp-110) cc_final: 0.7951 (ttp-170) REVERT: E 342 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8728 (mt) REVERT: F 37 ARG cc_start: 0.6950 (mmt90) cc_final: 0.6678 (mtm-85) REVERT: F 342 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8507 (mt) REVERT: F 368 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7396 (mmmt) REVERT: F 396 ARG cc_start: 0.8170 (ttp-110) cc_final: 0.7763 (ttp80) REVERT: G 342 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8451 (mt) REVERT: H 9 ASN cc_start: 0.6212 (OUTLIER) cc_final: 0.5851 (p0) REVERT: I 9 ASN cc_start: 0.6219 (OUTLIER) cc_final: 0.5775 (p0) REVERT: J 27 SER cc_start: 0.8028 (t) cc_final: 0.7681 (t) REVERT: J 200 TYR cc_start: 0.7360 (m-10) cc_final: 0.7141 (m-10) REVERT: J 259 MET cc_start: 0.8747 (ttp) cc_final: 0.8371 (ttp) REVERT: J 368 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7867 (mttm) REVERT: K 259 MET cc_start: 0.8590 (ttp) cc_final: 0.8365 (ttp) REVERT: K 319 GLU cc_start: 0.6497 (tt0) cc_final: 0.6254 (tt0) REVERT: K 368 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7713 (mmmt) outliers start: 39 outliers final: 4 residues processed: 536 average time/residue: 0.2398 time to fit residues: 205.3327 Evaluate side-chains 458 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 442 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASN Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 368 LYS Chi-restraints excluded: chain G residue 342 ILE Chi-restraints excluded: chain H residue 9 ASN Chi-restraints excluded: chain I residue 9 ASN Chi-restraints excluded: chain I residue 267 ASP Chi-restraints excluded: chain J residue 368 LYS Chi-restraints excluded: chain K residue 368 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 0.3980 chunk 401 optimal weight: 5.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN A 66 HIS ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 GLN G 66 HIS ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 9 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.172743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.152136 restraints weight = 46919.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.148368 restraints weight = 73432.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.145476 restraints weight = 79210.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.144299 restraints weight = 95874.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.142895 restraints weight = 84678.442| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 39068 Z= 0.158 Angle : 0.583 9.523 53364 Z= 0.311 Chirality : 0.044 0.332 5961 Planarity : 0.005 0.073 6479 Dihedral : 15.203 175.662 6579 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 2.50 % Allowed : 24.41 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.87 (0.12), residues: 4532 helix: -0.26 (0.11), residues: 2123 sheet: None (None), residues: 0 loop : -2.22 (0.12), residues: 2409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 50 TYR 0.039 0.002 TYR I 52 PHE 0.018 0.002 PHE J 211 TRP 0.011 0.001 TRP K 298 HIS 0.003 0.001 HIS G 66 Details of bonding type rmsd covalent geometry : bond 0.00362 (39068) covalent geometry : angle 0.58274 (53364) hydrogen bonds : bond 0.04470 ( 1254) hydrogen bonds : angle 3.99797 ( 3432) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 458 time to evaluate : 1.582 Fit side-chains REVERT: A 249 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7054 (mt0) REVERT: A 332 MET cc_start: 0.8609 (ttt) cc_final: 0.8097 (ttt) REVERT: A 368 LYS cc_start: 0.8118 (mmtm) cc_final: 0.7730 (mmmt) REVERT: B 60 LYS cc_start: 0.6376 (mmtm) cc_final: 0.5997 (mmtm) REVERT: B 70 TYR cc_start: 0.6382 (t80) cc_final: 0.5956 (t80) REVERT: B 249 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7522 (mp10) REVERT: B 271 SER cc_start: 0.8650 (t) cc_final: 0.8450 (t) REVERT: C 249 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.7139 (mt0) REVERT: C 381 ASP cc_start: 0.7547 (t70) cc_final: 0.7198 (t0) REVERT: D 249 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8240 (mm-40) REVERT: E 63 ARG cc_start: 0.6322 (tpp-160) cc_final: 0.6070 (tpp-160) REVERT: E 249 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7971 (mm-40) REVERT: E 342 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8767 (mt) REVERT: E 390 MET cc_start: 0.9174 (mtp) cc_final: 0.8971 (mtm) REVERT: F 249 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7089 (mt0) REVERT: F 260 MET cc_start: 0.8680 (mmt) cc_final: 0.8210 (mmt) REVERT: G 24 ASP cc_start: 0.6761 (OUTLIER) cc_final: 0.6413 (t0) REVERT: G 249 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8197 (mm-40) REVERT: H 9 ASN cc_start: 0.6216 (OUTLIER) cc_final: 0.5748 (p0) REVERT: H 249 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7873 (mm-40) REVERT: I 9 ASN cc_start: 0.5708 (OUTLIER) cc_final: 0.5301 (p0) REVERT: I 249 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7555 (mp10) REVERT: I 259 MET cc_start: 0.8527 (ttp) cc_final: 0.8316 (ttp) REVERT: I 381 ASP cc_start: 0.7948 (t70) cc_final: 0.7640 (t0) REVERT: J 249 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7178 (mt0) REVERT: J 259 MET cc_start: 0.8749 (ttp) cc_final: 0.8459 (ttp) REVERT: J 260 MET cc_start: 0.8792 (mmt) cc_final: 0.8580 (mmm) REVERT: J 368 LYS cc_start: 0.8425 (mmtt) cc_final: 0.8041 (mttm) REVERT: J 390 MET cc_start: 0.8993 (mtp) cc_final: 0.8725 (mtm) REVERT: K 249 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.8061 (mm-40) REVERT: K 259 MET cc_start: 0.8512 (ttp) cc_final: 0.8284 (ttp) REVERT: K 368 LYS cc_start: 0.8306 (mmtt) cc_final: 0.8040 (mptt) outliers start: 97 outliers final: 28 residues processed: 538 average time/residue: 0.2154 time to fit residues: 194.6033 Evaluate side-chains 464 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 421 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 249 GLN Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain E residue 9 ASN Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 259 MET Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 9 ASN Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 249 GLN Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 249 GLN Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain H residue 9 ASN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 235 ILE Chi-restraints excluded: chain H residue 249 GLN Chi-restraints excluded: chain I residue 9 ASN Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 249 GLN Chi-restraints excluded: chain I residue 363 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 249 GLN Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 249 GLN Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 408 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 421 optimal weight: 40.0000 chunk 93 optimal weight: 40.0000 chunk 344 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 427 optimal weight: 10.0000 chunk 354 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 159 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 187 optimal weight: 4.9990 chunk 380 optimal weight: 30.0000 overall best weight: 8.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 GLN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN C 51 GLN ** C 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 GLN ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 GLN ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 188 ASN ** H 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 GLN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 51 GLN J 51 GLN K 51 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.166073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.144722 restraints weight = 46987.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.140764 restraints weight = 82271.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.138721 restraints weight = 82465.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.137078 restraints weight = 96294.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.135292 restraints weight = 93331.971| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.076 39068 Z= 0.408 Angle : 0.816 10.111 53364 Z= 0.434 Chirality : 0.055 0.352 5961 Planarity : 0.007 0.076 6479 Dihedral : 15.393 178.458 6545 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.44 % Favored : 87.56 % Rotamer: Outliers : 5.12 % Allowed : 23.38 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.48 (0.11), residues: 4532 helix: -0.81 (0.11), residues: 2123 sheet: None (None), residues: 0 loop : -2.51 (0.11), residues: 2409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 396 TYR 0.034 0.003 TYR J 140 PHE 0.036 0.004 PHE F 29 TRP 0.018 0.003 TRP I 412 HIS 0.006 0.002 HIS G 177 Details of bonding type rmsd covalent geometry : bond 0.00968 (39068) covalent geometry : angle 0.81555 (53364) hydrogen bonds : bond 0.07015 ( 1254) hydrogen bonds : angle 4.75446 ( 3432) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 443 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7182 (mm) REVERT: A 198 MET cc_start: 0.7117 (ttt) cc_final: 0.6530 (ttm) REVERT: A 249 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.7380 (mt0) REVERT: A 343 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7793 (tt0) REVERT: A 368 LYS cc_start: 0.8207 (mmtm) cc_final: 0.7833 (mmtt) REVERT: B 60 LYS cc_start: 0.6653 (mmtm) cc_final: 0.6314 (mmtm) REVERT: B 81 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7168 (mm) REVERT: B 87 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7297 (t0) REVERT: B 249 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8085 (mp10) REVERT: C 16 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8148 (pp) REVERT: C 70 TYR cc_start: 0.7141 (t80) cc_final: 0.6877 (t80) REVERT: C 81 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.6997 (mm) REVERT: C 87 ASP cc_start: 0.7445 (OUTLIER) cc_final: 0.7172 (m-30) REVERT: C 249 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.7631 (mt0) REVERT: C 343 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7827 (tt0) REVERT: C 392 MET cc_start: 0.6976 (ttm) cc_final: 0.6721 (ttp) REVERT: D 70 TYR cc_start: 0.7077 (t80) cc_final: 0.6649 (t80) REVERT: D 81 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7065 (mm) REVERT: D 105 LEU cc_start: 0.4585 (OUTLIER) cc_final: 0.4215 (mt) REVERT: D 249 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.7824 (mt0) REVERT: D 343 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: E 70 TYR cc_start: 0.6929 (t80) cc_final: 0.6675 (t80) REVERT: E 105 LEU cc_start: 0.4766 (OUTLIER) cc_final: 0.4405 (mt) REVERT: F 60 LYS cc_start: 0.6478 (mmtm) cc_final: 0.6114 (mmtm) REVERT: F 81 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.6842 (mm) REVERT: F 249 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.7629 (mt0) REVERT: F 273 MET cc_start: 0.7428 (tmm) cc_final: 0.7123 (tmm) REVERT: F 343 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7727 (tt0) REVERT: G 70 TYR cc_start: 0.6875 (t80) cc_final: 0.6550 (t80) REVERT: G 81 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.6733 (mm) REVERT: G 87 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.7679 (m-30) REVERT: G 105 LEU cc_start: 0.5178 (OUTLIER) cc_final: 0.4914 (mt) REVERT: G 192 ILE cc_start: 0.7746 (mt) cc_final: 0.7538 (mm) REVERT: H 70 TYR cc_start: 0.7018 (t80) cc_final: 0.6669 (t80) REVERT: H 81 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7584 (mm) REVERT: H 105 LEU cc_start: 0.5186 (OUTLIER) cc_final: 0.4844 (mt) REVERT: H 249 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8135 (mm-40) REVERT: I 70 TYR cc_start: 0.6999 (t80) cc_final: 0.6726 (t80) REVERT: I 81 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.6744 (mm) REVERT: I 249 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.7460 (mt0) REVERT: I 259 MET cc_start: 0.8602 (ttp) cc_final: 0.8359 (ttp) REVERT: I 343 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7823 (tt0) REVERT: J 81 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.6963 (mm) REVERT: J 249 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.7584 (mt0) REVERT: J 279 MET cc_start: 0.7403 (mmt) cc_final: 0.6992 (mmm) REVERT: J 368 LYS cc_start: 0.8479 (mmtt) cc_final: 0.7841 (mmmt) REVERT: J 390 MET cc_start: 0.9044 (mtp) cc_final: 0.8777 (mtm) REVERT: K 70 TYR cc_start: 0.6791 (t80) cc_final: 0.6566 (t80) REVERT: K 81 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7001 (mm) REVERT: K 249 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8260 (mm-40) REVERT: K 368 LYS cc_start: 0.8521 (mmtt) cc_final: 0.8101 (mptt) outliers start: 199 outliers final: 104 residues processed: 603 average time/residue: 0.2253 time to fit residues: 223.9311 Evaluate side-chains 543 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 407 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASN Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 249 GLN Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 393 MET Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain E residue 9 ASN Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 259 MET Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain F residue 9 ASN Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 107 ARG Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 249 GLN Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 343 GLU Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 107 ARG Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 207 ILE Chi-restraints excluded: chain G residue 235 ILE Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain H residue 235 ILE Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 249 GLN Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 249 GLN Chi-restraints excluded: chain I residue 250 THR Chi-restraints excluded: chain I residue 343 GLU Chi-restraints excluded: chain I residue 408 SER Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 ASP Chi-restraints excluded: chain J residue 107 ARG Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain J residue 235 ILE Chi-restraints excluded: chain J residue 249 GLN Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 176 THR Chi-restraints excluded: chain K residue 207 ILE Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain K residue 249 GLN Chi-restraints excluded: chain K residue 408 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 335 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 232 optimal weight: 2.9990 chunk 289 optimal weight: 8.9990 chunk 202 optimal weight: 0.6980 chunk 272 optimal weight: 2.9990 chunk 329 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 170 optimal weight: 10.0000 chunk 256 optimal weight: 10.0000 chunk 354 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.170011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.149435 restraints weight = 46706.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.145627 restraints weight = 74615.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.142752 restraints weight = 87218.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.141516 restraints weight = 104447.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.139564 restraints weight = 96293.302| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 39068 Z= 0.164 Angle : 0.602 9.621 53364 Z= 0.321 Chirality : 0.045 0.342 5961 Planarity : 0.005 0.085 6479 Dihedral : 15.037 178.595 6539 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 4.04 % Allowed : 24.39 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.12), residues: 4532 helix: -0.24 (0.11), residues: 2112 sheet: None (None), residues: 0 loop : -2.32 (0.12), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 37 TYR 0.044 0.002 TYR K 52 PHE 0.016 0.002 PHE K 295 TRP 0.011 0.002 TRP G 246 HIS 0.003 0.001 HIS H 231 Details of bonding type rmsd covalent geometry : bond 0.00377 (39068) covalent geometry : angle 0.60213 (53364) hydrogen bonds : bond 0.04483 ( 1254) hydrogen bonds : angle 4.13532 ( 3432) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 444 time to evaluate : 1.463 Fit side-chains REVERT: A 81 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7202 (mm) REVERT: A 249 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.6886 (mt0) REVERT: A 332 MET cc_start: 0.9014 (ttt) cc_final: 0.8293 (ttt) REVERT: A 368 LYS cc_start: 0.8158 (mmtm) cc_final: 0.7744 (mmmt) REVERT: B 87 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7409 (t0) REVERT: B 105 LEU cc_start: 0.4519 (OUTLIER) cc_final: 0.4248 (mt) REVERT: B 249 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7760 (mp10) REVERT: C 81 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7005 (mm) REVERT: C 249 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.7228 (mt0) REVERT: D 81 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7101 (mm) REVERT: D 107 ARG cc_start: 0.5928 (OUTLIER) cc_final: 0.5461 (ptp-170) REVERT: D 151 ARG cc_start: 0.6494 (mmt180) cc_final: 0.6059 (mmt180) REVERT: D 249 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8343 (mm-40) REVERT: D 343 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7898 (tt0) REVERT: E 107 ARG cc_start: 0.5517 (OUTLIER) cc_final: 0.5156 (ptp-170) REVERT: E 249 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7968 (mm-40) REVERT: E 342 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8716 (mt) REVERT: F 81 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.6912 (mm) REVERT: F 105 LEU cc_start: 0.5401 (OUTLIER) cc_final: 0.5006 (mt) REVERT: F 159 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7879 (tt) REVERT: F 249 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7147 (mt0) REVERT: F 343 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7815 (tt0) REVERT: G 37 ARG cc_start: 0.7312 (mmt90) cc_final: 0.7024 (mmt180) REVERT: G 81 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.6814 (mm) REVERT: G 87 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7625 (m-30) REVERT: G 192 ILE cc_start: 0.7788 (mt) cc_final: 0.7558 (mm) REVERT: G 249 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8288 (mm-40) REVERT: H 81 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7581 (mm) REVERT: H 249 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.8052 (mm-40) REVERT: H 326 SER cc_start: 0.8757 (OUTLIER) cc_final: 0.8461 (m) REVERT: I 81 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.6785 (mm) REVERT: I 105 LEU cc_start: 0.5188 (OUTLIER) cc_final: 0.4834 (mt) REVERT: I 249 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7527 (mp10) REVERT: I 259 MET cc_start: 0.8594 (ttp) cc_final: 0.8379 (ttp) REVERT: J 81 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7019 (mm) REVERT: J 105 LEU cc_start: 0.5833 (OUTLIER) cc_final: 0.5513 (mt) REVERT: J 249 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8144 (mm-40) REVERT: J 326 SER cc_start: 0.8529 (OUTLIER) cc_final: 0.8137 (m) REVERT: J 368 LYS cc_start: 0.8487 (mmtt) cc_final: 0.7772 (mmmt) REVERT: J 390 MET cc_start: 0.8977 (mtp) cc_final: 0.8699 (mtm) REVERT: K 9 ASN cc_start: 0.7042 (OUTLIER) cc_final: 0.6406 (p0) REVERT: K 70 TYR cc_start: 0.6614 (t80) cc_final: 0.6315 (t80) REVERT: K 81 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7028 (mm) REVERT: K 249 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8223 (mm-40) REVERT: K 368 LYS cc_start: 0.8467 (mmtt) cc_final: 0.8032 (mptt) outliers start: 157 outliers final: 75 residues processed: 569 average time/residue: 0.2142 time to fit residues: 203.0353 Evaluate side-chains 521 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 412 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 249 GLN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain E residue 9 ASN Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain E residue 107 ARG Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 259 MET Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain F residue 9 ASN Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 107 ARG Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 249 GLN Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 343 GLU Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 107 ARG Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 235 ILE Chi-restraints excluded: chain G residue 249 GLN Chi-restraints excluded: chain G residue 332 MET Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 107 ARG Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 235 ILE Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 249 GLN Chi-restraints excluded: chain H residue 326 SER Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain I residue 9 ASN Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 107 ARG Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 249 GLN Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 ASP Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 107 ARG Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain J residue 178 LYS Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain J residue 235 ILE Chi-restraints excluded: chain J residue 249 GLN Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain K residue 9 ASN Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 174 THR Chi-restraints excluded: chain K residue 176 THR Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 249 GLN Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain K residue 408 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 318 optimal weight: 8.9990 chunk 241 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 255 optimal weight: 1.9990 chunk 400 optimal weight: 0.0170 chunk 332 optimal weight: 20.0000 chunk 264 optimal weight: 5.9990 chunk 246 optimal weight: 8.9990 chunk 398 optimal weight: 0.8980 chunk 200 optimal weight: 9.9990 chunk 357 optimal weight: 2.9990 overall best weight: 2.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.171509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.151540 restraints weight = 46742.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.147517 restraints weight = 74509.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.145618 restraints weight = 79664.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.144645 restraints weight = 95308.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.142784 restraints weight = 92623.945| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 39068 Z= 0.142 Angle : 0.569 10.977 53364 Z= 0.301 Chirality : 0.044 0.330 5961 Planarity : 0.005 0.089 6479 Dihedral : 14.763 178.885 6539 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.21 % Favored : 88.79 % Rotamer: Outliers : 4.64 % Allowed : 24.41 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.12), residues: 4532 helix: 0.07 (0.12), residues: 2101 sheet: None (None), residues: 0 loop : -2.25 (0.12), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 37 TYR 0.039 0.002 TYR K 52 PHE 0.016 0.001 PHE K 295 TRP 0.008 0.001 TRP G 246 HIS 0.002 0.001 HIS K 177 Details of bonding type rmsd covalent geometry : bond 0.00327 (39068) covalent geometry : angle 0.56902 (53364) hydrogen bonds : bond 0.04060 ( 1254) hydrogen bonds : angle 3.92089 ( 3432) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 445 time to evaluate : 1.593 Fit side-chains REVERT: A 249 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.6929 (mt0) REVERT: A 332 MET cc_start: 0.8882 (ttt) cc_final: 0.8412 (ttt) REVERT: A 368 LYS cc_start: 0.8080 (mmtm) cc_final: 0.7731 (mmmt) REVERT: B 81 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7267 (mm) REVERT: B 87 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7427 (t0) REVERT: B 105 LEU cc_start: 0.4453 (OUTLIER) cc_final: 0.4235 (mt) REVERT: B 188 ASN cc_start: 0.8181 (m-40) cc_final: 0.7873 (m-40) REVERT: B 249 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7470 (mp10) REVERT: C 81 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7027 (mm) REVERT: C 87 ASP cc_start: 0.7441 (OUTLIER) cc_final: 0.7104 (m-30) REVERT: C 249 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.7168 (mt0) REVERT: D 60 LYS cc_start: 0.6999 (mmtm) cc_final: 0.6719 (mmtm) REVERT: D 107 ARG cc_start: 0.5921 (OUTLIER) cc_final: 0.5278 (ptp-170) REVERT: E 107 ARG cc_start: 0.5601 (OUTLIER) cc_final: 0.5344 (ptp-170) REVERT: E 180 PHE cc_start: 0.7202 (p90) cc_final: 0.6970 (p90) REVERT: E 249 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7909 (mm-40) REVERT: E 342 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8740 (mt) REVERT: F 70 TYR cc_start: 0.6639 (t80) cc_final: 0.6098 (t80) REVERT: F 81 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.6892 (mm) REVERT: F 105 LEU cc_start: 0.5350 (OUTLIER) cc_final: 0.4953 (mt) REVERT: F 249 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.6927 (mt0) REVERT: F 343 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7781 (tt0) REVERT: G 87 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7556 (m-30) REVERT: G 105 LEU cc_start: 0.5065 (OUTLIER) cc_final: 0.4855 (mt) REVERT: G 211 PHE cc_start: 0.7906 (m-80) cc_final: 0.7648 (m-80) REVERT: G 249 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8257 (mm-40) REVERT: G 343 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7721 (tt0) REVERT: H 70 TYR cc_start: 0.6610 (t80) cc_final: 0.6127 (t80) REVERT: H 81 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7526 (mm) REVERT: H 159 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7764 (tt) REVERT: I 37 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.7070 (mpt-90) REVERT: I 81 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.6764 (mm) REVERT: I 105 LEU cc_start: 0.5116 (OUTLIER) cc_final: 0.4826 (mt) REVERT: I 249 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7718 (mp10) REVERT: I 259 MET cc_start: 0.8605 (ttp) cc_final: 0.8380 (ttp) REVERT: J 81 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.6991 (mm) REVERT: J 105 LEU cc_start: 0.5821 (OUTLIER) cc_final: 0.5553 (mt) REVERT: J 249 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7966 (mm-40) REVERT: J 279 MET cc_start: 0.7062 (mmt) cc_final: 0.6631 (mmm) REVERT: J 326 SER cc_start: 0.8500 (OUTLIER) cc_final: 0.8075 (m) REVERT: J 368 LYS cc_start: 0.8462 (mmtt) cc_final: 0.7712 (mmmt) REVERT: J 390 MET cc_start: 0.9005 (mtp) cc_final: 0.8733 (mtm) REVERT: K 9 ASN cc_start: 0.6870 (OUTLIER) cc_final: 0.6261 (p0) REVERT: K 81 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7014 (mm) REVERT: K 368 LYS cc_start: 0.8434 (mmtt) cc_final: 0.8019 (mptt) outliers start: 180 outliers final: 99 residues processed: 591 average time/residue: 0.2371 time to fit residues: 233.9317 Evaluate side-chains 548 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 417 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 249 GLN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 347 SER Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 393 MET Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain E residue 107 ARG Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 259 MET Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain F residue 9 ASN Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 107 ARG Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 249 GLN Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 343 GLU Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 235 ILE Chi-restraints excluded: chain G residue 249 GLN Chi-restraints excluded: chain G residue 332 MET Chi-restraints excluded: chain G residue 343 GLU Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 107 ARG Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 235 ILE Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 382 VAL Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain I residue 37 ARG Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 107 ARG Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 249 GLN Chi-restraints excluded: chain I residue 363 VAL Chi-restraints excluded: chain I residue 408 SER Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 ASP Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 107 ARG Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain J residue 178 LYS Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain J residue 235 ILE Chi-restraints excluded: chain J residue 249 GLN Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 347 SER Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain K residue 9 ASN Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 107 ARG Chi-restraints excluded: chain K residue 174 THR Chi-restraints excluded: chain K residue 176 THR Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 326 SER Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain K residue 408 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 110 optimal weight: 5.9990 chunk 352 optimal weight: 7.9990 chunk 179 optimal weight: 20.0000 chunk 450 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 193 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 286 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.172134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.151296 restraints weight = 46876.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.147210 restraints weight = 73581.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.145361 restraints weight = 83313.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.144037 restraints weight = 98736.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.141735 restraints weight = 95949.791| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 39068 Z= 0.135 Angle : 0.568 9.628 53364 Z= 0.298 Chirality : 0.043 0.326 5961 Planarity : 0.005 0.085 6479 Dihedral : 14.626 179.279 6539 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer: Outliers : 4.51 % Allowed : 24.36 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.12), residues: 4532 helix: 0.21 (0.12), residues: 2101 sheet: None (None), residues: 0 loop : -2.17 (0.12), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 37 TYR 0.036 0.002 TYR K 52 PHE 0.016 0.001 PHE K 295 TRP 0.011 0.001 TRP K 183 HIS 0.002 0.001 HIS K 231 Details of bonding type rmsd covalent geometry : bond 0.00308 (39068) covalent geometry : angle 0.56780 (53364) hydrogen bonds : bond 0.03903 ( 1254) hydrogen bonds : angle 3.83851 ( 3432) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 452 time to evaluate : 1.488 Fit side-chains REVERT: A 81 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7048 (mm) REVERT: A 249 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.6714 (mt0) REVERT: A 332 MET cc_start: 0.8881 (ttt) cc_final: 0.8427 (ttt) REVERT: A 368 LYS cc_start: 0.8050 (mmtm) cc_final: 0.7711 (mmmt) REVERT: B 81 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7235 (mm) REVERT: B 87 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7358 (t0) REVERT: B 105 LEU cc_start: 0.4594 (OUTLIER) cc_final: 0.4308 (mt) REVERT: B 188 ASN cc_start: 0.8227 (m-40) cc_final: 0.7858 (m-40) REVERT: B 249 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7577 (mm110) REVERT: B 271 SER cc_start: 0.8400 (t) cc_final: 0.8173 (t) REVERT: C 81 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7117 (mm) REVERT: C 87 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.7107 (m-30) REVERT: C 105 LEU cc_start: 0.5126 (OUTLIER) cc_final: 0.4638 (mt) REVERT: C 249 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.7193 (mt0) REVERT: D 60 LYS cc_start: 0.6520 (mmtm) cc_final: 0.4894 (mmmt) REVERT: D 81 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7100 (mm) REVERT: D 105 LEU cc_start: 0.4653 (OUTLIER) cc_final: 0.4245 (mt) REVERT: D 107 ARG cc_start: 0.5918 (OUTLIER) cc_final: 0.5234 (ptp-170) REVERT: D 343 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7858 (tt0) REVERT: E 107 ARG cc_start: 0.5586 (OUTLIER) cc_final: 0.5325 (ptp-170) REVERT: E 180 PHE cc_start: 0.7261 (p90) cc_final: 0.7012 (p90) REVERT: E 249 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7923 (mm-40) REVERT: E 342 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8718 (mt) REVERT: F 81 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.6840 (mm) REVERT: F 105 LEU cc_start: 0.5367 (OUTLIER) cc_final: 0.5004 (mt) REVERT: F 159 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7928 (tt) REVERT: F 249 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.6898 (mt0) REVERT: G 81 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7014 (mm) REVERT: G 87 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7560 (m-30) REVERT: G 105 LEU cc_start: 0.5065 (OUTLIER) cc_final: 0.4835 (mt) REVERT: G 211 PHE cc_start: 0.7937 (m-80) cc_final: 0.7692 (m-80) REVERT: G 249 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8195 (mm-40) REVERT: G 250 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8711 (m) REVERT: H 70 TYR cc_start: 0.6622 (t80) cc_final: 0.6342 (t80) REVERT: H 105 LEU cc_start: 0.4937 (OUTLIER) cc_final: 0.4642 (mt) REVERT: H 159 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7874 (tt) REVERT: H 326 SER cc_start: 0.8776 (OUTLIER) cc_final: 0.8478 (m) REVERT: I 37 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7084 (mpt-90) REVERT: I 81 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.6733 (mm) REVERT: I 105 LEU cc_start: 0.5238 (OUTLIER) cc_final: 0.4919 (mt) REVERT: I 249 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7735 (mp10) REVERT: I 259 MET cc_start: 0.8547 (ttp) cc_final: 0.8342 (ttp) REVERT: I 343 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7652 (tt0) REVERT: J 81 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.6989 (mm) REVERT: J 105 LEU cc_start: 0.5860 (OUTLIER) cc_final: 0.5554 (mt) REVERT: J 279 MET cc_start: 0.7006 (mmt) cc_final: 0.6768 (mmt) REVERT: J 326 SER cc_start: 0.8629 (OUTLIER) cc_final: 0.8146 (m) REVERT: J 368 LYS cc_start: 0.8456 (mmtt) cc_final: 0.7728 (mmmt) REVERT: J 390 MET cc_start: 0.8995 (mtp) cc_final: 0.8715 (mtm) REVERT: K 9 ASN cc_start: 0.6912 (OUTLIER) cc_final: 0.6374 (p0) REVERT: K 81 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7029 (mm) REVERT: K 273 MET cc_start: 0.7578 (tmm) cc_final: 0.7358 (tmm) REVERT: K 368 LYS cc_start: 0.8437 (mmtt) cc_final: 0.8027 (mptt) outliers start: 175 outliers final: 99 residues processed: 592 average time/residue: 0.2388 time to fit residues: 234.1194 Evaluate side-chains 560 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 422 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 249 GLN Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 107 ARG Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 259 MET Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 9 ASN Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 107 ARG Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 249 GLN Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 107 ARG Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 249 GLN Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 332 MET Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 107 ARG Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 235 ILE Chi-restraints excluded: chain H residue 259 MET Chi-restraints excluded: chain H residue 326 SER Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 382 VAL Chi-restraints excluded: chain I residue 37 ARG Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 107 ARG Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 249 GLN Chi-restraints excluded: chain I residue 343 GLU Chi-restraints excluded: chain I residue 363 VAL Chi-restraints excluded: chain I residue 408 SER Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 ASP Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 107 ARG Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain J residue 235 ILE Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 347 SER Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain K residue 9 ASN Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 107 ARG Chi-restraints excluded: chain K residue 174 THR Chi-restraints excluded: chain K residue 176 THR Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 326 SER Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain K residue 408 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 287 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 271 optimal weight: 9.9990 chunk 233 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 403 optimal weight: 5.9990 chunk 399 optimal weight: 6.9990 chunk 367 optimal weight: 6.9990 chunk 213 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.169024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.148726 restraints weight = 46782.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.145386 restraints weight = 78185.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.142896 restraints weight = 77286.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.141326 restraints weight = 94172.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.139550 restraints weight = 91054.145| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 39068 Z= 0.223 Angle : 0.639 9.825 53364 Z= 0.337 Chirality : 0.047 0.334 5961 Planarity : 0.005 0.094 6479 Dihedral : 14.791 179.161 6539 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.92 % Favored : 88.08 % Rotamer: Outliers : 4.97 % Allowed : 24.39 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.12), residues: 4532 helix: -0.12 (0.12), residues: 2145 sheet: None (None), residues: 0 loop : -2.26 (0.12), residues: 2387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 37 TYR 0.034 0.002 TYR K 52 PHE 0.021 0.002 PHE K 295 TRP 0.011 0.002 TRP K 298 HIS 0.004 0.001 HIS I 66 Details of bonding type rmsd covalent geometry : bond 0.00527 (39068) covalent geometry : angle 0.63905 (53364) hydrogen bonds : bond 0.04988 ( 1254) hydrogen bonds : angle 4.15958 ( 3432) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 437 time to evaluate : 1.465 Fit side-chains revert: symmetry clash REVERT: A 60 LYS cc_start: 0.7347 (mmtm) cc_final: 0.7100 (mmtm) REVERT: A 81 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7045 (mm) REVERT: A 249 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7065 (mt0) REVERT: A 332 MET cc_start: 0.8928 (ttt) cc_final: 0.8555 (ttt) REVERT: A 343 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7615 (tt0) REVERT: A 368 LYS cc_start: 0.8071 (mmtm) cc_final: 0.7758 (mmmt) REVERT: B 60 LYS cc_start: 0.6625 (mmtm) cc_final: 0.6274 (mmtm) REVERT: B 81 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7230 (mm) REVERT: B 87 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7403 (t0) REVERT: B 105 LEU cc_start: 0.4640 (OUTLIER) cc_final: 0.4416 (mt) REVERT: B 188 ASN cc_start: 0.8158 (m-40) cc_final: 0.7813 (m-40) REVERT: B 249 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7798 (mp10) REVERT: C 81 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.6965 (mm) REVERT: C 87 ASP cc_start: 0.7365 (OUTLIER) cc_final: 0.7049 (m-30) REVERT: C 105 LEU cc_start: 0.5242 (OUTLIER) cc_final: 0.5017 (mt) REVERT: C 249 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.7317 (mt0) REVERT: D 60 LYS cc_start: 0.6590 (mmtm) cc_final: 0.6273 (mmtm) REVERT: D 81 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7028 (mm) REVERT: D 105 LEU cc_start: 0.4690 (OUTLIER) cc_final: 0.4401 (mt) REVERT: D 107 ARG cc_start: 0.6071 (OUTLIER) cc_final: 0.5304 (ptp-170) REVERT: D 151 ARG cc_start: 0.6922 (mmt180) cc_final: 0.6637 (mmt180) REVERT: D 343 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7842 (tt0) REVERT: E 37 ARG cc_start: 0.7584 (mmt-90) cc_final: 0.7355 (mmt90) REVERT: E 159 ILE cc_start: 0.7808 (OUTLIER) cc_final: 0.7604 (tt) REVERT: E 180 PHE cc_start: 0.7228 (p90) cc_final: 0.7017 (p90) REVERT: E 342 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8722 (mt) REVERT: F 70 TYR cc_start: 0.6592 (t80) cc_final: 0.5980 (t80) REVERT: F 81 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.6820 (mm) REVERT: F 105 LEU cc_start: 0.5527 (OUTLIER) cc_final: 0.5099 (mt) REVERT: F 159 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7988 (tt) REVERT: F 249 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7255 (mt0) REVERT: F 259 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8077 (ttm) REVERT: F 343 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7688 (tt0) REVERT: G 81 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.6917 (mm) REVERT: G 87 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7678 (m-30) REVERT: G 105 LEU cc_start: 0.5250 (OUTLIER) cc_final: 0.4988 (mt) REVERT: G 211 PHE cc_start: 0.7915 (m-80) cc_final: 0.7678 (m-80) REVERT: G 249 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.7488 (mt0) REVERT: G 250 THR cc_start: 0.8931 (OUTLIER) cc_final: 0.8720 (m) REVERT: G 343 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7764 (tt0) REVERT: H 81 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7522 (mm) REVERT: H 105 LEU cc_start: 0.4419 (OUTLIER) cc_final: 0.4150 (mt) REVERT: H 159 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7849 (tt) REVERT: H 326 SER cc_start: 0.8802 (OUTLIER) cc_final: 0.8547 (m) REVERT: I 24 ASP cc_start: 0.6813 (OUTLIER) cc_final: 0.6466 (m-30) REVERT: I 37 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7136 (mpt-90) REVERT: I 81 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.6719 (mm) REVERT: I 105 LEU cc_start: 0.5606 (OUTLIER) cc_final: 0.5299 (mt) REVERT: I 249 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.7558 (mt0) REVERT: I 343 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7680 (tt0) REVERT: J 81 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.6955 (mm) REVERT: J 105 LEU cc_start: 0.5943 (OUTLIER) cc_final: 0.5656 (mt) REVERT: J 326 SER cc_start: 0.8794 (OUTLIER) cc_final: 0.8421 (m) REVERT: J 368 LYS cc_start: 0.8452 (mmtt) cc_final: 0.7749 (mmmt) REVERT: J 390 MET cc_start: 0.9006 (mtp) cc_final: 0.8749 (mtm) REVERT: K 9 ASN cc_start: 0.6630 (OUTLIER) cc_final: 0.6154 (p0) REVERT: K 81 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.6994 (mm) REVERT: K 368 LYS cc_start: 0.8453 (mmtt) cc_final: 0.8035 (mptt) outliers start: 193 outliers final: 114 residues processed: 599 average time/residue: 0.2434 time to fit residues: 240.7253 Evaluate side-chains 574 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 416 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASN Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain B residue 390 MET Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 249 GLN Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 347 SER Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 393 MET Chi-restraints excluded: chain E residue 9 ASN Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain E residue 107 ARG Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 162 CYS Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 259 MET Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain F residue 9 ASN Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 107 ARG Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 162 CYS Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 249 GLN Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 343 GLU Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 107 ARG Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 249 GLN Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 343 GLU Chi-restraints excluded: chain G residue 347 SER Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 107 ARG Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 235 ILE Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 259 MET Chi-restraints excluded: chain H residue 326 SER Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 382 VAL Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain I residue 24 ASP Chi-restraints excluded: chain I residue 37 ARG Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 107 ARG Chi-restraints excluded: chain I residue 159 ILE Chi-restraints excluded: chain I residue 162 CYS Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 249 GLN Chi-restraints excluded: chain I residue 343 GLU Chi-restraints excluded: chain I residue 363 VAL Chi-restraints excluded: chain I residue 408 SER Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 ASP Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 107 ARG Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain J residue 235 ILE Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain K residue 9 ASN Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 162 CYS Chi-restraints excluded: chain K residue 174 THR Chi-restraints excluded: chain K residue 176 THR Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 326 SER Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain K residue 408 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 353 optimal weight: 0.9980 chunk 77 optimal weight: 0.0970 chunk 372 optimal weight: 8.9990 chunk 436 optimal weight: 3.9990 chunk 253 optimal weight: 9.9990 chunk 349 optimal weight: 3.9990 chunk 181 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 311 optimal weight: 4.9990 chunk 268 optimal weight: 0.8980 overall best weight: 1.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 96 GLN K 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.172486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.152029 restraints weight = 46688.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.148237 restraints weight = 73572.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.145862 restraints weight = 79958.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.144984 restraints weight = 95957.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.143428 restraints weight = 86878.098| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 39068 Z= 0.131 Angle : 0.573 9.732 53364 Z= 0.301 Chirality : 0.044 0.329 5961 Planarity : 0.005 0.092 6479 Dihedral : 14.594 178.669 6539 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 4.02 % Allowed : 25.26 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.12), residues: 4532 helix: 0.24 (0.12), residues: 2101 sheet: None (None), residues: 0 loop : -2.14 (0.12), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG K 107 TYR 0.040 0.002 TYR A 70 PHE 0.013 0.001 PHE K 295 TRP 0.009 0.001 TRP G 246 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00295 (39068) covalent geometry : angle 0.57315 (53364) hydrogen bonds : bond 0.03827 ( 1254) hydrogen bonds : angle 3.87774 ( 3432) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 438 time to evaluate : 1.580 Fit side-chains revert: symmetry clash REVERT: A 81 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7050 (mm) REVERT: A 249 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.6691 (mt0) REVERT: A 332 MET cc_start: 0.8963 (ttt) cc_final: 0.8349 (ttt) REVERT: A 368 LYS cc_start: 0.8006 (mmtm) cc_final: 0.7675 (mmmt) REVERT: B 81 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7247 (mm) REVERT: B 87 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7312 (t0) REVERT: B 105 LEU cc_start: 0.4551 (OUTLIER) cc_final: 0.4334 (mt) REVERT: B 188 ASN cc_start: 0.8226 (m-40) cc_final: 0.7865 (m-40) REVERT: B 249 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7552 (mm110) REVERT: B 271 SER cc_start: 0.8332 (t) cc_final: 0.8106 (t) REVERT: C 81 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.6983 (mm) REVERT: C 87 ASP cc_start: 0.7398 (OUTLIER) cc_final: 0.7161 (m-30) REVERT: C 105 LEU cc_start: 0.5280 (OUTLIER) cc_final: 0.4827 (mt) REVERT: C 151 ARG cc_start: 0.6593 (mmt180) cc_final: 0.6393 (mmt180) REVERT: C 249 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.7231 (mt0) REVERT: D 60 LYS cc_start: 0.7019 (mmtm) cc_final: 0.5175 (mmmt) REVERT: D 81 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7080 (mm) REVERT: D 105 LEU cc_start: 0.5389 (OUTLIER) cc_final: 0.5088 (mt) REVERT: D 107 ARG cc_start: 0.5848 (OUTLIER) cc_final: 0.5106 (ptp-170) REVERT: D 151 ARG cc_start: 0.6794 (mmt180) cc_final: 0.6418 (mmt180) REVERT: E 180 PHE cc_start: 0.7116 (p90) cc_final: 0.6881 (p90) REVERT: E 342 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8722 (mt) REVERT: F 70 TYR cc_start: 0.6498 (t80) cc_final: 0.6034 (t80) REVERT: F 81 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6829 (mm) REVERT: F 105 LEU cc_start: 0.5417 (OUTLIER) cc_final: 0.5069 (mt) REVERT: F 249 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.6889 (mt0) REVERT: F 259 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.7971 (ttm) REVERT: G 81 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7031 (mm) REVERT: G 87 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7462 (m-30) REVERT: G 249 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8204 (mm-40) REVERT: G 250 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8679 (m) REVERT: G 279 MET cc_start: 0.7193 (mmt) cc_final: 0.6903 (mmp) REVERT: H 81 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7502 (mm) REVERT: H 105 LEU cc_start: 0.5150 (OUTLIER) cc_final: 0.4841 (mt) REVERT: H 159 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7814 (tt) REVERT: H 273 MET cc_start: 0.7603 (tmm) cc_final: 0.7383 (tmm) REVERT: H 326 SER cc_start: 0.8598 (OUTLIER) cc_final: 0.8382 (m) REVERT: I 37 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.7104 (mpt-90) REVERT: I 81 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.6697 (mm) REVERT: I 105 LEU cc_start: 0.5630 (OUTLIER) cc_final: 0.5311 (mt) REVERT: I 249 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7724 (mp10) REVERT: I 343 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7581 (tt0) REVERT: J 81 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.6973 (mm) REVERT: J 105 LEU cc_start: 0.5870 (OUTLIER) cc_final: 0.5568 (mt) REVERT: J 279 MET cc_start: 0.7054 (mmt) cc_final: 0.6652 (mmm) REVERT: J 326 SER cc_start: 0.8784 (OUTLIER) cc_final: 0.8314 (m) REVERT: J 368 LYS cc_start: 0.8444 (mmtt) cc_final: 0.7719 (mmmt) REVERT: J 390 MET cc_start: 0.8973 (mtp) cc_final: 0.8708 (mtm) REVERT: K 9 ASN cc_start: 0.6781 (OUTLIER) cc_final: 0.6190 (p0) REVERT: K 81 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.6936 (mm) REVERT: K 200 TYR cc_start: 0.7320 (m-10) cc_final: 0.7002 (m-10) REVERT: K 319 GLU cc_start: 0.6430 (tt0) cc_final: 0.6146 (tt0) REVERT: K 368 LYS cc_start: 0.8430 (mmtt) cc_final: 0.8029 (mptt) outliers start: 156 outliers final: 106 residues processed: 565 average time/residue: 0.2428 time to fit residues: 227.3592 Evaluate side-chains 559 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 417 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain B residue 390 MET Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 249 GLN Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 393 MET Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain E residue 107 ARG Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 259 MET Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain F residue 9 ASN Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 107 ARG Chi-restraints excluded: chain F residue 162 CYS Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 249 GLN Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 107 ARG Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 249 GLN Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 347 SER Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 107 ARG Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 235 ILE Chi-restraints excluded: chain H residue 259 MET Chi-restraints excluded: chain H residue 326 SER Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 382 VAL Chi-restraints excluded: chain I residue 37 ARG Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 107 ARG Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 249 GLN Chi-restraints excluded: chain I residue 343 GLU Chi-restraints excluded: chain I residue 363 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 ASP Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain J residue 178 LYS Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 347 SER Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain K residue 9 ASN Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 174 THR Chi-restraints excluded: chain K residue 176 THR Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 382 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 316 optimal weight: 6.9990 chunk 231 optimal weight: 5.9990 chunk 87 optimal weight: 30.0000 chunk 334 optimal weight: 20.0000 chunk 124 optimal weight: 0.0980 chunk 3 optimal weight: 8.9990 chunk 46 optimal weight: 30.0000 chunk 57 optimal weight: 7.9990 chunk 193 optimal weight: 1.9990 chunk 221 optimal weight: 5.9990 chunk 336 optimal weight: 10.0000 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 ASN ** F 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.169384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.149807 restraints weight = 46915.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.146549 restraints weight = 81431.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.144499 restraints weight = 78746.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.142656 restraints weight = 92745.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.140895 restraints weight = 90892.745| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 39068 Z= 0.208 Angle : 0.631 9.773 53364 Z= 0.333 Chirality : 0.046 0.334 5961 Planarity : 0.005 0.092 6479 Dihedral : 14.690 179.994 6539 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % Rotamer: Outliers : 4.43 % Allowed : 24.77 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.12), residues: 4532 helix: 0.03 (0.12), residues: 2112 sheet: None (None), residues: 0 loop : -2.22 (0.12), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 107 TYR 0.042 0.002 TYR A 52 PHE 0.020 0.002 PHE K 295 TRP 0.011 0.002 TRP K 298 HIS 0.003 0.001 HIS G 177 Details of bonding type rmsd covalent geometry : bond 0.00491 (39068) covalent geometry : angle 0.63120 (53364) hydrogen bonds : bond 0.04795 ( 1254) hydrogen bonds : angle 4.11256 ( 3432) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 430 time to evaluate : 1.432 Fit side-chains revert: symmetry clash REVERT: A 60 LYS cc_start: 0.7205 (mmtm) cc_final: 0.5697 (mmmt) REVERT: A 81 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7048 (mm) REVERT: A 249 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7005 (mt0) REVERT: A 332 MET cc_start: 0.8842 (ttt) cc_final: 0.8434 (ttt) REVERT: A 368 LYS cc_start: 0.8059 (mmtm) cc_final: 0.7758 (mmmt) REVERT: B 81 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7133 (mm) REVERT: B 87 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7392 (t0) REVERT: B 105 LEU cc_start: 0.4693 (OUTLIER) cc_final: 0.4470 (mt) REVERT: B 188 ASN cc_start: 0.8175 (m-40) cc_final: 0.7908 (m-40) REVERT: B 249 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7789 (mp10) REVERT: C 81 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.6975 (mm) REVERT: C 87 ASP cc_start: 0.7334 (OUTLIER) cc_final: 0.7098 (m-30) REVERT: C 105 LEU cc_start: 0.5273 (OUTLIER) cc_final: 0.5047 (mt) REVERT: C 249 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.7314 (mt0) REVERT: D 60 LYS cc_start: 0.7080 (mmtm) cc_final: 0.5190 (mmmt) REVERT: D 81 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.6991 (mm) REVERT: D 105 LEU cc_start: 0.5411 (OUTLIER) cc_final: 0.5101 (mt) REVERT: D 107 ARG cc_start: 0.6145 (OUTLIER) cc_final: 0.5439 (ptp-170) REVERT: D 151 ARG cc_start: 0.6991 (mmt180) cc_final: 0.6706 (mmt180) REVERT: D 343 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7814 (tt0) REVERT: E 180 PHE cc_start: 0.7120 (p90) cc_final: 0.6892 (p90) REVERT: E 342 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8694 (mt) REVERT: F 70 TYR cc_start: 0.6461 (t80) cc_final: 0.6167 (t80) REVERT: F 81 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.6786 (mm) REVERT: F 105 LEU cc_start: 0.5524 (OUTLIER) cc_final: 0.5119 (mt) REVERT: F 159 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7991 (tt) REVERT: F 249 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7208 (mt0) REVERT: F 259 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8075 (ttm) REVERT: F 343 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7701 (tt0) REVERT: G 81 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.6962 (mm) REVERT: G 87 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7458 (m-30) REVERT: G 249 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8274 (mm-40) REVERT: G 250 THR cc_start: 0.8933 (OUTLIER) cc_final: 0.8732 (m) REVERT: G 343 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7718 (tt0) REVERT: H 81 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7499 (mm) REVERT: H 105 LEU cc_start: 0.5414 (OUTLIER) cc_final: 0.5086 (mt) REVERT: H 159 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7843 (tt) REVERT: H 326 SER cc_start: 0.8824 (OUTLIER) cc_final: 0.8534 (m) REVERT: I 24 ASP cc_start: 0.6790 (OUTLIER) cc_final: 0.6436 (m-30) REVERT: I 37 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7022 (mpt-90) REVERT: I 81 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.6686 (mm) REVERT: I 105 LEU cc_start: 0.5642 (OUTLIER) cc_final: 0.5338 (mt) REVERT: I 249 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7559 (mt0) REVERT: I 294 SER cc_start: 0.8052 (OUTLIER) cc_final: 0.7523 (p) REVERT: I 343 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7644 (tt0) REVERT: J 81 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.6940 (mm) REVERT: J 105 LEU cc_start: 0.5818 (OUTLIER) cc_final: 0.5514 (mt) REVERT: J 279 MET cc_start: 0.7020 (mmt) cc_final: 0.6604 (mmm) REVERT: J 326 SER cc_start: 0.8802 (OUTLIER) cc_final: 0.8430 (m) REVERT: J 368 LYS cc_start: 0.8335 (mmtt) cc_final: 0.7605 (mmmt) REVERT: J 390 MET cc_start: 0.9010 (mtp) cc_final: 0.8752 (mtm) REVERT: K 9 ASN cc_start: 0.6735 (OUTLIER) cc_final: 0.6191 (p0) REVERT: K 81 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.6955 (mm) REVERT: K 368 LYS cc_start: 0.8449 (mmtt) cc_final: 0.8045 (mptt) outliers start: 172 outliers final: 117 residues processed: 572 average time/residue: 0.2345 time to fit residues: 221.1882 Evaluate side-chains 571 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 412 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain B residue 390 MET Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 249 GLN Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain D residue 162 CYS Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 347 SER Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 393 MET Chi-restraints excluded: chain E residue 9 ASN Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 107 ARG Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 162 CYS Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 259 MET Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain F residue 9 ASN Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 107 ARG Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 162 CYS Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 249 GLN Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 343 GLU Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 107 ARG Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 249 GLN Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 343 GLU Chi-restraints excluded: chain G residue 347 SER Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 107 ARG Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 235 ILE Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 259 MET Chi-restraints excluded: chain H residue 326 SER Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 382 VAL Chi-restraints excluded: chain I residue 24 ASP Chi-restraints excluded: chain I residue 37 ARG Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 107 ARG Chi-restraints excluded: chain I residue 162 CYS Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 249 GLN Chi-restraints excluded: chain I residue 294 SER Chi-restraints excluded: chain I residue 338 SER Chi-restraints excluded: chain I residue 343 GLU Chi-restraints excluded: chain I residue 363 VAL Chi-restraints excluded: chain I residue 408 SER Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 ASP Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain J residue 195 CYS Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 347 SER Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain K residue 9 ASN Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 162 CYS Chi-restraints excluded: chain K residue 174 THR Chi-restraints excluded: chain K residue 176 THR Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 326 SER Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 382 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 113 optimal weight: 0.9980 chunk 452 optimal weight: 10.0000 chunk 347 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 chunk 144 optimal weight: 9.9990 chunk 154 optimal weight: 4.9990 chunk 345 optimal weight: 0.1980 chunk 359 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN E 231 HIS K 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.174275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.153849 restraints weight = 46468.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.149605 restraints weight = 70085.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.147599 restraints weight = 79172.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.146870 restraints weight = 92804.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.145699 restraints weight = 75260.932| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 39068 Z= 0.113 Angle : 0.564 10.652 53364 Z= 0.295 Chirality : 0.043 0.329 5961 Planarity : 0.004 0.092 6479 Dihedral : 14.363 176.893 6539 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 3.19 % Allowed : 26.11 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.12), residues: 4532 helix: 0.42 (0.12), residues: 2090 sheet: None (None), residues: 0 loop : -2.07 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 37 TYR 0.044 0.001 TYR A 52 PHE 0.019 0.001 PHE J 211 TRP 0.016 0.001 TRP G 169 HIS 0.002 0.000 HIS F 296 Details of bonding type rmsd covalent geometry : bond 0.00245 (39068) covalent geometry : angle 0.56418 (53364) hydrogen bonds : bond 0.03445 ( 1254) hydrogen bonds : angle 3.78856 ( 3432) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 451 time to evaluate : 1.486 Fit side-chains revert: symmetry clash REVERT: A 81 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7059 (mm) REVERT: A 249 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7699 (mm110) REVERT: A 332 MET cc_start: 0.8949 (ttt) cc_final: 0.8306 (ttt) REVERT: A 368 LYS cc_start: 0.7910 (mmtm) cc_final: 0.7588 (mmmt) REVERT: B 81 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7169 (mm) REVERT: B 87 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7270 (t0) REVERT: B 188 ASN cc_start: 0.8289 (m-40) cc_final: 0.8054 (m-40) REVERT: B 249 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7596 (mm110) REVERT: B 271 SER cc_start: 0.8322 (t) cc_final: 0.8076 (t) REVERT: C 81 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7040 (mm) REVERT: C 87 ASP cc_start: 0.7352 (OUTLIER) cc_final: 0.7132 (m-30) REVERT: C 105 LEU cc_start: 0.5235 (OUTLIER) cc_final: 0.4826 (mt) REVERT: C 249 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8036 (mm-40) REVERT: D 60 LYS cc_start: 0.7015 (mmtm) cc_final: 0.5187 (mmmt) REVERT: D 81 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.6971 (mm) REVERT: D 105 LEU cc_start: 0.5398 (OUTLIER) cc_final: 0.4996 (mt) REVERT: D 107 ARG cc_start: 0.5709 (OUTLIER) cc_final: 0.5295 (ptp-170) REVERT: D 151 ARG cc_start: 0.6734 (mmt180) cc_final: 0.6399 (mmt180) REVERT: E 105 LEU cc_start: 0.5412 (OUTLIER) cc_final: 0.4876 (mt) REVERT: E 107 ARG cc_start: 0.5661 (OUTLIER) cc_final: 0.5246 (ptp-170) REVERT: E 180 PHE cc_start: 0.7197 (p90) cc_final: 0.6991 (p90) REVERT: E 342 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8780 (mt) REVERT: F 70 TYR cc_start: 0.6543 (t80) cc_final: 0.6210 (t80) REVERT: F 81 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.6896 (mm) REVERT: F 105 LEU cc_start: 0.5375 (OUTLIER) cc_final: 0.5027 (mt) REVERT: F 249 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.6666 (mt0) REVERT: F 259 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8376 (ttp) REVERT: G 24 ASP cc_start: 0.6619 (OUTLIER) cc_final: 0.6300 (t0) REVERT: G 81 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.6966 (mm) REVERT: G 249 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7902 (mm-40) REVERT: G 250 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8585 (m) REVERT: G 279 MET cc_start: 0.6784 (mmm) cc_final: 0.6514 (mmm) REVERT: H 81 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7465 (mm) REVERT: H 105 LEU cc_start: 0.5100 (OUTLIER) cc_final: 0.4807 (mt) REVERT: H 107 ARG cc_start: 0.5332 (OUTLIER) cc_final: 0.4990 (ptp-170) REVERT: H 326 SER cc_start: 0.8791 (OUTLIER) cc_final: 0.8588 (m) REVERT: I 37 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.6964 (mpt-90) REVERT: I 81 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.6733 (mm) REVERT: I 105 LEU cc_start: 0.5607 (OUTLIER) cc_final: 0.5327 (mt) REVERT: I 249 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7603 (mp10) REVERT: J 81 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7005 (mm) REVERT: J 105 LEU cc_start: 0.5856 (OUTLIER) cc_final: 0.5531 (mt) REVERT: J 279 MET cc_start: 0.6869 (mmt) cc_final: 0.6544 (mmm) REVERT: J 326 SER cc_start: 0.8822 (OUTLIER) cc_final: 0.8476 (m) REVERT: J 368 LYS cc_start: 0.8315 (mmtt) cc_final: 0.7544 (mmmt) REVERT: J 390 MET cc_start: 0.8999 (mtp) cc_final: 0.8714 (mtm) REVERT: K 9 ASN cc_start: 0.6952 (OUTLIER) cc_final: 0.6391 (p0) REVERT: K 81 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.6966 (mm) REVERT: K 200 TYR cc_start: 0.7319 (m-10) cc_final: 0.7082 (m-10) REVERT: K 368 LYS cc_start: 0.8435 (mmtt) cc_final: 0.7958 (mptt) outliers start: 124 outliers final: 73 residues processed: 552 average time/residue: 0.2270 time to fit residues: 207.3667 Evaluate side-chains 531 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 422 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 249 GLN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain D residue 162 CYS Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain E residue 9 ASN Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 107 ARG Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 259 MET Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 9 ASN Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 107 ARG Chi-restraints excluded: chain F residue 162 CYS Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 249 GLN Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 107 ARG Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 249 GLN Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 107 ARG Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 259 MET Chi-restraints excluded: chain H residue 326 SER Chi-restraints excluded: chain H residue 382 VAL Chi-restraints excluded: chain I residue 37 ARG Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 107 ARG Chi-restraints excluded: chain I residue 162 CYS Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 249 GLN Chi-restraints excluded: chain I residue 363 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain J residue 195 CYS Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 347 SER Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain K residue 9 ASN Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 68 ASN Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 174 THR Chi-restraints excluded: chain K residue 176 THR Chi-restraints excluded: chain K residue 326 SER Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 382 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 276 optimal weight: 8.9990 chunk 142 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 chunk 291 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 447 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 371 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 274 optimal weight: 0.0670 chunk 422 optimal weight: 5.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.173847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.153645 restraints weight = 46641.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.149638 restraints weight = 69461.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.147538 restraints weight = 84738.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.146503 restraints weight = 90050.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.144388 restraints weight = 89399.774| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.203 39068 Z= 0.150 Angle : 0.672 59.197 53364 Z= 0.377 Chirality : 0.044 0.351 5961 Planarity : 0.004 0.089 6479 Dihedral : 14.364 176.986 6539 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 3.22 % Allowed : 26.45 % Favored : 70.33 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.12), residues: 4532 helix: 0.42 (0.12), residues: 2090 sheet: None (None), residues: 0 loop : -2.07 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 107 TYR 0.051 0.002 TYR F 70 PHE 0.020 0.001 PHE J 211 TRP 0.043 0.002 TRP E 131 HIS 0.005 0.001 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00346 (39068) covalent geometry : angle 0.67188 (53364) hydrogen bonds : bond 0.03528 ( 1254) hydrogen bonds : angle 3.82164 ( 3432) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5415.98 seconds wall clock time: 95 minutes 1.70 seconds (5701.70 seconds total)