Starting phenix.real_space_refine on Tue Sep 15 07:35:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yg7_33810/09_2026/7yg7_33810.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yg7_33810/09_2026/7yg7_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_33810/09_2026/7yg7_33810.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yg7_33810/09_2026/7yg7_33810.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7yg7_33810/09_2026/7yg7_33810.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yg7_33810/09_2026/7yg7_33810.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yg7_33810/09_2026/7yg7_33810.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yg7_33810/09_2026/7yg7_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: {'RNAv2': 99} Modifications used: {'rna2p_pyr': 13, 'rna3p_pyr': 86} Link IDs: {'rna2p': 13, 'rna3p': 85} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.29, per 1000 atoms: 0.22 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: 3.25 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 4.11 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: 6.55 Time building geometry restraints manager: 4.39 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: 51741 2.07 - 4.14: 1317 4.14 - 6.21: 207 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 - 34.53: 22151 34.53 - 69.05: 1092 69.05 - 103.58: 50 103.58 - 138.11: 0 138.11 - 172.63: 1 Dihedral angle restraints: 23294 sinusoidal: 10028 harmonic: 13266 Sorted by residual: dihedral pdb=" C4' U U 38 " pdb=" C3' U U 38 " pdb=" C2' U U 38 " pdb=" C1' U U 38 " ideal model delta sinusoidal sigma weight residual 36.35 -36.01 72.36 1 3.10e+00 1.04e-01 6.96e+02 dihedral pdb=" C4' U U 67 " pdb=" C3' U U 67 " pdb=" C2' U U 67 " pdb=" C1' U U 67 " ideal model delta sinusoidal sigma weight residual 36.34 -35.02 71.37 1 3.10e+00 1.04e-01 6.80e+02 dihedral pdb=" C4' U U 31 " pdb=" C3' U U 31 " pdb=" C2' U U 31 " pdb=" C1' U U 31 " ideal model delta sinusoidal sigma weight residual 36.35 -34.99 71.34 1 3.10e+00 1.04e-01 6.79e+02 ... (remaining 23291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 4737 0.064 - 0.127: 995 0.127 - 0.191: 100 0.191 - 0.255: 112 0.255 - 0.318: 17 Chirality restraints: 5961 Sorted by residual: chirality pdb=" C2' U U 38 " pdb=" C3' U U 38 " pdb=" O2' U U 38 " pdb=" C1' U U 38 " both_signs ideal model delta sigma weight residual False -2.79 -2.47 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" C2' U U 14 " pdb=" C3' U U 14 " pdb=" O2' U U 14 " pdb=" C1' U U 14 " both_signs ideal model delta sigma weight residual False -2.79 -2.48 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" C3' U U 13 " pdb=" C4' U U 13 " pdb=" O3' U U 13 " pdb=" C2' U U 13 " both_signs ideal model delta sigma weight residual False -2.50 -2.77 0.28 2.00e-01 2.50e+01 1.90e+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: 0.440 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: 0.050 Extract box with map and model: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 36.130 Find NCS groups from input model: 0.650 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 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= 0.209 Angle : 0.826 10.357 53364 Z= 0.412 Chirality : 0.059 0.318 5961 Planarity : 0.007 0.105 6479 Dihedral : 17.985 172.631 14780 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 are 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/Z covalent geometry : bond 0.00449 / 0.21 (39068) covalent geometry : angle 0.82590 / 0.41 (53364) hydrogen bonds : bond 0.15541 / 10.41 ( 1254) hydrogen bonds : angle 5.09380 / 3.55 ( 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 : 1.432 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: 0.8726 (OUTLIER) cc_final: 0.8454 (mt) REVERT: H 9 ASN cc_start: 0.6212 (OUTLIER) cc_final: 0.5852 (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: 0.8589 (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: 0.2499 time to fit residues: 215.0405 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 : 1.319 ------------------------------------------------------------------------------- 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: 9.9990 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... 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 = 0.3795 r_free = 0.3795 target = 0.173000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.153080 restraints weight = 46895.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.149368 restraints weight = 73634.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.147192 restraints weight = 84893.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.146640 restraints weight = 90814.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.145208 restraints weight = 81143.432| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 39068 Z= 0.161 Angle : 0.735 14.318 53364 Z= 0.334 Chirality : 0.065 0.784 5961 Planarity : 0.005 0.074 6479 Dihedral : 10.187 174.397 6185 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 2.42 % Allowed : 24.39 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.12), residues: 4532 helix: -0.27 (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 0.040 0.002 TYR I 52 PHE 0.019 0.002 PHE J 211 TRP 0.010 0.001 TRP K 298 HIS 0.003 0.001 HIS G 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (39068) covalent geometry : angle 0.73505 / 0.33 (53364) hydrogen bonds : bond 0.04591 / 3.08 ( 1254) hydrogen bonds : angle 3.99203 / 2.80 ( 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: 94 poor density : 461 time to evaluate : 1.536 Fit side-chains REVERT: A 249 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7049 (mt0) REVERT: A 332 MET cc_start: 0.8611 (ttt) cc_final: 0.8112 (ttt) REVERT: A 368 LYS cc_start: 0.8114 (mmtm) cc_final: 0.7729 (mmmt) REVERT: B 60 LYS cc_start: 0.6385 (mmtm) cc_final: 0.5996 (mmtm) REVERT: B 70 TYR cc_start: 0.6342 (t80) cc_final: 0.5932 (t80) REVERT: B 249 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7549 (mp10) REVERT: B 271 SER cc_start: 0.8653 (t) cc_final: 0.8447 (t) REVERT: C 249 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.7122 (mt0) REVERT: C 381 ASP cc_start: 0.7553 (t70) cc_final: 0.7202 (t0) REVERT: D 249 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8247 (mm-40) REVERT: E 63 ARG cc_start: 0.6311 (tpp-160) cc_final: 0.6061 (tpp-160) REVERT: E 249 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7997 (mm-40) REVERT: E 342 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8796 (mt) REVERT: E 390 MET cc_start: 0.9162 (mtp) cc_final: 0.8949 (mtm) REVERT: F 249 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7082 (mt0) REVERT: F 260 MET cc_start: 0.8672 (mmt) cc_final: 0.8211 (mmt) REVERT: G 24 ASP cc_start: 0.6743 (OUTLIER) cc_final: 0.6400 (t0) REVERT: G 249 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8203 (mm-40) REVERT: H 9 ASN cc_start: 0.6195 (OUTLIER) cc_final: 0.5724 (p0) REVERT: H 249 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7851 (mm-40) REVERT: I 9 ASN cc_start: 0.5709 (OUTLIER) cc_final: 0.5300 (p0) REVERT: I 249 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7572 (mp10) REVERT: I 259 MET cc_start: 0.8524 (ttp) cc_final: 0.8315 (ttp) REVERT: I 381 ASP cc_start: 0.7954 (t70) cc_final: 0.7637 (t0) REVERT: J 249 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7208 (mt0) REVERT: J 259 MET cc_start: 0.8736 (ttp) cc_final: 0.8448 (ttp) REVERT: J 260 MET cc_start: 0.8786 (mmt) cc_final: 0.8584 (mmm) REVERT: J 368 LYS cc_start: 0.8416 (mmtt) cc_final: 0.8032 (mttm) REVERT: J 390 MET cc_start: 0.8984 (mtp) cc_final: 0.8714 (mtm) REVERT: K 249 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.8069 (mm-40) REVERT: K 259 MET cc_start: 0.8495 (ttp) cc_final: 0.8272 (ttp) REVERT: K 368 LYS cc_start: 0.8296 (mmtt) cc_final: 0.8041 (mptt) outliers start: 94 outliers final: 27 residues processed: 538 average time/residue: 0.2201 time to fit residues: 198.5916 Evaluate side-chains 467 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 425 time to evaluate : 1.337 ------------------------------------------------------------------------------- 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 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 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 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: 6.9990 chunk 354 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 159 optimal weight: 0.3980 chunk 12 optimal weight: 7.9990 chunk 187 optimal weight: 5.9990 chunk 380 optimal weight: 0.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 GLN E 51 GLN F 51 GLN G 51 GLN G 66 HIS G 188 ASN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.170439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.149802 restraints weight = 46937.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.146626 restraints weight = 78019.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.144391 restraints weight = 80242.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.142943 restraints weight = 96103.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.140993 restraints weight = 89448.303| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 39068 Z= 0.218 Angle : 0.738 10.842 53364 Z= 0.347 Chirality : 0.062 0.573 5961 Planarity : 0.005 0.069 6479 Dihedral : 10.071 174.416 6151 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.98 % Favored : 88.02 % Rotamer: Outliers : 4.20 % Allowed : 23.18 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.12), residues: 4532 helix: -0.20 (0.11), residues: 2112 sheet: None (None), residues: 0 loop : -2.29 (0.12), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 37 TYR 0.032 0.002 TYR I 52 PHE 0.021 0.002 PHE G 295 TRP 0.014 0.002 TRP K 298 HIS 0.003 0.001 HIS G 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.22 (39068) covalent geometry : angle 0.73840 / 0.35 (53364) hydrogen bonds : bond 0.05114 / 3.44 ( 1254) hydrogen bonds : angle 4.16693 / 2.94 ( 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 608 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 445 time to evaluate : 1.502 Fit side-chains REVERT: A 70 TYR cc_start: 0.6536 (t80) cc_final: 0.6229 (t80) REVERT: A 249 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7038 (mt0) REVERT: A 332 MET cc_start: 0.8483 (ttt) cc_final: 0.8016 (ttt) REVERT: A 368 LYS cc_start: 0.8113 (mmtm) cc_final: 0.7754 (mmmt) REVERT: B 60 LYS cc_start: 0.6489 (mmtm) cc_final: 0.6134 (mmtm) REVERT: B 87 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7450 (t0) REVERT: B 249 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7860 (mp10) REVERT: C 16 LEU cc_start: 0.8424 (pt) cc_final: 0.8138 (pp) REVERT: C 81 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7025 (mm) REVERT: C 249 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.7290 (mt0) REVERT: C 381 ASP cc_start: 0.7584 (t70) cc_final: 0.7354 (t0) REVERT: D 63 ARG cc_start: 0.6591 (tpp-160) cc_final: 0.6312 (tpp-160) REVERT: D 70 TYR cc_start: 0.6861 (t80) cc_final: 0.6511 (t80) REVERT: D 81 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7048 (mm) REVERT: D 151 ARG cc_start: 0.6700 (mmt180) cc_final: 0.6362 (mmt-90) REVERT: D 249 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8337 (mm-40) REVERT: D 343 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7863 (tt0) REVERT: E 70 TYR cc_start: 0.6657 (t80) cc_final: 0.6435 (t80) REVERT: E 249 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8162 (mm-40) REVERT: E 390 MET cc_start: 0.9256 (mtp) cc_final: 0.9040 (mtm) REVERT: F 60 LYS cc_start: 0.6454 (mmtm) cc_final: 0.6020 (mmtm) REVERT: F 81 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.6902 (mm) REVERT: F 249 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7235 (mt0) REVERT: F 343 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7814 (tt0) REVERT: G 24 ASP cc_start: 0.6681 (OUTLIER) cc_final: 0.6293 (t0) REVERT: G 70 TYR cc_start: 0.6692 (t80) cc_final: 0.6401 (t80) REVERT: G 81 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.6747 (mm) REVERT: G 87 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7616 (m-30) REVERT: G 249 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8323 (mm-40) REVERT: H 9 ASN cc_start: 0.6489 (OUTLIER) cc_final: 0.6167 (p0) REVERT: H 70 TYR cc_start: 0.6752 (t80) cc_final: 0.6422 (t80) REVERT: H 81 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7589 (mm) REVERT: H 249 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8068 (mm-40) REVERT: I 70 TYR cc_start: 0.6646 (t80) cc_final: 0.6345 (t80) REVERT: I 81 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.6763 (mm) REVERT: I 249 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7447 (mt0) REVERT: I 259 MET cc_start: 0.8634 (ttp) cc_final: 0.8415 (ttp) REVERT: I 343 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7766 (tt0) REVERT: J 70 TYR cc_start: 0.6996 (t80) cc_final: 0.6628 (t80) REVERT: J 81 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.6954 (mm) REVERT: J 249 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7992 (mm-40) REVERT: J 279 MET cc_start: 0.7266 (mmt) cc_final: 0.6762 (mmm) REVERT: J 368 LYS cc_start: 0.8486 (mmtt) cc_final: 0.7739 (mmmt) REVERT: J 390 MET cc_start: 0.8984 (mtp) cc_final: 0.8711 (mtm) REVERT: K 70 TYR cc_start: 0.6558 (t80) cc_final: 0.6296 (t80) REVERT: K 81 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7246 (mm) REVERT: K 249 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8235 (mm-40) REVERT: K 368 LYS cc_start: 0.8438 (mmtt) cc_final: 0.8086 (mptt) outliers start: 163 outliers final: 78 residues processed: 582 average time/residue: 0.2216 time to fit residues: 214.9913 Evaluate side-chains 518 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 415 time to evaluate : 1.424 ------------------------------------------------------------------------------- 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 24 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 87 ASP 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 363 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 174 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain C residue 24 ASP 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 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 250 THR 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 176 THR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 363 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 100 ILE 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 363 VAL Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain F residue 9 ASN Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 100 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 250 THR Chi-restraints excluded: chain F residue 343 GLU 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 100 ILE 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 363 VAL Chi-restraints excluded: chain H residue 9 ASN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 81 LEU 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 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 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 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 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 100 ILE 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 363 VAL 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: 30.0000 chunk 86 optimal weight: 9.9990 chunk 232 optimal weight: 5.9990 chunk 289 optimal weight: 10.0000 chunk 202 optimal weight: 0.2980 chunk 272 optimal weight: 5.9990 chunk 329 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 chunk 170 optimal weight: 9.9990 chunk 256 optimal weight: 40.0000 chunk 354 optimal weight: 7.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 GLN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 GLN D 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.170069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.149590 restraints weight = 46972.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.145797 restraints weight = 78148.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.143432 restraints weight = 80308.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.141692 restraints weight = 96212.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.140028 restraints weight = 94158.641| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 39068 Z= 0.216 Angle : 0.725 11.331 53364 Z= 0.342 Chirality : 0.060 0.567 5961 Planarity : 0.005 0.081 6479 Dihedral : 9.990 173.792 6147 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer: Outliers : 4.87 % Allowed : 23.20 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.12), residues: 4532 helix: -0.18 (0.11), residues: 2112 sheet: None (None), residues: 0 loop : -2.25 (0.12), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 37 TYR 0.032 0.002 TYR B 52 PHE 0.020 0.002 PHE G 295 TRP 0.014 0.002 TRP K 298 HIS 0.003 0.001 HIS E 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.22 (39068) covalent geometry : angle 0.72488 / 0.34 (53364) hydrogen bonds : bond 0.04939 / 3.33 ( 1254) hydrogen bonds : angle 4.14226 / 2.92 ( 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 632 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 443 time to evaluate : 1.477 Fit side-chains REVERT: A 60 LYS cc_start: 0.6879 (mmtm) cc_final: 0.6653 (mmtm) REVERT: A 70 TYR cc_start: 0.6401 (t80) cc_final: 0.6165 (t80) REVERT: A 81 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7048 (mm) REVERT: A 249 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.6996 (mt0) REVERT: A 343 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7656 (tt0) REVERT: A 368 LYS cc_start: 0.8196 (mmtm) cc_final: 0.7801 (mmmt) REVERT: B 60 LYS cc_start: 0.6316 (mmtm) cc_final: 0.6043 (mmtm) REVERT: B 81 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7216 (mm) REVERT: B 87 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7446 (t0) REVERT: B 249 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7894 (mp10) REVERT: C 70 TYR cc_start: 0.6976 (t80) cc_final: 0.6744 (t80) REVERT: C 81 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.6989 (mm) REVERT: C 87 ASP cc_start: 0.7385 (OUTLIER) cc_final: 0.7078 (m-30) REVERT: C 249 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.7297 (mt0) REVERT: C 343 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7875 (tt0) REVERT: C 381 ASP cc_start: 0.7627 (t70) cc_final: 0.7379 (t0) REVERT: D 81 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7033 (mm) REVERT: D 105 LEU cc_start: 0.4596 (OUTLIER) cc_final: 0.4218 (mt) REVERT: D 107 ARG cc_start: 0.5809 (OUTLIER) cc_final: 0.5421 (ptp-170) REVERT: D 151 ARG cc_start: 0.6721 (mmt180) cc_final: 0.6266 (mmt-90) REVERT: D 249 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8363 (mm-40) REVERT: D 343 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7869 (tt0) REVERT: E 70 TYR cc_start: 0.6744 (t80) cc_final: 0.6469 (t80) REVERT: E 105 LEU cc_start: 0.5250 (OUTLIER) cc_final: 0.4818 (mt) REVERT: E 249 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7933 (mm-40) REVERT: E 390 MET cc_start: 0.9272 (mtp) cc_final: 0.9072 (mtm) REVERT: F 70 TYR cc_start: 0.6687 (t80) cc_final: 0.6303 (t80) REVERT: F 81 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.6908 (mm) REVERT: F 249 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7218 (mt0) REVERT: F 259 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8023 (ttm) REVERT: F 343 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7760 (tt0) REVERT: G 70 TYR cc_start: 0.6715 (t80) cc_final: 0.6375 (t80) REVERT: G 81 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.6735 (mm) REVERT: G 87 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7609 (m-30) REVERT: G 105 LEU cc_start: 0.4837 (OUTLIER) cc_final: 0.4536 (mt) REVERT: H 9 ASN cc_start: 0.6636 (OUTLIER) cc_final: 0.6186 (p0) REVERT: H 70 TYR cc_start: 0.6563 (t80) cc_final: 0.6258 (t80) REVERT: H 81 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7528 (mm) REVERT: H 105 LEU cc_start: 0.5065 (OUTLIER) cc_final: 0.4723 (mt) REVERT: H 249 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7932 (mm-40) REVERT: I 70 TYR cc_start: 0.6764 (t80) cc_final: 0.6407 (t80) REVERT: I 81 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.6740 (mm) REVERT: I 105 LEU cc_start: 0.5069 (OUTLIER) cc_final: 0.4698 (mt) REVERT: I 249 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7452 (mt0) REVERT: I 259 MET cc_start: 0.8595 (ttp) cc_final: 0.8375 (ttp) REVERT: I 343 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7752 (tt0) REVERT: J 81 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.6966 (mm) REVERT: J 105 LEU cc_start: 0.5974 (OUTLIER) cc_final: 0.5650 (mt) REVERT: J 249 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.8044 (mm-40) REVERT: J 368 LYS cc_start: 0.8472 (mmtt) cc_final: 0.7712 (mmmt) REVERT: J 390 MET cc_start: 0.9002 (mtp) cc_final: 0.8720 (mtm) REVERT: K 9 ASN cc_start: 0.7115 (OUTLIER) cc_final: 0.6499 (p0) REVERT: K 70 TYR cc_start: 0.6596 (t80) cc_final: 0.6283 (t80) REVERT: K 81 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7233 (mm) REVERT: K 249 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8214 (mm-40) REVERT: K 368 LYS cc_start: 0.8430 (mmtt) cc_final: 0.8065 (mptt) outliers start: 189 outliers final: 105 residues processed: 599 average time/residue: 0.2237 time to fit residues: 223.5420 Evaluate side-chains 561 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 418 time to evaluate : 1.373 ------------------------------------------------------------------------------- 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 81 LEU Chi-restraints excluded: chain A residue 87 ASP 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 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 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 207 ILE Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain C residue 24 ASP 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 382 VAL Chi-restraints excluded: chain D residue 9 ASN 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 107 ARG Chi-restraints excluded: chain D residue 176 THR 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 363 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 100 ILE Chi-restraints excluded: chain E residue 105 LEU 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 363 VAL Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain F residue 9 ASN Chi-restraints excluded: chain F residue 24 ASP 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 343 GLU Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain G residue 24 ASP 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 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 235 ILE Chi-restraints excluded: chain G residue 332 MET 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 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 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 9 ASN 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 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 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 363 VAL Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain K residue 9 ASN Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 107 ARG 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 249 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 318 optimal weight: 3.9990 chunk 241 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 255 optimal weight: 20.0000 chunk 400 optimal weight: 6.9990 chunk 332 optimal weight: 0.7980 chunk 264 optimal weight: 10.0000 chunk 246 optimal weight: 0.0370 chunk 398 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 chunk 357 optimal weight: 3.9990 overall best weight: 1.5662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.173840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.153858 restraints weight = 46839.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.150080 restraints weight = 68601.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.147730 restraints weight = 77737.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.146639 restraints weight = 88210.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.145327 restraints weight = 91512.131| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.1910 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= 0.116 Angle : 0.630 10.627 53364 Z= 0.295 Chirality : 0.053 0.509 5961 Planarity : 0.004 0.086 6479 Dihedral : 9.739 174.859 6147 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 4.17 % Allowed : 23.92 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.12), residues: 4532 helix: 0.23 (0.12), residues: 2101 sheet: None (None), residues: 0 loop : -2.11 (0.12), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 37 TYR 0.048 0.001 TYR K 52 PHE 0.011 0.001 PHE J 30 TRP 0.008 0.001 TRP G 246 HIS 0.003 0.000 HIS K 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (39068) covalent geometry : angle 0.62996 / 0.30 (53364) hydrogen bonds : bond 0.03598 / 2.43 ( 1254) hydrogen bonds : angle 3.79055 / 2.66 ( 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 617 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 455 time to evaluate : 1.390 Fit side-chains REVERT: A 81 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7057 (mm) REVERT: A 249 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.6714 (mt0) REVERT: A 368 LYS cc_start: 0.8156 (mmtm) cc_final: 0.7710 (mmmt) REVERT: B 81 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7232 (mm) REVERT: B 87 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7366 (t0) REVERT: B 249 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7532 (mm110) REVERT: C 81 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7031 (mm) REVERT: C 87 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.7142 (m-30) REVERT: C 249 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7077 (mt0) REVERT: C 381 ASP cc_start: 0.7538 (t70) cc_final: 0.7279 (t0) REVERT: D 60 LYS cc_start: 0.6942 (mmtm) cc_final: 0.6649 (mmtm) REVERT: D 63 ARG cc_start: 0.6534 (tpp-160) cc_final: 0.6304 (tpp-160) REVERT: D 105 LEU cc_start: 0.4583 (OUTLIER) cc_final: 0.4184 (mt) REVERT: D 107 ARG cc_start: 0.5792 (OUTLIER) cc_final: 0.5296 (ptp-170) REVERT: D 151 ARG cc_start: 0.6717 (mmt180) cc_final: 0.6514 (mmt180) REVERT: D 249 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8264 (mm-40) REVERT: D 343 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7841 (tt0) REVERT: E 249 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7903 (mm-40) REVERT: E 390 MET cc_start: 0.9266 (mtp) cc_final: 0.9032 (mtm) REVERT: F 70 TYR cc_start: 0.6686 (t80) cc_final: 0.6172 (t80) REVERT: F 105 LEU cc_start: 0.5382 (OUTLIER) cc_final: 0.4992 (mt) REVERT: F 249 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.6885 (mt0) REVERT: F 259 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.7898 (ttm) REVERT: F 343 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7712 (tt0) REVERT: G 24 ASP cc_start: 0.6530 (OUTLIER) cc_final: 0.6148 (t0) REVERT: G 87 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7536 (m-30) REVERT: G 211 PHE cc_start: 0.7790 (m-80) cc_final: 0.7578 (m-80) REVERT: G 249 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7994 (mm-40) REVERT: H 249 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7876 (mm-40) REVERT: H 326 SER cc_start: 0.8869 (OUTLIER) cc_final: 0.8554 (m) REVERT: I 81 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.6773 (mm) REVERT: I 249 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7685 (mp10) REVERT: J 81 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.6964 (mm) REVERT: J 249 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7093 (mt0) REVERT: J 279 MET cc_start: 0.7029 (mmt) cc_final: 0.6602 (mmm) REVERT: J 368 LYS cc_start: 0.8416 (mmtt) cc_final: 0.7708 (mmmt) REVERT: J 390 MET cc_start: 0.8995 (mtp) cc_final: 0.8720 (mtm) REVERT: K 9 ASN cc_start: 0.6801 (OUTLIER) cc_final: 0.6289 (p0) REVERT: K 81 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7227 (mm) REVERT: K 200 TYR cc_start: 0.7361 (m-10) cc_final: 0.7001 (m-10) REVERT: K 368 LYS cc_start: 0.8385 (mmtt) cc_final: 0.8009 (mptt) outliers start: 162 outliers final: 80 residues processed: 585 average time/residue: 0.2240 time to fit residues: 219.2934 Evaluate side-chains 529 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 422 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP 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 159 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 107 ARG Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 249 GLN 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 249 GLN Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain D residue 159 ILE 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 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 81 LEU Chi-restraints excluded: chain E residue 87 ASP 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 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 24 ASP Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 107 ARG 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 326 SER 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 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 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 G residue 382 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 107 ARG Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 235 ILE Chi-restraints excluded: chain H residue 249 GLN 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 71 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 249 GLN 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 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 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 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 100 ILE Chi-restraints excluded: chain K residue 235 ILE 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: 3.9990 chunk 352 optimal weight: 7.9990 chunk 179 optimal weight: 5.9990 chunk 450 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 193 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 286 optimal weight: 2.9990 chunk 120 optimal weight: 0.3980 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 ASN G 66 HIS H 66 HIS K 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.172927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.152877 restraints weight = 46967.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.149228 restraints weight = 70376.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.146362 restraints weight = 87276.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.145190 restraints weight = 102468.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.143331 restraints weight = 90962.237| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1988 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= 0.143 Angle : 0.653 9.705 53364 Z= 0.306 Chirality : 0.054 0.471 5961 Planarity : 0.004 0.085 6479 Dihedral : 9.720 171.401 6145 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 4.40 % Allowed : 23.85 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.12), residues: 4532 helix: 0.25 (0.12), residues: 2101 sheet: None (None), residues: 0 loop : -2.12 (0.12), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 37 TYR 0.042 0.002 TYR K 52 PHE 0.015 0.001 PHE G 295 TRP 0.009 0.001 TRP K 298 HIS 0.003 0.001 HIS C 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (39068) covalent geometry : angle 0.65279 / 0.31 (53364) hydrogen bonds : bond 0.04043 / 2.72 ( 1254) hydrogen bonds : angle 3.85255 / 2.70 ( 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 626 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 455 time to evaluate : 1.471 Fit side-chains revert: symmetry clash REVERT: A 60 LYS cc_start: 0.7223 (mmtm) cc_final: 0.6813 (mmtm) REVERT: A 81 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7040 (mm) REVERT: A 249 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.6730 (mt0) REVERT: A 343 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7591 (tt0) REVERT: A 368 LYS cc_start: 0.8096 (mmtm) cc_final: 0.7711 (mmmt) REVERT: B 60 LYS cc_start: 0.6556 (mmtm) cc_final: 0.6153 (mmtm) REVERT: B 81 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7257 (mm) REVERT: B 87 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7315 (t0) REVERT: B 249 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7591 (mp10) REVERT: C 81 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7003 (mm) REVERT: C 87 ASP cc_start: 0.7417 (OUTLIER) cc_final: 0.7169 (m-30) REVERT: C 105 LEU cc_start: 0.5265 (OUTLIER) cc_final: 0.4801 (mt) REVERT: C 249 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7172 (mt0) REVERT: C 381 ASP cc_start: 0.7566 (t70) cc_final: 0.7309 (t0) REVERT: D 60 LYS cc_start: 0.6505 (mmtm) cc_final: 0.6146 (mmtm) REVERT: D 63 ARG cc_start: 0.6574 (tpp-160) cc_final: 0.6284 (tpp-160) REVERT: D 81 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7023 (mm) REVERT: D 105 LEU cc_start: 0.4548 (OUTLIER) cc_final: 0.4134 (mt) REVERT: D 107 ARG cc_start: 0.5891 (OUTLIER) cc_final: 0.5260 (ptp-170) REVERT: D 151 ARG cc_start: 0.6787 (mmt180) cc_final: 0.6568 (mmt180) REVERT: D 249 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8294 (mm-40) REVERT: D 343 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7798 (tt0) REVERT: E 180 PHE cc_start: 0.7334 (p90) cc_final: 0.7093 (p90) REVERT: E 249 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7973 (mm-40) REVERT: F 81 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.6840 (mm) REVERT: F 105 LEU cc_start: 0.5299 (OUTLIER) cc_final: 0.4939 (mt) REVERT: F 249 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.6947 (mt0) REVERT: F 259 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.7943 (ttm) REVERT: F 343 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7749 (tt0) REVERT: G 24 ASP cc_start: 0.6592 (OUTLIER) cc_final: 0.6192 (t0) REVERT: G 81 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.6918 (mm) REVERT: G 87 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7609 (m-30) REVERT: G 211 PHE cc_start: 0.7869 (m-80) cc_final: 0.7554 (m-80) REVERT: G 249 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8313 (mm-40) REVERT: H 81 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7517 (mm) REVERT: H 326 SER cc_start: 0.8665 (OUTLIER) cc_final: 0.8399 (m) REVERT: I 81 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.6700 (mm) REVERT: I 249 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7668 (mp10) REVERT: J 81 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.6946 (mm) REVERT: J 105 LEU cc_start: 0.5762 (OUTLIER) cc_final: 0.5445 (mt) REVERT: J 249 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7968 (mm-40) REVERT: J 279 MET cc_start: 0.7024 (mmt) cc_final: 0.6774 (mmt) REVERT: J 326 SER cc_start: 0.8834 (OUTLIER) cc_final: 0.8373 (m) REVERT: J 368 LYS cc_start: 0.8424 (mmtt) cc_final: 0.7708 (mmmt) REVERT: J 390 MET cc_start: 0.8993 (mtp) cc_final: 0.8717 (mtm) REVERT: K 9 ASN cc_start: 0.6345 (OUTLIER) cc_final: 0.5869 (p0) REVERT: K 81 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7055 (mm) REVERT: K 178 LYS cc_start: 0.7243 (mtmt) cc_final: 0.7041 (mtmt) REVERT: K 200 TYR cc_start: 0.7336 (m-10) cc_final: 0.6995 (m-10) REVERT: K 368 LYS cc_start: 0.8421 (mmtt) cc_final: 0.8032 (mptt) outliers start: 171 outliers final: 98 residues processed: 597 average time/residue: 0.2222 time to fit residues: 221.4843 Evaluate side-chains 565 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 432 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP 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 159 ILE 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 343 GLU 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 107 ARG Chi-restraints excluded: chain B residue 173 VAL 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 24 ASP 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 174 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 249 GLN Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 363 VAL 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 105 LEU Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain D residue 159 ILE 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 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 87 ASP 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 363 VAL Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 9 ASN Chi-restraints excluded: chain F residue 24 ASP 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 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 326 SER Chi-restraints excluded: chain F residue 343 GLU 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 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 176 THR 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 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 173 VAL 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 363 VAL Chi-restraints excluded: chain H residue 382 VAL 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 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 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 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 195 CYS 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 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 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 100 ILE Chi-restraints excluded: chain K residue 174 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 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: 0.2980 chunk 135 optimal weight: 7.9990 chunk 108 optimal weight: 0.0970 chunk 403 optimal weight: 0.0060 chunk 399 optimal weight: 5.9990 chunk 367 optimal weight: 1.9990 chunk 213 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 overall best weight: 1.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.174693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.154068 restraints weight = 46814.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.150580 restraints weight = 68983.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.148908 restraints weight = 84132.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.148009 restraints weight = 76353.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.146545 restraints weight = 78315.760| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2049 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= 0.119 Angle : 0.631 9.615 53364 Z= 0.297 Chirality : 0.052 0.474 5961 Planarity : 0.004 0.088 6479 Dihedral : 9.590 163.313 6145 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 3.91 % Allowed : 24.16 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.12), residues: 4532 helix: 0.38 (0.12), residues: 2101 sheet: None (None), residues: 0 loop : -2.07 (0.12), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 37 TYR 0.040 0.001 TYR K 52 PHE 0.011 0.001 PHE A 295 TRP 0.007 0.001 TRP B 375 HIS 0.004 0.001 HIS I 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (39068) covalent geometry : angle 0.63096 / 0.30 (53364) hydrogen bonds : bond 0.03567 / 2.40 ( 1254) hydrogen bonds : angle 3.72499 / 2.60 ( 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 610 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 458 time to evaluate : 1.541 Fit side-chains revert: symmetry clash REVERT: A 81 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7036 (mm) REVERT: A 249 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.6703 (mt0) REVERT: A 368 LYS cc_start: 0.8070 (mmtm) cc_final: 0.7624 (mmmt) REVERT: B 81 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7303 (mm) REVERT: B 87 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7282 (t0) REVERT: B 249 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7550 (mm110) REVERT: C 81 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7048 (mm) REVERT: C 87 ASP cc_start: 0.7388 (OUTLIER) cc_final: 0.7153 (m-30) REVERT: C 249 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.7107 (mt0) REVERT: C 381 ASP cc_start: 0.7538 (t70) cc_final: 0.7276 (t0) REVERT: D 60 LYS cc_start: 0.6462 (mmtm) cc_final: 0.6166 (mmtm) REVERT: D 81 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7017 (mm) REVERT: D 105 LEU cc_start: 0.4392 (OUTLIER) cc_final: 0.4081 (mt) REVERT: D 107 ARG cc_start: 0.5807 (OUTLIER) cc_final: 0.5273 (ptp-170) REVERT: D 151 ARG cc_start: 0.6635 (mmt180) cc_final: 0.6428 (mmt180) REVERT: D 249 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8284 (mm-40) REVERT: E 105 LEU cc_start: 0.5367 (OUTLIER) cc_final: 0.4966 (mt) REVERT: E 180 PHE cc_start: 0.7268 (p90) cc_final: 0.7066 (p90) REVERT: E 249 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7896 (mm-40) REVERT: E 326 SER cc_start: 0.9108 (OUTLIER) cc_final: 0.8888 (m) REVERT: F 81 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.6829 (mm) REVERT: F 105 LEU cc_start: 0.5308 (OUTLIER) cc_final: 0.4881 (mt) REVERT: F 249 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.6760 (mt0) REVERT: F 259 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.7901 (ttm) REVERT: F 343 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7757 (tt0) REVERT: G 8 THR cc_start: 0.5475 (OUTLIER) cc_final: 0.5170 (t) REVERT: G 24 ASP cc_start: 0.6577 (OUTLIER) cc_final: 0.6182 (t0) REVERT: G 81 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.6980 (mm) REVERT: G 279 MET cc_start: 0.6882 (mmt) cc_final: 0.6465 (mmm) REVERT: H 9 ASN cc_start: 0.5764 (OUTLIER) cc_final: 0.5343 (p0) REVERT: H 81 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7510 (mm) REVERT: H 107 ARG cc_start: 0.4771 (OUTLIER) cc_final: 0.4447 (ptp-170) REVERT: H 326 SER cc_start: 0.8821 (OUTLIER) cc_final: 0.8562 (m) REVERT: I 81 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.6697 (mm) REVERT: I 105 LEU cc_start: 0.5107 (OUTLIER) cc_final: 0.4812 (mt) REVERT: I 249 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7606 (mp10) REVERT: J 81 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.6818 (mm) REVERT: J 105 LEU cc_start: 0.5740 (OUTLIER) cc_final: 0.5419 (mt) REVERT: J 249 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7807 (mm-40) REVERT: J 326 SER cc_start: 0.8807 (OUTLIER) cc_final: 0.8415 (m) REVERT: J 368 LYS cc_start: 0.8406 (mmtt) cc_final: 0.7688 (mmmt) REVERT: J 390 MET cc_start: 0.8996 (mtp) cc_final: 0.8723 (mtm) REVERT: K 9 ASN cc_start: 0.6036 (OUTLIER) cc_final: 0.5599 (p0) REVERT: K 81 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7029 (mm) REVERT: K 200 TYR cc_start: 0.7254 (m-10) cc_final: 0.6954 (m-10) REVERT: K 368 LYS cc_start: 0.8433 (mmtt) cc_final: 0.8019 (mptt) outliers start: 152 outliers final: 90 residues processed: 583 average time/residue: 0.2338 time to fit residues: 228.0434 Evaluate side-chains 552 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 426 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 24 ASP 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 159 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 107 ARG Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 24 ASP 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 235 ILE Chi-restraints excluded: chain C residue 249 GLN Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 382 VAL 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 159 ILE 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 260 MET 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 87 ASP Chi-restraints excluded: chain E residue 105 LEU 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 326 SER 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 24 ASP 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 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 343 GLU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain G residue 8 THR 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 100 ILE Chi-restraints excluded: chain G residue 107 ARG Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 176 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 9 ASN 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 173 VAL 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 363 VAL Chi-restraints excluded: chain H residue 382 VAL 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 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 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 195 CYS Chi-restraints excluded: chain J residue 249 GLN Chi-restraints excluded: chain J residue 326 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 75 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 235 ILE 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: 8.9990 chunk 77 optimal weight: 3.9990 chunk 372 optimal weight: 0.5980 chunk 436 optimal weight: 7.9990 chunk 253 optimal weight: 20.0000 chunk 349 optimal weight: 0.0980 chunk 181 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 311 optimal weight: 2.9990 chunk 268 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 66 HIS ** 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 = 0.3816 r_free = 0.3816 target = 0.174809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.154329 restraints weight = 46706.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.150793 restraints weight = 66078.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.148594 restraints weight = 76239.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.147899 restraints weight = 86605.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.146205 restraints weight = 75832.143| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2119 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= 0.122 Angle : 0.632 10.190 53364 Z= 0.298 Chirality : 0.051 0.452 5961 Planarity : 0.004 0.088 6479 Dihedral : 9.555 160.324 6145 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 4.02 % Allowed : 24.39 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.12), residues: 4532 helix: 0.45 (0.12), residues: 2090 sheet: None (None), residues: 0 loop : -2.06 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 37 TYR 0.041 0.002 TYR K 70 PHE 0.018 0.001 PHE J 211 TRP 0.014 0.001 TRP K 183 HIS 0.003 0.001 HIS I 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (39068) covalent geometry : angle 0.63208 / 0.30 (53364) hydrogen bonds : bond 0.03657 / 2.45 ( 1254) hydrogen bonds : angle 3.73555 / 2.61 ( 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 604 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 448 time to evaluate : 1.516 Fit side-chains REVERT: A 81 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7041 (mm) REVERT: A 249 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.6693 (mt0) REVERT: A 368 LYS cc_start: 0.8030 (mmtm) cc_final: 0.7597 (mmmt) REVERT: B 81 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7271 (mm) REVERT: B 87 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.7252 (t0) REVERT: B 249 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7637 (mm110) REVERT: C 81 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.6929 (mm) REVERT: C 87 ASP cc_start: 0.7363 (OUTLIER) cc_final: 0.7136 (m-30) REVERT: C 319 GLU cc_start: 0.6242 (tt0) cc_final: 0.5923 (tt0) REVERT: C 343 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7963 (tt0) REVERT: C 381 ASP cc_start: 0.7522 (t70) cc_final: 0.7242 (t0) REVERT: D 24 ASP cc_start: 0.6650 (OUTLIER) cc_final: 0.6220 (m-30) REVERT: D 60 LYS cc_start: 0.7067 (mmtm) cc_final: 0.5113 (mmmt) REVERT: D 81 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.6997 (mm) REVERT: D 105 LEU cc_start: 0.4522 (OUTLIER) cc_final: 0.4167 (mt) REVERT: D 107 ARG cc_start: 0.5806 (OUTLIER) cc_final: 0.5307 (ptp-170) REVERT: D 151 ARG cc_start: 0.6629 (mmt180) cc_final: 0.6395 (mmt180) REVERT: D 249 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8270 (mm-40) REVERT: D 343 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7869 (tt0) REVERT: E 105 LEU cc_start: 0.5333 (OUTLIER) cc_final: 0.4962 (mt) REVERT: E 249 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7924 (mm-40) REVERT: E 319 GLU cc_start: 0.6602 (tt0) cc_final: 0.6364 (tt0) REVERT: F 81 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6812 (mm) REVERT: F 105 LEU cc_start: 0.5277 (OUTLIER) cc_final: 0.4907 (mt) REVERT: F 249 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.6808 (mt0) REVERT: F 259 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.7907 (ttm) REVERT: F 343 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7693 (tt0) REVERT: G 8 THR cc_start: 0.5594 (OUTLIER) cc_final: 0.5315 (t) REVERT: G 24 ASP cc_start: 0.6639 (OUTLIER) cc_final: 0.6308 (t0) REVERT: G 81 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.6825 (mm) REVERT: G 87 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.7599 (m-30) REVERT: H 9 ASN cc_start: 0.5764 (OUTLIER) cc_final: 0.5336 (p0) REVERT: H 81 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7426 (mm) REVERT: H 105 LEU cc_start: 0.4860 (OUTLIER) cc_final: 0.4548 (mt) REVERT: H 273 MET cc_start: 0.7319 (tmm) cc_final: 0.7066 (tmm) REVERT: H 326 SER cc_start: 0.8771 (OUTLIER) cc_final: 0.8459 (m) REVERT: I 81 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.6675 (mm) REVERT: I 105 LEU cc_start: 0.5126 (OUTLIER) cc_final: 0.4814 (mt) REVERT: I 249 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7616 (mp10) REVERT: J 105 LEU cc_start: 0.5736 (OUTLIER) cc_final: 0.5422 (mt) REVERT: J 249 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7813 (mm-40) REVERT: J 279 MET cc_start: 0.6984 (mmt) cc_final: 0.6603 (mmm) REVERT: J 326 SER cc_start: 0.8712 (OUTLIER) cc_final: 0.8298 (m) REVERT: J 368 LYS cc_start: 0.8417 (mmtt) cc_final: 0.7699 (mmmt) REVERT: J 390 MET cc_start: 0.9014 (mtp) cc_final: 0.8740 (mtm) REVERT: K 9 ASN cc_start: 0.6279 (OUTLIER) cc_final: 0.5852 (p0) REVERT: K 81 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7058 (mm) REVERT: K 200 TYR cc_start: 0.7254 (m-10) cc_final: 0.7003 (m-10) REVERT: K 368 LYS cc_start: 0.8430 (mmtt) cc_final: 0.8019 (mptt) outliers start: 156 outliers final: 100 residues processed: 575 average time/residue: 0.2316 time to fit residues: 223.1559 Evaluate side-chains 566 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 430 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 24 ASP 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 159 ILE 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 107 ARG Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 24 ASP 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 162 CYS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain D residue 24 ASP 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 159 ILE 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 260 MET 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 75 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 174 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 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 24 ASP 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 326 SER Chi-restraints excluded: chain F residue 343 GLU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain G residue 8 THR 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 107 ARG Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 210 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 9 ASN 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 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 363 VAL Chi-restraints excluded: chain H residue 382 VAL 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 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 363 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 75 LEU 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 195 CYS Chi-restraints excluded: chain J residue 249 GLN Chi-restraints excluded: chain J residue 326 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 75 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 174 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 Chi-restraints excluded: chain K residue 408 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 316 optimal weight: 5.9990 chunk 231 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 334 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 193 optimal weight: 0.8980 chunk 221 optimal weight: 0.0010 chunk 336 optimal weight: 8.9990 overall best weight: 1.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.175365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.152552 restraints weight = 47006.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.148675 restraints weight = 65096.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.145982 restraints weight = 76793.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.145029 restraints weight = 84077.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.143271 restraints weight = 73073.097| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2177 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= 0.118 Angle : 0.629 10.012 53364 Z= 0.297 Chirality : 0.051 0.449 5961 Planarity : 0.004 0.083 6479 Dihedral : 9.503 159.303 6145 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 3.63 % Allowed : 24.85 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.13), residues: 4532 helix: 0.52 (0.12), residues: 2079 sheet: None (None), residues: 0 loop : -2.03 (0.12), residues: 2453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 37 TYR 0.041 0.002 TYR K 52 PHE 0.017 0.001 PHE J 211 TRP 0.013 0.001 TRP E 169 HIS 0.003 0.000 HIS I 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (39068) covalent geometry : angle 0.62897 / 0.30 (53364) hydrogen bonds : bond 0.03542 / 2.38 ( 1254) hydrogen bonds : angle 3.75033 / 2.60 ( 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 587 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 446 time to evaluate : 1.434 Fit side-chains REVERT: A 81 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7024 (mm) REVERT: A 249 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7764 (mm110) REVERT: A 343 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7801 (tt0) REVERT: A 368 LYS cc_start: 0.7978 (mmtm) cc_final: 0.7593 (mmmt) REVERT: B 81 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7148 (mm) REVERT: B 87 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7248 (t0) REVERT: B 249 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7625 (mm110) REVERT: C 81 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.6918 (mm) REVERT: C 87 ASP cc_start: 0.7488 (OUTLIER) cc_final: 0.7272 (m-30) REVERT: C 105 LEU cc_start: 0.5274 (OUTLIER) cc_final: 0.4813 (mt) REVERT: C 151 ARG cc_start: 0.6451 (mmt180) cc_final: 0.6235 (mmt180) REVERT: C 319 GLU cc_start: 0.6501 (tt0) cc_final: 0.6299 (tt0) REVERT: D 60 LYS cc_start: 0.7029 (mmtm) cc_final: 0.5112 (mmmt) REVERT: D 81 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.6943 (mm) REVERT: D 105 LEU cc_start: 0.4857 (OUTLIER) cc_final: 0.4490 (mt) REVERT: D 107 ARG cc_start: 0.5783 (OUTLIER) cc_final: 0.5243 (ptp-170) REVERT: D 151 ARG cc_start: 0.6541 (mmt180) cc_final: 0.6332 (mmt180) REVERT: D 249 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8241 (mm-40) REVERT: D 343 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7902 (tt0) REVERT: E 27 SER cc_start: 0.7811 (t) cc_final: 0.7552 (t) REVERT: E 105 LEU cc_start: 0.5359 (OUTLIER) cc_final: 0.4948 (mt) REVERT: E 249 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7911 (mm-40) REVERT: F 81 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6812 (mm) REVERT: F 105 LEU cc_start: 0.5315 (OUTLIER) cc_final: 0.4970 (mt) REVERT: F 249 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.6775 (mt0) REVERT: F 259 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.7923 (ttm) REVERT: F 343 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7677 (tt0) REVERT: G 8 THR cc_start: 0.5527 (OUTLIER) cc_final: 0.5257 (t) REVERT: G 24 ASP cc_start: 0.6689 (OUTLIER) cc_final: 0.6337 (t0) REVERT: G 81 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.6877 (mm) REVERT: G 87 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7640 (m-30) REVERT: G 279 MET cc_start: 0.7193 (mmt) cc_final: 0.6926 (mmp) REVERT: H 81 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7413 (mm) REVERT: H 105 LEU cc_start: 0.4853 (OUTLIER) cc_final: 0.4570 (mt) REVERT: H 273 MET cc_start: 0.7449 (tmm) cc_final: 0.7221 (tmm) REVERT: H 326 SER cc_start: 0.8791 (OUTLIER) cc_final: 0.8487 (m) REVERT: I 81 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.6644 (mm) REVERT: I 105 LEU cc_start: 0.5140 (OUTLIER) cc_final: 0.4912 (mt) REVERT: I 249 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7649 (mp10) REVERT: J 105 LEU cc_start: 0.5775 (OUTLIER) cc_final: 0.5504 (mt) REVERT: J 249 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7787 (mm-40) REVERT: J 279 MET cc_start: 0.6835 (mmt) cc_final: 0.6486 (mmm) REVERT: J 326 SER cc_start: 0.8681 (OUTLIER) cc_final: 0.8260 (m) REVERT: J 368 LYS cc_start: 0.8350 (mmtt) cc_final: 0.7690 (mmtt) REVERT: J 382 VAL cc_start: 0.8686 (OUTLIER) cc_final: 0.8473 (t) REVERT: J 390 MET cc_start: 0.9000 (mtp) cc_final: 0.8738 (mtm) REVERT: K 9 ASN cc_start: 0.6253 (OUTLIER) cc_final: 0.5786 (p0) REVERT: K 81 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7028 (mm) REVERT: K 200 TYR cc_start: 0.7306 (m-10) cc_final: 0.7046 (m-10) REVERT: K 368 LYS cc_start: 0.8442 (mmtt) cc_final: 0.8018 (mptt) outliers start: 141 outliers final: 97 residues processed: 560 average time/residue: 0.2354 time to fit residues: 221.1379 Evaluate side-chains 563 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 431 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 24 ASP 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 159 ILE 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 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 159 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 24 ASP 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 235 ILE Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 363 VAL 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 159 ILE 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 260 MET 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 81 LEU Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain E residue 105 LEU 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 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 24 ASP 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 326 SER Chi-restraints excluded: chain F residue 343 GLU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain G residue 8 THR 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 107 ARG Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 210 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 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 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 363 VAL Chi-restraints excluded: chain H residue 382 VAL 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 363 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 75 LEU 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 195 CYS Chi-restraints excluded: chain J residue 249 GLN Chi-restraints excluded: chain J residue 326 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 81 LEU Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 174 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 Chi-restraints excluded: chain K residue 408 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 113 optimal weight: 0.0050 chunk 452 optimal weight: 9.9990 chunk 347 optimal weight: 9.9990 chunk 85 optimal weight: 20.0000 chunk 281 optimal weight: 0.0010 chunk 144 optimal weight: 9.9990 chunk 154 optimal weight: 6.9990 chunk 345 optimal weight: 20.0000 chunk 359 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 overall best weight: 4.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 HIS K 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.170732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.150917 restraints weight = 46794.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.147699 restraints weight = 75206.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.144709 restraints weight = 86796.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.143059 restraints weight = 105330.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.140438 restraints weight = 97076.507| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2286 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= 0.217 Angle : 0.723 10.404 53364 Z= 0.345 Chirality : 0.057 0.516 5961 Planarity : 0.005 0.085 6479 Dihedral : 9.752 163.290 6145 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % Rotamer: Outliers : 3.63 % Allowed : 25.01 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.12), residues: 4532 helix: 0.08 (0.12), residues: 2112 sheet: None (None), residues: 0 loop : -2.15 (0.12), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 37 TYR 0.043 0.002 TYR H 52 PHE 0.021 0.002 PHE G 295 TRP 0.014 0.002 TRP K 298 HIS 0.004 0.001 HIS E 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.22 (39068) covalent geometry : angle 0.72297 / 0.34 (53364) hydrogen bonds : bond 0.04841 / 3.25 ( 1254) hydrogen bonds : angle 4.13284 / 2.90 ( 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 574 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 433 time to evaluate : 1.460 Fit side-chains revert: symmetry clash REVERT: A 81 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7027 (mm) REVERT: A 249 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7139 (mt0) REVERT: A 343 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7821 (tt0) REVERT: A 368 LYS cc_start: 0.8040 (mmtm) cc_final: 0.7735 (mmmt) REVERT: B 81 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7141 (mm) REVERT: B 87 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7322 (t0) REVERT: B 105 LEU cc_start: 0.5071 (OUTLIER) cc_final: 0.4862 (mt) REVERT: B 249 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7894 (mp10) REVERT: B 279 MET cc_start: 0.7102 (mmm) cc_final: 0.6821 (mmm) REVERT: C 81 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.6880 (mm) REVERT: C 87 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.7099 (m-30) REVERT: C 343 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7949 (tt0) REVERT: C 381 ASP cc_start: 0.7585 (t70) cc_final: 0.7331 (t0) REVERT: D 60 LYS cc_start: 0.7238 (mmtm) cc_final: 0.6875 (mmtm) REVERT: D 81 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7154 (mm) REVERT: D 105 LEU cc_start: 0.4732 (OUTLIER) cc_final: 0.4456 (mt) REVERT: D 107 ARG cc_start: 0.5897 (OUTLIER) cc_final: 0.5179 (ptp-170) REVERT: D 151 ARG cc_start: 0.6744 (mmt180) cc_final: 0.6476 (mmt180) REVERT: D 249 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8406 (mm-40) REVERT: D 343 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7960 (tt0) REVERT: E 105 LEU cc_start: 0.5200 (OUTLIER) cc_final: 0.4857 (mt) REVERT: F 81 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6818 (mm) REVERT: F 105 LEU cc_start: 0.5505 (OUTLIER) cc_final: 0.5062 (mt) REVERT: F 249 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7263 (mt0) REVERT: F 259 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8253 (ttm) REVERT: F 343 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7577 (tt0) REVERT: G 8 THR cc_start: 0.5667 (OUTLIER) cc_final: 0.5374 (t) REVERT: G 81 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.6831 (mm) REVERT: G 87 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.7617 (m-30) REVERT: G 279 MET cc_start: 0.7091 (mmt) cc_final: 0.6806 (mmp) REVERT: G 343 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7766 (tt0) REVERT: H 81 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7455 (mm) REVERT: H 105 LEU cc_start: 0.5148 (OUTLIER) cc_final: 0.4770 (mt) REVERT: H 326 SER cc_start: 0.8836 (OUTLIER) cc_final: 0.8495 (m) REVERT: I 81 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.6616 (mm) REVERT: I 105 LEU cc_start: 0.5447 (OUTLIER) cc_final: 0.5052 (mt) REVERT: I 249 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7535 (mt0) REVERT: I 343 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7778 (tt0) REVERT: J 81 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.6893 (mm) REVERT: J 105 LEU cc_start: 0.5857 (OUTLIER) cc_final: 0.5560 (mt) REVERT: J 249 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8050 (mm-40) REVERT: J 279 MET cc_start: 0.7036 (mmt) cc_final: 0.6580 (mmm) REVERT: J 326 SER cc_start: 0.8743 (OUTLIER) cc_final: 0.8413 (m) REVERT: J 368 LYS cc_start: 0.8211 (mmtt) cc_final: 0.7628 (mmtt) REVERT: J 390 MET cc_start: 0.9020 (mtp) cc_final: 0.8763 (mtm) REVERT: K 81 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7101 (mm) REVERT: K 368 LYS cc_start: 0.8473 (mmtt) cc_final: 0.8029 (mptt) outliers start: 141 outliers final: 96 residues processed: 548 average time/residue: 0.2432 time to fit residues: 220.1377 Evaluate side-chains 542 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 413 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 24 ASP 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 159 ILE 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 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 159 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 390 MET Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 24 ASP 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 162 CYS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 343 GLU 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 81 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain D residue 159 ILE 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 260 MET Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 382 VAL 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 235 ILE Chi-restraints excluded: chain E residue 259 MET 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 24 ASP 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 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 382 VAL Chi-restraints excluded: chain G residue 8 THR 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 107 ARG Chi-restraints excluded: chain G residue 159 ILE 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 210 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 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 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 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 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 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 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 195 CYS Chi-restraints excluded: chain J residue 249 GLN Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain J residue 406 ASP Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 174 THR Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain K residue 408 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 276 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 291 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 447 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 371 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 274 optimal weight: 0.7980 chunk 422 optimal weight: 6.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN K 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.171945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.152342 restraints weight = 46844.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.148568 restraints weight = 74404.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.145980 restraints weight = 81047.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.144491 restraints weight = 100704.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.143132 restraints weight = 89465.930| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 39068 Z= 0.168 Angle : 0.685 10.366 53364 Z= 0.326 Chirality : 0.055 0.519 5961 Planarity : 0.005 0.088 6479 Dihedral : 9.682 160.509 6145 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.55 % Favored : 89.45 % Rotamer: Outliers : 3.71 % Allowed : 25.32 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.12), residues: 4532 helix: 0.18 (0.12), residues: 2090 sheet: None (None), residues: 0 loop : -2.09 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 37 TYR 0.042 0.002 TYR K 52 PHE 0.017 0.002 PHE J 211 TRP 0.010 0.002 TRP K 298 HIS 0.003 0.001 HIS H 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (39068) covalent geometry : angle 0.68548 / 0.33 (53364) hydrogen bonds : bond 0.04258 / 2.87 ( 1254) hydrogen bonds : angle 4.04930 / 2.83 ( 3432) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5660.32 seconds wall clock time: 99 minutes 18.86 seconds (5958.86 seconds total)