Starting phenix.real_space_refine on Mon Jul 6 16:40:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yg7_33810/07_2026/7yg7_33810.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yg7_33810/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7yg7_33810/07_2026/7yg7_33810.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yg7_33810/07_2026/7yg7_33810.map" model { file = "/net/cci-nas-00/data/ceres_data/7yg7_33810/07_2026/7yg7_33810.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yg7_33810/07_2026/7yg7_33810.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7yg7_33810/07_2026/7yg7_33810.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yg7_33810/07_2026/7yg7_33810.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 98 5.49 5 S 187 5.16 5 C 23925 2.51 5 N 6281 2.21 5 O 7544 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: {'RNA': 99} Modifications used: {'5*END': 1, 'rna2p_pyr': 13, 'rna3p_pyr': 86} Link IDs: {'rna2p': 13, 'rna3p': 85} Time building chain proxies: 6.90, per 1000 atoms: 0.18 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: 2.59 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: 3.43 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: 5.56 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7628 1.33 - 1.45: 9682 1.45 - 1.57: 21243 1.57 - 1.69: 196 1.69 - 1.81: 319 Bond restraints: 39068 Sorted by residual: bond pdb=" SD MET H 279 " pdb=" CE MET H 279 " ideal model delta sigma weight residual 1.791 1.743 0.048 2.50e-02 1.60e+03 3.65e+00 bond pdb=" SD MET F 279 " pdb=" CE MET F 279 " ideal model delta sigma weight residual 1.791 1.743 0.048 2.50e-02 1.60e+03 3.63e+00 bond pdb=" SD MET D 279 " pdb=" CE MET D 279 " ideal model delta sigma weight residual 1.791 1.744 0.047 2.50e-02 1.60e+03 3.56e+00 bond pdb=" SD MET I 279 " pdb=" CE MET I 279 " ideal model delta sigma weight residual 1.791 1.744 0.047 2.50e-02 1.60e+03 3.55e+00 bond pdb=" SD MET B 279 " pdb=" CE MET B 279 " ideal model delta sigma weight residual 1.791 1.744 0.047 2.50e-02 1.60e+03 3.54e+00 ... (remaining 39063 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 51953 2.07 - 4.14: 1145 4.14 - 6.21: 167 6.21 - 8.29: 55 8.29 - 10.36: 44 Bond angle restraints: 53364 Sorted by residual: angle pdb=" C ARG F 353 " pdb=" N LYS F 354 " pdb=" CA LYS F 354 " ideal model delta sigma weight residual 121.80 130.22 -8.42 2.44e+00 1.68e-01 1.19e+01 angle pdb=" C ARG C 353 " pdb=" N LYS C 354 " pdb=" CA LYS C 354 " ideal model delta sigma weight residual 121.80 130.21 -8.41 2.44e+00 1.68e-01 1.19e+01 angle pdb=" C ARG B 353 " pdb=" N LYS B 354 " pdb=" CA LYS B 354 " ideal model delta sigma weight residual 121.80 130.20 -8.40 2.44e+00 1.68e-01 1.18e+01 angle pdb=" C ARG I 353 " pdb=" N LYS I 354 " pdb=" CA LYS I 354 " ideal model delta sigma weight residual 121.80 130.20 -8.40 2.44e+00 1.68e-01 1.18e+01 angle pdb=" C ARG A 353 " pdb=" N LYS A 354 " pdb=" CA LYS A 354 " ideal model delta sigma weight residual 121.80 130.20 -8.40 2.44e+00 1.68e-01 1.18e+01 ... (remaining 53359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.72: 22262 34.72 - 69.44: 976 69.44 - 104.16: 40 104.16 - 138.88: 4 138.88 - 173.60: 12 Dihedral angle restraints: 23294 sinusoidal: 10028 harmonic: 13266 Sorted by residual: dihedral pdb=" O4' U U 95 " pdb=" C1' U U 95 " pdb=" N1 U U 95 " pdb=" C2 U U 95 " ideal model delta sinusoidal sigma weight residual -160.00 13.60 -173.60 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' U U 97 " pdb=" C1' U U 97 " pdb=" N1 U U 97 " pdb=" C2 U U 97 " ideal model delta sinusoidal sigma weight residual 200.00 26.52 173.48 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' U U 5 " pdb=" C1' U U 5 " pdb=" N1 U U 5 " pdb=" C2 U U 5 " ideal model delta sinusoidal sigma weight residual -160.00 12.68 -172.68 1 1.50e+01 4.44e-03 8.50e+01 ... (remaining 23291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4079 0.045 - 0.090: 1497 0.090 - 0.135: 297 0.135 - 0.180: 48 0.180 - 0.224: 40 Chirality restraints: 5961 Sorted by residual: chirality pdb=" CG LEU D 132 " pdb=" CB LEU D 132 " pdb=" CD1 LEU D 132 " pdb=" CD2 LEU D 132 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CG LEU C 132 " pdb=" CB LEU C 132 " pdb=" CD1 LEU C 132 " pdb=" CD2 LEU C 132 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CG LEU F 132 " pdb=" CB LEU F 132 " pdb=" CD1 LEU F 132 " pdb=" CD2 LEU F 132 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 5958 not shown) Planarity restraints: 6479 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU K 16 " 0.070 5.00e-02 4.00e+02 1.05e-01 1.75e+01 pdb=" N PRO K 17 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO K 17 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO K 17 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G 16 " -0.070 5.00e-02 4.00e+02 1.05e-01 1.75e+01 pdb=" N PRO G 17 " 0.181 5.00e-02 4.00e+02 pdb=" CA PRO G 17 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO G 17 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 16 " 0.070 5.00e-02 4.00e+02 1.05e-01 1.75e+01 pdb=" N PRO B 17 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO B 17 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 17 " 0.056 5.00e-02 4.00e+02 ... (remaining 6476 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 396 2.63 - 3.20: 32506 3.20 - 3.77: 58402 3.77 - 4.33: 79342 4.33 - 4.90: 126441 Nonbonded interactions: 297087 Sorted by model distance: nonbonded pdb=" O2' U U 38 " pdb=" O5' U U 39 " model vdw 2.065 3.040 nonbonded pdb=" O2' U U 38 " pdb=" O4' U U 39 " model vdw 2.221 3.040 nonbonded pdb=" O2' U U 41 " pdb=" OP1 U U 43 " model vdw 2.235 3.040 nonbonded pdb=" N THR A 289 " pdb=" OP2 U U 76 " model vdw 2.293 3.120 nonbonded pdb=" OH TYR F 150 " pdb=" OP2 U U 26 " model vdw 2.304 3.040 ... (remaining 297082 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 30.930 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.070 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.780 ------------------------------------------------------------------------------- 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= 0.210 Angle : 0.796 10.357 53364 Z= 0.415 Chirality : 0.050 0.224 5961 Planarity : 0.007 0.105 6479 Dihedral : 18.086 173.599 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 0.00446 / 0.21 (39068) covalent geometry : angle 0.79568 / 0.42 (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 : 1.384 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: 0.2275 time to fit residues: 195.9162 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 : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASN Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 368 LYS Chi-restraints excluded: chain G residue 342 ILE Chi-restraints excluded: chain H residue 9 ASN Chi-restraints excluded: chain I residue 9 ASN Chi-restraints excluded: chain I residue 267 ASP Chi-restraints excluded: chain J residue 368 LYS Chi-restraints excluded: chain K residue 368 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 0.3980 chunk 401 optimal weight: 5.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3793 r_free = 0.3793 target = 0.172889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.152160 restraints weight = 46882.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.148758 restraints weight = 72191.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.146882 restraints weight = 72287.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.145897 restraints weight = 75339.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.143988 restraints weight = 75557.701| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1129 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= 0.158 Angle : 0.583 9.047 53364 Z= 0.311 Chirality : 0.044 0.325 5961 Planarity : 0.005 0.073 6479 Dihedral : 12.382 175.735 6185 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 2.40 % Allowed : 24.49 % Favored : 73.11 % 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: -1.86 (0.12), residues: 4532 helix: -0.24 (0.11), residues: 2112 sheet: None (None), residues: 0 loop : -2.23 (0.12), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 50 TYR 0.038 0.002 TYR I 52 PHE 0.016 0.002 PHE J 30 TRP 0.011 0.001 TRP K 298 HIS 0.003 0.001 HIS G 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (39068) covalent geometry : angle 0.58253 / 0.31 (53364) hydrogen bonds : bond 0.04612 / 3.09 ( 1254) hydrogen bonds : angle 4.00874 / 2.81 ( 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 553 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 460 time to evaluate : 1.304 Fit side-chains REVERT: A 249 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7047 (mt0) REVERT: A 332 MET cc_start: 0.8630 (ttt) cc_final: 0.8078 (ttt) REVERT: A 368 LYS cc_start: 0.8121 (mmtm) cc_final: 0.7734 (mmmt) REVERT: B 60 LYS cc_start: 0.6378 (mmtm) cc_final: 0.5993 (mmtm) REVERT: B 70 TYR cc_start: 0.6274 (t80) cc_final: 0.5918 (t80) REVERT: B 249 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7526 (mp10) REVERT: C 249 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.7153 (mt0) REVERT: C 381 ASP cc_start: 0.7535 (t70) cc_final: 0.7194 (t0) REVERT: D 249 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8212 (mm-40) REVERT: E 63 ARG cc_start: 0.6314 (tpp-160) cc_final: 0.6060 (tpp-160) REVERT: E 249 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7954 (mm-40) REVERT: E 342 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8808 (mt) REVERT: E 390 MET cc_start: 0.9162 (mtp) cc_final: 0.8955 (mtm) REVERT: F 249 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7079 (mt0) REVERT: F 260 MET cc_start: 0.8716 (mmt) cc_final: 0.8261 (mmt) REVERT: F 368 LYS cc_start: 0.8163 (mmtt) cc_final: 0.7720 (mmmt) REVERT: G 24 ASP cc_start: 0.6656 (OUTLIER) cc_final: 0.6345 (t0) REVERT: G 249 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8228 (mm-40) REVERT: H 9 ASN cc_start: 0.6203 (OUTLIER) cc_final: 0.5731 (p0) REVERT: H 249 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7991 (mm-40) REVERT: I 9 ASN cc_start: 0.5705 (OUTLIER) cc_final: 0.5301 (p0) REVERT: I 249 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7553 (mp10) REVERT: I 259 MET cc_start: 0.8526 (ttp) cc_final: 0.8317 (ttp) REVERT: I 381 ASP cc_start: 0.7951 (t70) cc_final: 0.7640 (t0) REVERT: J 249 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7196 (mt0) REVERT: J 259 MET cc_start: 0.8748 (ttp) cc_final: 0.8454 (ttp) REVERT: J 260 MET cc_start: 0.8788 (mmt) cc_final: 0.8576 (mmm) REVERT: J 368 LYS cc_start: 0.8424 (mmtt) cc_final: 0.8038 (mttm) REVERT: J 390 MET cc_start: 0.8987 (mtp) cc_final: 0.8734 (mtm) REVERT: K 249 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.8069 (mm-40) REVERT: K 259 MET cc_start: 0.8512 (ttp) cc_final: 0.8280 (ttp) REVERT: K 368 LYS cc_start: 0.8310 (mmtt) cc_final: 0.8039 (mptt) outliers start: 93 outliers final: 28 residues processed: 535 average time/residue: 0.2000 time to fit residues: 178.9263 Evaluate side-chains 464 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 421 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain K residue 408 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 421 optimal weight: 40.0000 chunk 93 optimal weight: 50.0000 chunk 344 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 427 optimal weight: 0.9990 chunk 354 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 159 optimal weight: 0.0070 chunk 12 optimal weight: 10.0000 chunk 187 optimal weight: 3.9990 chunk 380 optimal weight: 30.0000 overall best weight: 2.4604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 GLN E 51 GLN G 66 HIS H 51 GLN H 66 HIS K 51 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.172969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.152968 restraints weight = 46857.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.149240 restraints weight = 75964.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.147723 restraints weight = 89256.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.147265 restraints weight = 84552.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.145061 restraints weight = 90884.765| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 39068 Z= 0.142 Angle : 0.561 10.077 53364 Z= 0.295 Chirality : 0.044 0.320 5961 Planarity : 0.005 0.064 6479 Dihedral : 12.058 178.887 6151 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % Rotamer: Outliers : 3.66 % Allowed : 23.31 % Favored : 73.04 % 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: -1.60 (0.12), residues: 4532 helix: 0.06 (0.12), residues: 2112 sheet: None (None), residues: 0 loop : -2.19 (0.12), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 37 TYR 0.036 0.002 TYR I 52 PHE 0.016 0.001 PHE G 295 TRP 0.010 0.001 TRP K 298 HIS 0.002 0.001 HIS J 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (39068) covalent geometry : angle 0.56125 / 0.30 (53364) hydrogen bonds : bond 0.04099 / 2.76 ( 1254) hydrogen bonds : angle 3.85658 / 2.70 ( 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 604 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 462 time to evaluate : 1.022 Fit side-chains REVERT: A 249 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.6945 (mt0) REVERT: A 332 MET cc_start: 0.8560 (ttt) cc_final: 0.8096 (ttt) REVERT: A 368 LYS cc_start: 0.8153 (mmtm) cc_final: 0.7754 (mmmt) REVERT: B 60 LYS cc_start: 0.6413 (mmtm) cc_final: 0.6040 (mmtm) REVERT: B 70 TYR cc_start: 0.6488 (t80) cc_final: 0.6265 (t80) REVERT: B 87 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7361 (t0) REVERT: B 249 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7399 (mp10) REVERT: C 16 LEU cc_start: 0.8347 (pt) cc_final: 0.8049 (pp) REVERT: C 81 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7111 (mm) REVERT: C 249 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.7175 (mt0) REVERT: C 381 ASP cc_start: 0.7495 (t70) cc_final: 0.7242 (t0) REVERT: D 60 LYS cc_start: 0.6884 (mmtm) cc_final: 0.6564 (mmtm) REVERT: D 63 ARG cc_start: 0.6583 (tpp-160) cc_final: 0.6301 (tpp-160) REVERT: D 81 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7083 (mm) REVERT: D 249 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8273 (mm-40) REVERT: E 107 ARG cc_start: 0.5434 (OUTLIER) cc_final: 0.5137 (ptp-170) REVERT: E 180 PHE cc_start: 0.7164 (p90) cc_final: 0.6932 (p90) REVERT: E 249 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7787 (mm-40) REVERT: E 390 MET cc_start: 0.9259 (mtp) cc_final: 0.9034 (mtm) REVERT: F 81 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.6938 (mm) REVERT: F 200 TYR cc_start: 0.7751 (m-10) cc_final: 0.7422 (m-10) REVERT: F 249 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.6989 (mt0) REVERT: F 273 MET cc_start: 0.7217 (tmm) cc_final: 0.6995 (tmm) REVERT: F 343 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7786 (tt0) REVERT: F 368 LYS cc_start: 0.8223 (mmtt) cc_final: 0.7891 (mmmt) REVERT: G 24 ASP cc_start: 0.6602 (OUTLIER) cc_final: 0.6305 (t0) REVERT: G 70 TYR cc_start: 0.6518 (t80) cc_final: 0.6261 (t80) REVERT: G 81 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.6820 (mm) REVERT: G 249 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8259 (mm-40) REVERT: H 81 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7514 (mm) REVERT: H 249 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7882 (mm-40) REVERT: I 9 ASN cc_start: 0.5732 (OUTLIER) cc_final: 0.5491 (p0) REVERT: I 81 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.6791 (mm) REVERT: I 151 ARG cc_start: 0.6841 (mmt180) cc_final: 0.6640 (mmt180) REVERT: I 249 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7574 (mp10) REVERT: I 259 MET cc_start: 0.8551 (ttp) cc_final: 0.8350 (ttp) REVERT: I 381 ASP cc_start: 0.7828 (t70) cc_final: 0.7603 (t0) REVERT: J 70 TYR cc_start: 0.6874 (t80) cc_final: 0.6515 (t80) REVERT: J 81 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.6855 (mm) REVERT: J 249 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7878 (mm-40) REVERT: J 259 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8380 (ttp) REVERT: J 279 MET cc_start: 0.7033 (mmt) cc_final: 0.6527 (mmm) REVERT: J 368 LYS cc_start: 0.8439 (mmtt) cc_final: 0.8031 (mptt) REVERT: J 390 MET cc_start: 0.8986 (mtp) cc_final: 0.8719 (mtm) REVERT: K 81 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7132 (mm) REVERT: K 200 TYR cc_start: 0.7526 (m-10) cc_final: 0.7168 (m-80) REVERT: K 249 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8183 (mm-40) REVERT: K 259 MET cc_start: 0.8455 (ttp) cc_final: 0.8239 (ttp) REVERT: K 368 LYS cc_start: 0.8336 (mmtt) cc_final: 0.7973 (mptt) outliers start: 142 outliers final: 69 residues processed: 582 average time/residue: 0.2032 time to fit residues: 194.6865 Evaluate side-chains 514 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 420 time to evaluate : 1.258 ------------------------------------------------------------------------------- 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 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 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 249 GLN Chi-restraints excluded: chain B residue 363 VAL 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 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 C residue 363 VAL 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 363 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 100 ILE Chi-restraints excluded: chain E residue 107 ARG Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 259 MET Chi-restraints excluded: chain E residue 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 343 GLU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 100 ILE 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 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 H residue 363 VAL Chi-restraints excluded: chain I residue 9 ASN Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 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 174 THR Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain J residue 235 ILE Chi-restraints excluded: chain J residue 249 GLN Chi-restraints excluded: chain J residue 259 MET Chi-restraints excluded: chain J residue 363 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: 20.0000 chunk 86 optimal weight: 6.9990 chunk 232 optimal weight: 9.9990 chunk 289 optimal weight: 9.9990 chunk 202 optimal weight: 1.9990 chunk 272 optimal weight: 9.9990 chunk 329 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 170 optimal weight: 20.0000 chunk 256 optimal weight: 20.0000 chunk 354 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN F 51 GLN G 51 GLN ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 51 GLN J 51 GLN K 68 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.168061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.147315 restraints weight = 46946.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.143728 restraints weight = 78645.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.141163 restraints weight = 83679.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.139598 restraints weight = 100235.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.137491 restraints weight = 94917.299| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 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 : 0.007 0.058 39068 Z= 0.297 Angle : 0.700 10.483 53364 Z= 0.372 Chirality : 0.050 0.334 5961 Planarity : 0.006 0.082 6479 Dihedral : 12.346 179.564 6147 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.14 % Favored : 87.86 % Rotamer: Outliers : 5.15 % Allowed : 22.92 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.04 (0.12), residues: 4532 helix: -0.43 (0.11), residues: 2156 sheet: None (None), residues: 0 loop : -2.32 (0.12), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 107 TYR 0.043 0.003 TYR K 52 PHE 0.026 0.003 PHE F 29 TRP 0.017 0.002 TRP K 298 HIS 0.005 0.001 HIS G 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00704 / 0.30 (39068) covalent geometry : angle 0.70030 / 0.37 (53364) hydrogen bonds : bond 0.05856 / 3.94 ( 1254) hydrogen bonds : angle 4.36070 / 3.08 ( 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 636 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 436 time to evaluate : 1.078 Fit side-chains REVERT: A 70 TYR cc_start: 0.6530 (t80) cc_final: 0.6242 (t80) REVERT: A 81 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7041 (mm) REVERT: A 249 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.7258 (mt0) REVERT: A 343 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7668 (tt0) REVERT: A 368 LYS cc_start: 0.8170 (mmtm) cc_final: 0.7835 (mmmt) REVERT: B 60 LYS cc_start: 0.6412 (mmtm) cc_final: 0.6163 (mmtm) REVERT: B 81 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7206 (mm) REVERT: B 87 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7371 (t0) REVERT: B 249 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7957 (mp10) REVERT: C 16 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8108 (pp) REVERT: C 70 TYR cc_start: 0.7025 (t80) cc_final: 0.6722 (t80) REVERT: C 81 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.6959 (mm) REVERT: C 87 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.7109 (m-30) REVERT: C 249 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.7449 (mt0) REVERT: C 343 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7836 (tt0) REVERT: C 381 ASP cc_start: 0.7623 (t70) cc_final: 0.7387 (t0) REVERT: C 392 MET cc_start: 0.6990 (ttm) cc_final: 0.6742 (ttt) REVERT: D 60 LYS cc_start: 0.6713 (mmtm) cc_final: 0.6428 (mmtm) REVERT: D 63 ARG cc_start: 0.6620 (tpp-160) cc_final: 0.6405 (tpp-160) REVERT: D 70 TYR cc_start: 0.6926 (t80) cc_final: 0.6500 (t80) REVERT: D 81 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7035 (mm) REVERT: D 105 LEU cc_start: 0.4485 (OUTLIER) cc_final: 0.4029 (mt) REVERT: D 107 ARG cc_start: 0.5862 (OUTLIER) cc_final: 0.5466 (ptp-170) REVERT: D 249 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.7679 (mt0) REVERT: D 343 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7858 (tt0) REVERT: E 70 TYR cc_start: 0.6855 (t80) cc_final: 0.6410 (t80) REVERT: E 249 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8245 (mm-40) REVERT: E 390 MET cc_start: 0.9265 (mtp) cc_final: 0.9057 (mtm) REVERT: F 60 LYS cc_start: 0.6410 (mmtm) cc_final: 0.6078 (mmtm) REVERT: F 70 TYR cc_start: 0.6501 (t80) cc_final: 0.6217 (t80) REVERT: F 81 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.6861 (mm) REVERT: F 249 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.7413 (mt0) REVERT: F 259 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.7701 (ttm) REVERT: F 343 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7705 (tt0) REVERT: F 368 LYS cc_start: 0.8332 (mmtt) cc_final: 0.8052 (mmmt) REVERT: G 70 TYR cc_start: 0.6686 (t80) cc_final: 0.6429 (t80) REVERT: G 81 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.6658 (mm) REVERT: G 87 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7671 (m-30) REVERT: G 105 LEU cc_start: 0.4985 (OUTLIER) cc_final: 0.4642 (mt) REVERT: G 249 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.7519 (mt0) REVERT: H 70 TYR cc_start: 0.6657 (t80) cc_final: 0.6293 (t80) REVERT: H 81 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7499 (mm) REVERT: H 105 LEU cc_start: 0.5158 (OUTLIER) cc_final: 0.4795 (mt) REVERT: H 249 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8102 (mm-40) REVERT: H 343 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7671 (tt0) REVERT: I 70 TYR cc_start: 0.6750 (t80) cc_final: 0.6466 (t80) REVERT: I 81 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.6723 (mm) REVERT: I 151 ARG cc_start: 0.6963 (mmt180) cc_final: 0.6752 (mmt180) REVERT: I 249 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.7474 (mt0) REVERT: I 259 MET cc_start: 0.8634 (ttp) cc_final: 0.8387 (ttp) REVERT: I 343 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7806 (tt0) REVERT: J 70 TYR cc_start: 0.7002 (t80) cc_final: 0.6648 (t80) REVERT: J 81 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.6957 (mm) REVERT: J 105 LEU cc_start: 0.5949 (OUTLIER) cc_final: 0.5619 (mt) REVERT: J 249 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.7473 (mt0) REVERT: J 368 LYS cc_start: 0.8451 (mmtt) cc_final: 0.7787 (mmmt) REVERT: J 390 MET cc_start: 0.8980 (mtp) cc_final: 0.8714 (mtm) REVERT: K 9 ASN cc_start: 0.6729 (OUTLIER) cc_final: 0.6411 (p0) REVERT: K 70 TYR cc_start: 0.6562 (t80) cc_final: 0.6227 (t80) REVERT: K 81 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7197 (mm) REVERT: K 249 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8212 (mm-40) REVERT: K 368 LYS cc_start: 0.8470 (mmtt) cc_final: 0.8083 (mptt) outliers start: 200 outliers final: 105 residues processed: 606 average time/residue: 0.2029 time to fit residues: 204.2657 Evaluate side-chains 552 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 410 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASN Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 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 174 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 249 GLN Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 382 VAL 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 196 VAL Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 343 GLU 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 196 VAL 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 382 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 F residue 408 SER Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 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 207 ILE Chi-restraints excluded: chain G residue 235 ILE Chi-restraints excluded: chain G residue 249 GLN Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 332 MET Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 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 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 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 195 CYS Chi-restraints excluded: chain J residue 235 ILE Chi-restraints excluded: chain J residue 249 GLN Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain K residue 9 ASN Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 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 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: 1.9990 chunk 241 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 255 optimal weight: 7.9990 chunk 400 optimal weight: 2.9990 chunk 332 optimal weight: 0.9990 chunk 264 optimal weight: 0.7980 chunk 246 optimal weight: 9.9990 chunk 398 optimal weight: 1.9990 chunk 200 optimal weight: 10.0000 chunk 357 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 231 HIS J 231 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.173533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.153065 restraints weight = 46705.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.148771 restraints weight = 68723.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.145730 restraints weight = 85689.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.144687 restraints weight = 100143.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.142303 restraints weight = 91157.035| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 39068 Z= 0.114 Angle : 0.546 9.510 53364 Z= 0.288 Chirality : 0.043 0.326 5961 Planarity : 0.004 0.086 6479 Dihedral : 11.926 179.459 6145 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 3.40 % Allowed : 24.26 % Favored : 72.34 % 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: -1.44 (0.12), residues: 4532 helix: 0.22 (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 0.006 0.000 ARG K 37 TYR 0.039 0.001 TYR K 52 PHE 0.011 0.001 PHE J 30 TRP 0.009 0.001 TRP G 246 HIS 0.002 0.000 HIS K 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (39068) covalent geometry : angle 0.54606 / 0.29 (53364) hydrogen bonds : bond 0.03500 / 2.37 ( 1254) hydrogen bonds : angle 3.76719 / 2.64 ( 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 595 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 463 time to evaluate : 1.021 Fit side-chains REVERT: A 60 LYS cc_start: 0.7210 (mmtm) cc_final: 0.6744 (mmtm) REVERT: A 81 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7111 (mm) REVERT: A 249 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.6639 (mt0) REVERT: A 332 MET cc_start: 0.8968 (ttt) cc_final: 0.8204 (ttt) REVERT: A 368 LYS cc_start: 0.8094 (mmtm) cc_final: 0.7673 (mmmt) REVERT: B 81 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7287 (mm) REVERT: B 87 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7387 (t0) REVERT: B 249 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7475 (mm110) REVERT: B 250 THR cc_start: 0.8636 (OUTLIER) cc_final: 0.8373 (m) REVERT: C 81 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7039 (mm) REVERT: C 87 ASP cc_start: 0.7417 (OUTLIER) cc_final: 0.7162 (m-30) REVERT: C 381 ASP cc_start: 0.7524 (t70) cc_final: 0.7260 (t0) REVERT: D 60 LYS cc_start: 0.6481 (mmtm) cc_final: 0.6152 (mmtm) REVERT: D 63 ARG cc_start: 0.6580 (tpp-160) cc_final: 0.6335 (tpp-160) REVERT: D 81 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7102 (mm) REVERT: D 192 ILE cc_start: 0.7520 (OUTLIER) cc_final: 0.7179 (pt) REVERT: D 249 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8233 (mm-40) REVERT: E 105 LEU cc_start: 0.5393 (OUTLIER) cc_final: 0.4949 (mt) REVERT: E 249 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7876 (mm-40) REVERT: E 390 MET cc_start: 0.9257 (mtp) cc_final: 0.9017 (mtm) REVERT: F 70 TYR cc_start: 0.6557 (t80) cc_final: 0.6059 (t80) REVERT: F 81 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.6907 (mm) REVERT: F 105 LEU cc_start: 0.5245 (OUTLIER) cc_final: 0.4833 (mt) REVERT: F 249 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.6770 (mt0) REVERT: F 259 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8212 (ttm) REVERT: F 368 LYS cc_start: 0.8297 (mmtt) cc_final: 0.8053 (mmmt) REVERT: G 24 ASP cc_start: 0.6592 (OUTLIER) cc_final: 0.6230 (t0) REVERT: G 81 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6737 (mm) REVERT: G 87 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7602 (m-30) REVERT: G 211 PHE cc_start: 0.7905 (m-80) cc_final: 0.7646 (m-80) REVERT: H 70 TYR cc_start: 0.6429 (t80) cc_final: 0.6035 (t80) REVERT: H 81 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7508 (mm) REVERT: H 343 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7669 (tt0) REVERT: I 70 TYR cc_start: 0.6704 (t80) cc_final: 0.6491 (t80) REVERT: I 81 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.6765 (mm) REVERT: I 105 LEU cc_start: 0.4985 (OUTLIER) cc_final: 0.4656 (mt) REVERT: I 151 ARG cc_start: 0.6785 (mmt180) cc_final: 0.6584 (mmt180) REVERT: I 249 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7705 (mp10) REVERT: J 81 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7008 (mm) REVERT: J 211 PHE cc_start: 0.7805 (m-80) cc_final: 0.7580 (m-80) REVERT: J 249 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7014 (mt0) REVERT: J 279 MET cc_start: 0.7031 (mmt) cc_final: 0.6556 (mmm) REVERT: J 368 LYS cc_start: 0.8435 (mmtt) cc_final: 0.7723 (mmmt) REVERT: J 390 MET cc_start: 0.8999 (mtp) cc_final: 0.8714 (mtm) REVERT: K 9 ASN cc_start: 0.6738 (OUTLIER) cc_final: 0.6231 (p0) REVERT: K 70 TYR cc_start: 0.6557 (t80) cc_final: 0.6150 (t80) REVERT: K 81 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7225 (mm) REVERT: K 200 TYR cc_start: 0.7363 (m-10) cc_final: 0.7042 (m-10) REVERT: K 368 LYS cc_start: 0.8436 (mmtt) cc_final: 0.8017 (mptt) outliers start: 132 outliers final: 51 residues processed: 566 average time/residue: 0.1994 time to fit residues: 188.0651 Evaluate side-chains 503 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 424 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASN Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 107 ARG 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 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 176 THR Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 250 THR 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 382 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 363 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 105 LEU Chi-restraints excluded: chain E residue 174 THR 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 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 235 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 382 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 107 ARG Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 235 ILE Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 173 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 249 GLN Chi-restraints excluded: chain I residue 363 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 ASP Chi-restraints excluded: chain J residue 107 ARG 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 16 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 382 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 110 optimal weight: 0.7980 chunk 352 optimal weight: 6.9990 chunk 179 optimal weight: 20.0000 chunk 450 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 193 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 286 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 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 = 0.3801 r_free = 0.3801 target = 0.173635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.156395 restraints weight = 46877.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.153650 restraints weight = 78147.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.151958 restraints weight = 75881.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.151120 restraints weight = 87202.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.145829 restraints weight = 78554.865| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1909 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 : 0.553 9.718 53364 Z= 0.289 Chirality : 0.043 0.323 5961 Planarity : 0.004 0.084 6479 Dihedral : 11.717 178.826 6145 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 3.71 % Allowed : 24.21 % Favored : 72.08 % 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: -1.32 (0.12), residues: 4532 helix: 0.35 (0.12), residues: 2101 sheet: None (None), residues: 0 loop : -2.09 (0.12), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 37 TYR 0.035 0.001 TYR K 52 PHE 0.013 0.001 PHE K 295 TRP 0.008 0.001 TRP K 298 HIS 0.002 0.001 HIS G 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (39068) covalent geometry : angle 0.55272 / 0.29 (53364) hydrogen bonds : bond 0.03669 / 2.48 ( 1254) hydrogen bonds : angle 3.72210 / 2.61 ( 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 580 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 436 time to evaluate : 1.390 Fit side-chains revert: symmetry clash REVERT: A 81 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7089 (mm) REVERT: A 249 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.6772 (mt0) REVERT: A 332 MET cc_start: 0.8829 (ttt) cc_final: 0.8219 (ttt) REVERT: A 368 LYS cc_start: 0.8026 (mmtm) cc_final: 0.7683 (mmmt) REVERT: B 81 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7253 (mm) REVERT: B 87 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7351 (t0) REVERT: B 249 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7492 (mm110) REVERT: B 250 THR cc_start: 0.8668 (OUTLIER) cc_final: 0.8444 (m) REVERT: C 81 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7004 (mm) REVERT: C 87 ASP cc_start: 0.7452 (OUTLIER) cc_final: 0.7222 (m-30) REVERT: C 105 LEU cc_start: 0.5244 (OUTLIER) cc_final: 0.4755 (mt) REVERT: C 381 ASP cc_start: 0.7541 (t70) cc_final: 0.7278 (t0) REVERT: D 60 LYS cc_start: 0.6975 (mmtm) cc_final: 0.6315 (mmtm) REVERT: D 105 LEU cc_start: 0.4505 (OUTLIER) cc_final: 0.4086 (mt) REVERT: D 249 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8290 (mm-40) REVERT: E 105 LEU cc_start: 0.5439 (OUTLIER) cc_final: 0.5033 (mt) REVERT: E 249 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7928 (mm-40) REVERT: F 70 TYR cc_start: 0.6472 (t80) cc_final: 0.6109 (t80) REVERT: F 105 LEU cc_start: 0.5387 (OUTLIER) cc_final: 0.5030 (mt) REVERT: F 249 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.6892 (mt0) REVERT: F 259 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8027 (ttm) REVERT: F 368 LYS cc_start: 0.8270 (mmtt) cc_final: 0.8043 (mmmt) REVERT: G 24 ASP cc_start: 0.6607 (OUTLIER) cc_final: 0.6241 (t0) REVERT: G 87 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7613 (m-30) REVERT: G 211 PHE cc_start: 0.7936 (m-80) cc_final: 0.7622 (m-80) REVERT: I 81 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.6749 (mm) REVERT: I 105 LEU cc_start: 0.5114 (OUTLIER) cc_final: 0.4769 (mt) REVERT: I 151 ARG cc_start: 0.6675 (mmt180) cc_final: 0.6467 (mmt180) REVERT: I 249 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7665 (mp10) REVERT: J 27 SER cc_start: 0.7937 (t) cc_final: 0.7666 (t) REVERT: J 81 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.6986 (mm) REVERT: J 105 LEU cc_start: 0.5912 (OUTLIER) cc_final: 0.5554 (mt) REVERT: J 178 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7311 (mtmt) REVERT: J 211 PHE cc_start: 0.7797 (m-80) cc_final: 0.7548 (m-80) REVERT: J 279 MET cc_start: 0.6972 (mmt) cc_final: 0.6734 (mmt) REVERT: J 368 LYS cc_start: 0.8342 (mmtt) cc_final: 0.7662 (mmmt) REVERT: J 390 MET cc_start: 0.8980 (mtp) cc_final: 0.8714 (mtm) REVERT: K 9 ASN cc_start: 0.6789 (OUTLIER) cc_final: 0.6323 (p0) REVERT: K 81 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7071 (mm) REVERT: K 200 TYR cc_start: 0.7233 (m-10) cc_final: 0.6958 (m-10) REVERT: K 368 LYS cc_start: 0.8336 (mmtt) cc_final: 0.7984 (mptt) outliers start: 144 outliers final: 79 residues processed: 554 average time/residue: 0.2059 time to fit residues: 190.0621 Evaluate side-chains 524 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 419 time to evaluate : 1.304 ------------------------------------------------------------------------------- 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 176 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain B residue 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 176 THR Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain D residue 105 LEU 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 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 105 LEU 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 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 363 VAL Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 107 ARG Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain H residue 12 VAL 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 382 VAL Chi-restraints excluded: chain H residue 408 SER 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 249 GLN Chi-restraints excluded: chain I residue 363 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 ASP Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 107 ARG Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain J residue 178 LYS Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain J residue 235 ILE Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain K residue 9 ASN Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 107 ARG 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 287 optimal weight: 0.0980 chunk 34 optimal weight: 7.9990 chunk 271 optimal weight: 0.8980 chunk 233 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 403 optimal weight: 7.9990 chunk 399 optimal weight: 6.9990 chunk 367 optimal weight: 0.7980 chunk 213 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.173402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.156502 restraints weight = 46709.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.153213 restraints weight = 79450.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.151308 restraints weight = 87209.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.150325 restraints weight = 98148.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.148352 restraints weight = 100352.546| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.1976 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= 0.132 Angle : 0.563 9.993 53364 Z= 0.294 Chirality : 0.043 0.317 5961 Planarity : 0.004 0.087 6479 Dihedral : 11.649 177.886 6145 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer: Outliers : 3.84 % Allowed : 23.64 % Favored : 72.52 % 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: -1.29 (0.12), residues: 4532 helix: 0.39 (0.12), residues: 2090 sheet: None (None), residues: 0 loop : -2.07 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 37 TYR 0.039 0.002 TYR A 70 PHE 0.014 0.001 PHE G 295 TRP 0.009 0.001 TRP K 298 HIS 0.002 0.001 HIS E 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (39068) covalent geometry : angle 0.56252 / 0.29 (53364) hydrogen bonds : bond 0.03778 / 2.54 ( 1254) hydrogen bonds : angle 3.74541 / 2.63 ( 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 590 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 441 time to evaluate : 1.305 Fit side-chains REVERT: A 81 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7098 (mm) REVERT: A 249 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.6787 (mt0) REVERT: A 332 MET cc_start: 0.8881 (ttt) cc_final: 0.8389 (ttt) REVERT: A 368 LYS cc_start: 0.8036 (mmtm) cc_final: 0.7593 (mmmt) REVERT: B 81 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7278 (mm) REVERT: B 87 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.7260 (t0) REVERT: B 249 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7612 (mm110) REVERT: B 250 THR cc_start: 0.8678 (OUTLIER) cc_final: 0.8453 (m) REVERT: C 81 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7016 (mm) REVERT: C 105 LEU cc_start: 0.5204 (OUTLIER) cc_final: 0.4722 (mt) REVERT: C 381 ASP cc_start: 0.7531 (t70) cc_final: 0.7267 (t0) REVERT: D 60 LYS cc_start: 0.7079 (mmtm) cc_final: 0.6511 (mmtm) REVERT: D 81 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7138 (mm) REVERT: D 151 ARG cc_start: 0.6688 (mmt180) cc_final: 0.6353 (mmt180) REVERT: D 249 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8336 (mm-40) REVERT: E 105 LEU cc_start: 0.5373 (OUTLIER) cc_final: 0.5004 (mt) REVERT: E 249 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7945 (mm-40) REVERT: F 81 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.6861 (mm) REVERT: F 105 LEU cc_start: 0.5283 (OUTLIER) cc_final: 0.4862 (mt) REVERT: F 249 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.6888 (mt0) REVERT: F 259 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.7981 (ttm) REVERT: F 343 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7657 (tt0) REVERT: F 368 LYS cc_start: 0.8325 (mmtt) cc_final: 0.8032 (mmmt) REVERT: G 8 THR cc_start: 0.5578 (OUTLIER) cc_final: 0.5299 (t) REVERT: G 24 ASP cc_start: 0.6552 (OUTLIER) cc_final: 0.6148 (t0) REVERT: G 81 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.6949 (mm) REVERT: G 87 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7526 (m-30) REVERT: G 279 MET cc_start: 0.7050 (mmt) cc_final: 0.6658 (mmm) REVERT: H 70 TYR cc_start: 0.6234 (t80) cc_final: 0.5698 (t80) REVERT: H 81 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7519 (mm) REVERT: H 343 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7608 (tt0) REVERT: I 81 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.6766 (mm) REVERT: I 151 ARG cc_start: 0.6693 (mmt180) cc_final: 0.6471 (mmt180) REVERT: I 249 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7750 (mp10) REVERT: I 279 MET cc_start: 0.6897 (OUTLIER) cc_final: 0.6603 (mmt) REVERT: J 27 SER cc_start: 0.7941 (t) cc_final: 0.7677 (t) REVERT: J 81 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7008 (mm) REVERT: J 105 LEU cc_start: 0.5682 (OUTLIER) cc_final: 0.5369 (mt) REVERT: J 178 LYS cc_start: 0.7444 (OUTLIER) cc_final: 0.7230 (mtmt) REVERT: J 279 MET cc_start: 0.6907 (mmt) cc_final: 0.6661 (mmt) REVERT: J 326 SER cc_start: 0.8567 (OUTLIER) cc_final: 0.8248 (m) REVERT: J 368 LYS cc_start: 0.8417 (mmtt) cc_final: 0.7736 (mmtt) REVERT: J 390 MET cc_start: 0.8995 (mtp) cc_final: 0.8730 (mtm) REVERT: K 9 ASN cc_start: 0.6266 (OUTLIER) cc_final: 0.5865 (p0) REVERT: K 68 ASN cc_start: 0.7778 (t160) cc_final: 0.7573 (t0) REVERT: K 81 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7046 (mm) REVERT: K 200 TYR cc_start: 0.7244 (m-10) cc_final: 0.6995 (m-10) REVERT: K 368 LYS cc_start: 0.8406 (mmtt) cc_final: 0.8001 (mptt) outliers start: 149 outliers final: 92 residues processed: 563 average time/residue: 0.1989 time to fit residues: 188.2061 Evaluate side-chains 546 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 423 time to evaluate : 1.356 ------------------------------------------------------------------------------- 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 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 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 100 ILE Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 81 LEU 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 235 ILE Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 81 LEU 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 363 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 105 LEU 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 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 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 64 ILE Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 107 ARG Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 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 173 VAL Chi-restraints excluded: chain H residue 235 ILE Chi-restraints excluded: chain H residue 259 MET 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 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 279 MET 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 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 195 CYS Chi-restraints excluded: chain J residue 235 ILE 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 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 107 ARG 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 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: 0.8980 chunk 372 optimal weight: 0.9980 chunk 436 optimal weight: 9.9990 chunk 253 optimal weight: 20.0000 chunk 349 optimal weight: 0.7980 chunk 181 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 311 optimal weight: 4.9990 chunk 268 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.175263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.155463 restraints weight = 46643.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.152138 restraints weight = 72974.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.150231 restraints weight = 75845.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.149739 restraints weight = 88842.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.147599 restraints weight = 81216.661| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 39068 Z= 0.110 Angle : 0.544 9.530 53364 Z= 0.283 Chirality : 0.042 0.317 5961 Planarity : 0.004 0.081 6479 Dihedral : 11.454 176.147 6145 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 3.12 % Allowed : 24.52 % Favored : 72.37 % 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: -1.15 (0.13), residues: 4532 helix: 0.56 (0.12), residues: 2079 sheet: None (None), residues: 0 loop : -2.05 (0.12), residues: 2453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 37 TYR 0.041 0.001 TYR K 70 PHE 0.011 0.001 PHE K 295 TRP 0.012 0.001 TRP G 131 HIS 0.005 0.001 HIS I 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (39068) covalent geometry : angle 0.54374 / 0.28 (53364) hydrogen bonds : bond 0.03393 / 2.29 ( 1254) hydrogen bonds : angle 3.64896 / 2.54 ( 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 574 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 453 time to evaluate : 1.349 Fit side-chains REVERT: A 81 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7092 (mm) REVERT: A 249 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7805 (mm110) REVERT: A 332 MET cc_start: 0.8843 (ttt) cc_final: 0.8430 (ttt) REVERT: A 368 LYS cc_start: 0.8029 (mmtm) cc_final: 0.7646 (mmmt) REVERT: B 81 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7254 (mm) REVERT: B 87 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.7228 (t0) REVERT: B 249 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7581 (mm110) REVERT: B 250 THR cc_start: 0.8623 (OUTLIER) cc_final: 0.8354 (m) REVERT: C 81 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7147 (mm) REVERT: C 87 ASP cc_start: 0.7444 (OUTLIER) cc_final: 0.7213 (m-30) REVERT: C 105 LEU cc_start: 0.5198 (OUTLIER) cc_final: 0.4791 (mt) REVERT: C 319 GLU cc_start: 0.6374 (tt0) cc_final: 0.6141 (tt0) REVERT: C 381 ASP cc_start: 0.7471 (t70) cc_final: 0.7209 (t0) REVERT: D 60 LYS cc_start: 0.7014 (mmtm) cc_final: 0.6661 (mmtm) REVERT: D 81 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7134 (mm) REVERT: D 151 ARG cc_start: 0.6628 (mmt180) cc_final: 0.6321 (mmt180) REVERT: D 249 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8196 (mm-40) REVERT: D 343 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7789 (tt0) REVERT: E 105 LEU cc_start: 0.5241 (OUTLIER) cc_final: 0.4855 (mt) REVERT: E 249 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7816 (mm-40) REVERT: E 319 GLU cc_start: 0.6739 (tt0) cc_final: 0.6523 (tt0) REVERT: F 81 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.6842 (mm) REVERT: F 105 LEU cc_start: 0.5185 (OUTLIER) cc_final: 0.4805 (mt) REVERT: F 249 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.6660 (mt0) REVERT: F 259 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.7978 (ttm) REVERT: F 343 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7608 (tt0) REVERT: F 368 LYS cc_start: 0.8354 (mmtt) cc_final: 0.7770 (mmmt) REVERT: G 8 THR cc_start: 0.5550 (OUTLIER) cc_final: 0.5256 (t) REVERT: G 24 ASP cc_start: 0.6626 (OUTLIER) cc_final: 0.6295 (t0) REVERT: G 81 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.6929 (mm) REVERT: G 87 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7623 (m-30) REVERT: H 70 TYR cc_start: 0.6307 (t80) cc_final: 0.5824 (t80) REVERT: H 81 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7437 (mm) REVERT: I 81 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.6755 (mm) REVERT: I 151 ARG cc_start: 0.6635 (mmt180) cc_final: 0.6409 (mmt180) REVERT: I 249 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7684 (mp10) REVERT: J 81 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.6989 (mm) REVERT: J 105 LEU cc_start: 0.5680 (OUTLIER) cc_final: 0.5353 (mt) REVERT: J 178 LYS cc_start: 0.7480 (OUTLIER) cc_final: 0.7235 (mtmt) REVERT: J 279 MET cc_start: 0.6902 (mmt) cc_final: 0.6688 (mmt) REVERT: J 368 LYS cc_start: 0.8412 (mmtt) cc_final: 0.7762 (mmtt) REVERT: J 382 VAL cc_start: 0.8692 (OUTLIER) cc_final: 0.8469 (t) REVERT: J 390 MET cc_start: 0.9014 (mtp) cc_final: 0.8743 (mtm) REVERT: K 9 ASN cc_start: 0.6181 (OUTLIER) cc_final: 0.5797 (p0) REVERT: K 68 ASN cc_start: 0.7668 (t160) cc_final: 0.7440 (t0) REVERT: K 81 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7032 (mm) REVERT: K 368 LYS cc_start: 0.8407 (mmtt) cc_final: 0.7989 (mptt) outliers start: 121 outliers final: 83 residues processed: 551 average time/residue: 0.1964 time to fit residues: 181.4746 Evaluate side-chains 537 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 423 time to evaluate : 1.408 ------------------------------------------------------------------------------- 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 176 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 250 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 159 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 E residue 24 ASP Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 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 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 64 ILE Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 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 363 VAL Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 259 MET 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 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 105 LEU Chi-restraints excluded: chain J residue 107 ARG 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 363 VAL Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain J residue 406 ASP Chi-restraints excluded: chain K residue 9 ASN Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 107 ARG Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 382 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 316 optimal weight: 6.9990 chunk 231 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 334 optimal weight: 9.9990 chunk 124 optimal weight: 0.4980 chunk 3 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 193 optimal weight: 5.9990 chunk 221 optimal weight: 0.5980 chunk 336 optimal weight: 9.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 HIS ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 188 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.171174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.153966 restraints weight = 47014.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.150923 restraints weight = 82271.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.148914 restraints weight = 91279.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.147031 restraints weight = 105754.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.144965 restraints weight = 96735.710| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 39068 Z= 0.198 Angle : 0.619 9.760 53364 Z= 0.326 Chirality : 0.045 0.327 5961 Planarity : 0.005 0.082 6479 Dihedral : 11.734 179.074 6145 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.74 % Favored : 88.26 % Rotamer: Outliers : 3.58 % Allowed : 24.52 % 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: -1.49 (0.12), residues: 4532 helix: 0.13 (0.12), residues: 2123 sheet: None (None), residues: 0 loop : -2.11 (0.12), residues: 2409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 37 TYR 0.039 0.002 TYR B 70 PHE 0.020 0.002 PHE G 295 TRP 0.014 0.002 TRP K 298 HIS 0.006 0.001 HIS E 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 (39068) covalent geometry : angle 0.61946 / 0.33 (53364) hydrogen bonds : bond 0.04637 / 3.12 ( 1254) hydrogen bonds : angle 4.03379 / 2.83 ( 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 576 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 437 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: A 81 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7057 (mm) REVERT: A 249 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.6999 (mt0) REVERT: A 332 MET cc_start: 0.8830 (ttt) cc_final: 0.8424 (ttt) REVERT: A 368 LYS cc_start: 0.7981 (mmtm) cc_final: 0.7710 (mmmt) REVERT: B 81 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7150 (mm) REVERT: B 87 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7253 (t0) REVERT: B 105 LEU cc_start: 0.4455 (OUTLIER) cc_final: 0.4238 (mt) REVERT: B 188 ASN cc_start: 0.8220 (m-40) cc_final: 0.7934 (m-40) REVERT: B 249 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7624 (mp10) REVERT: B 279 MET cc_start: 0.6956 (mmm) cc_final: 0.6682 (mmm) REVERT: C 81 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.6964 (mm) REVERT: C 87 ASP cc_start: 0.7287 (OUTLIER) cc_final: 0.7031 (m-30) REVERT: C 105 LEU cc_start: 0.5181 (OUTLIER) cc_final: 0.4735 (mt) REVERT: C 381 ASP cc_start: 0.7591 (t70) cc_final: 0.7345 (t0) REVERT: D 60 LYS cc_start: 0.7116 (mmtm) cc_final: 0.6815 (mmtm) REVERT: D 81 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7029 (mm) REVERT: D 151 ARG cc_start: 0.6800 (mmt180) cc_final: 0.6416 (mmt180) REVERT: D 249 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8362 (mm-40) REVERT: D 343 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7833 (tt0) REVERT: E 105 LEU cc_start: 0.5163 (OUTLIER) cc_final: 0.4858 (mt) REVERT: F 81 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.6840 (mm) REVERT: F 105 LEU cc_start: 0.5415 (OUTLIER) cc_final: 0.4999 (mt) REVERT: F 249 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7196 (mt0) REVERT: F 343 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7638 (tt0) REVERT: F 368 LYS cc_start: 0.8341 (mmtt) cc_final: 0.7808 (mmmt) REVERT: G 8 THR cc_start: 0.5597 (OUTLIER) cc_final: 0.5218 (t) REVERT: G 81 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.6892 (mm) REVERT: G 87 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7600 (m-30) REVERT: G 211 PHE cc_start: 0.7902 (m-80) cc_final: 0.7592 (m-80) REVERT: G 279 MET cc_start: 0.7201 (OUTLIER) cc_final: 0.7001 (mmm) REVERT: G 343 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7692 (tt0) REVERT: H 81 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7473 (mm) REVERT: H 343 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7656 (tt0) REVERT: I 81 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.6672 (mm) REVERT: I 151 ARG cc_start: 0.6798 (mmt180) cc_final: 0.6580 (mmt180) REVERT: I 249 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7545 (mt0) REVERT: J 81 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.6960 (mm) REVERT: J 105 LEU cc_start: 0.5821 (OUTLIER) cc_final: 0.5513 (mt) REVERT: J 326 SER cc_start: 0.8805 (OUTLIER) cc_final: 0.8444 (m) REVERT: J 368 LYS cc_start: 0.8451 (mmtt) cc_final: 0.7733 (mmmt) REVERT: J 390 MET cc_start: 0.8994 (mtp) cc_final: 0.8729 (mtm) REVERT: K 9 ASN cc_start: 0.6718 (OUTLIER) cc_final: 0.6216 (p0) REVERT: K 81 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7031 (mm) REVERT: K 199 PHE cc_start: 0.8191 (t80) cc_final: 0.7855 (t80) REVERT: K 368 LYS cc_start: 0.8424 (mmtt) cc_final: 0.8035 (mptt) outliers start: 139 outliers final: 94 residues processed: 552 average time/residue: 0.2052 time to fit residues: 187.6896 Evaluate side-chains 539 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 417 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 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 A residue 382 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain D residue 81 LEU 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 E residue 24 ASP Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 259 MET Chi-restraints excluded: chain E residue 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 249 GLN Chi-restraints excluded: chain F residue 250 THR 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 64 ILE Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 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 279 MET 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 173 VAL Chi-restraints excluded: chain H residue 235 ILE Chi-restraints excluded: chain H residue 259 MET 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 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 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 195 CYS 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 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 107 ARG Chi-restraints excluded: chain K residue 162 CYS 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: 0.8980 chunk 452 optimal weight: 10.0000 chunk 347 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 281 optimal weight: 0.0170 chunk 144 optimal weight: 9.9990 chunk 154 optimal weight: 5.9990 chunk 345 optimal weight: 0.7980 chunk 359 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.174767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.158122 restraints weight = 46527.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.155014 restraints weight = 77307.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.152959 restraints weight = 84177.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.152275 restraints weight = 96851.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.150296 restraints weight = 93929.091| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 39068 Z= 0.116 Angle : 0.562 10.356 53364 Z= 0.293 Chirality : 0.042 0.316 5961 Planarity : 0.004 0.079 6479 Dihedral : 11.472 176.500 6145 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 2.81 % Allowed : 25.68 % 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: -1.20 (0.13), residues: 4532 helix: 0.46 (0.12), residues: 2090 sheet: None (None), residues: 0 loop : -2.02 (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 H 52 PHE 0.024 0.001 PHE J 211 TRP 0.010 0.001 TRP C 131 HIS 0.005 0.000 HIS G 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (39068) covalent geometry : angle 0.56172 / 0.29 (53364) hydrogen bonds : bond 0.03470 / 2.34 ( 1254) hydrogen bonds : angle 3.78353 / 2.63 ( 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 539 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 430 time to evaluate : 1.367 Fit side-chains REVERT: A 81 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7080 (mm) REVERT: A 249 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7743 (mm110) REVERT: A 332 MET cc_start: 0.8889 (ttt) cc_final: 0.8338 (ttt) REVERT: A 368 LYS cc_start: 0.7911 (mmtm) cc_final: 0.7616 (mmmt) REVERT: B 81 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7188 (mm) REVERT: B 87 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7187 (t0) REVERT: B 188 ASN cc_start: 0.8237 (m-40) cc_final: 0.7997 (m-40) REVERT: B 249 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7734 (mm-40) REVERT: C 81 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.6965 (mm) REVERT: C 87 ASP cc_start: 0.7304 (OUTLIER) cc_final: 0.7071 (m-30) REVERT: C 105 LEU cc_start: 0.5092 (OUTLIER) cc_final: 0.4681 (mt) REVERT: C 381 ASP cc_start: 0.7513 (t70) cc_final: 0.7244 (t0) REVERT: D 60 LYS cc_start: 0.7076 (mmtm) cc_final: 0.5310 (mmmt) REVERT: D 81 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7025 (mm) REVERT: D 105 LEU cc_start: 0.5136 (OUTLIER) cc_final: 0.4822 (mt) REVERT: D 151 ARG cc_start: 0.6754 (mmt180) cc_final: 0.6432 (mmt180) REVERT: D 249 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8248 (mm-40) REVERT: D 343 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7762 (tt0) REVERT: F 81 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.6942 (mm) REVERT: F 105 LEU cc_start: 0.5281 (OUTLIER) cc_final: 0.4960 (mt) REVERT: F 249 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.6735 (mt0) REVERT: F 368 LYS cc_start: 0.8333 (mmtt) cc_final: 0.7762 (mmmt) REVERT: G 8 THR cc_start: 0.5362 (OUTLIER) cc_final: 0.5092 (t) REVERT: G 81 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.6893 (mm) REVERT: G 87 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7610 (m-30) REVERT: G 151 ARG cc_start: 0.6431 (mmt180) cc_final: 0.6013 (mmt180) REVERT: G 279 MET cc_start: 0.7066 (OUTLIER) cc_final: 0.6859 (mmm) REVERT: H 81 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7452 (mm) REVERT: I 81 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.6740 (mm) REVERT: I 151 ARG cc_start: 0.6676 (mmt180) cc_final: 0.6450 (mmt180) REVERT: I 249 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7726 (mp10) REVERT: I 279 MET cc_start: 0.7137 (mmt) cc_final: 0.6914 (mmt) REVERT: J 81 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7000 (mm) REVERT: J 105 LEU cc_start: 0.5717 (OUTLIER) cc_final: 0.5430 (mt) REVERT: J 279 MET cc_start: 0.6865 (mmt) cc_final: 0.6549 (mmm) REVERT: J 368 LYS cc_start: 0.8414 (mmtt) cc_final: 0.7686 (mmmt) REVERT: J 390 MET cc_start: 0.9003 (mtp) cc_final: 0.8724 (mtm) REVERT: K 9 ASN cc_start: 0.6919 (OUTLIER) cc_final: 0.6343 (p0) REVERT: K 81 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7058 (mm) REVERT: K 368 LYS cc_start: 0.8378 (mmtt) cc_final: 0.7962 (mptt) outliers start: 109 outliers final: 73 residues processed: 517 average time/residue: 0.2057 time to fit residues: 178.2277 Evaluate side-chains 514 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 416 time to evaluate : 1.219 ------------------------------------------------------------------------------- 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 176 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 347 SER 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 235 ILE Chi-restraints excluded: chain C residue 250 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 159 ILE Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 174 THR 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 249 GLN Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 326 SER 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 64 ILE Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 107 ARG Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 279 MET 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 173 VAL Chi-restraints excluded: chain H residue 259 MET 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 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 81 LEU Chi-restraints excluded: chain J residue 87 ASP Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 107 ARG Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain J residue 192 ILE 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 107 ARG 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 276 optimal weight: 7.9990 chunk 142 optimal weight: 9.9990 chunk 187 optimal weight: 6.9990 chunk 291 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 447 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 371 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 274 optimal weight: 0.7980 chunk 422 optimal weight: 7.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.170878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.153246 restraints weight = 46906.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.149966 restraints weight = 83095.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.147976 restraints weight = 94805.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.146769 restraints weight = 96827.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.145406 restraints weight = 93421.031| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 39068 Z= 0.199 Angle : 0.627 9.849 53364 Z= 0.330 Chirality : 0.045 0.334 5961 Planarity : 0.005 0.082 6479 Dihedral : 11.714 179.257 6145 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.87 % Favored : 88.13 % Rotamer: Outliers : 3.22 % Allowed : 25.42 % 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: -1.46 (0.12), residues: 4532 helix: 0.17 (0.12), residues: 2101 sheet: None (None), residues: 0 loop : -2.10 (0.12), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 37 TYR 0.040 0.002 TYR H 52 PHE 0.028 0.002 PHE J 211 TRP 0.014 0.002 TRP K 298 HIS 0.005 0.001 HIS G 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 (39068) covalent geometry : angle 0.62705 / 0.33 (53364) hydrogen bonds : bond 0.04611 / 3.10 ( 1254) hydrogen bonds : angle 4.08250 / 2.86 ( 3432) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4872.79 seconds wall clock time: 85 minutes 41.88 seconds (5141.88 seconds total)