Starting phenix.real_space_refine on Thu Aug 6 17:41:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e6n_47573/08_2026/9e6n_47573.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e6n_47573/08_2026/9e6n_47573.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e6n_47573/08_2026/9e6n_47573.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e6n_47573/08_2026/9e6n_47573.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e6n_47573/08_2026/9e6n_47573.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e6n_47573/08_2026/9e6n_47573.map" } resolution = 2.8 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= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 6 5.21 5 S 108 5.16 5 C 10268 2.51 5 N 2871 2.21 5 O 3233 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16522 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2442 Classifications: {'peptide': 321} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 307} Chain: "B" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2431 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 306} Chain: "C" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2442 Classifications: {'peptide': 321} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 307} Chain: "D" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2442 Classifications: {'peptide': 321} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 307} Chain: "E" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2431 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 306} Chain: "F" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2442 Classifications: {'peptide': 321} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 307} Chain: "G" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 263 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 31} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 267 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "I" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 276 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "J" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 267 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "K" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 267 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "X" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 360 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.23, per 1000 atoms: 0.20 Number of scatterers: 16522 At special positions: 0 Unit cell: (119.13, 113.715, 167.865, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 108 16.00 P 36 15.00 Mg 6 11.99 O 3233 8.00 N 2871 7.00 C 10268 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 591.4 milliseconds 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3812 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 18 sheets defined 50.7% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 82 through 87 Processing helix chain 'A' and resid 92 through 102 Processing helix chain 'A' and resid 106 through 113 Processing helix chain 'A' and resid 114 through 120 Processing helix chain 'A' and resid 125 through 140 Processing helix chain 'A' and resid 146 through 156 removed outlier: 3.660A pdb=" N GLU A 156 " --> pdb=" O MET A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 172 Processing helix chain 'A' and resid 190 through 202 removed outlier: 3.524A pdb=" N CYS A 202 " --> pdb=" O LEU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 225 through 236 removed outlier: 3.902A pdb=" N LEU A 229 " --> pdb=" O ARG A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 246 Processing helix chain 'A' and resid 254 through 272 removed outlier: 3.891A pdb=" N LEU A 262 " --> pdb=" O GLN A 258 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A 264 " --> pdb=" O ARG A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.799A pdb=" N PHE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 318 Processing helix chain 'A' and resid 347 through 354 removed outlier: 3.582A pdb=" N SER A 354 " --> pdb=" O MET A 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 87 Processing helix chain 'B' and resid 92 through 102 Processing helix chain 'B' and resid 106 through 113 Processing helix chain 'B' and resid 114 through 121 removed outlier: 3.551A pdb=" N LEU B 118 " --> pdb=" O PRO B 114 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE B 121 " --> pdb=" O ASP B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 140 removed outlier: 3.551A pdb=" N LEU B 139 " --> pdb=" O GLU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 155 Processing helix chain 'B' and resid 164 through 171 Processing helix chain 'B' and resid 190 through 202 removed outlier: 3.561A pdb=" N VAL B 200 " --> pdb=" O HIS B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 225 through 236 removed outlier: 4.010A pdb=" N LEU B 229 " --> pdb=" O ARG B 225 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 246 Processing helix chain 'B' and resid 254 through 270 removed outlier: 3.941A pdb=" N LEU B 262 " --> pdb=" O GLN B 258 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASP B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN B 267 " --> pdb=" O ASP B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 290 removed outlier: 4.485A pdb=" N TYR B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THR B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 318 Processing helix chain 'B' and resid 347 through 354 Processing helix chain 'C' and resid 82 through 87 removed outlier: 3.564A pdb=" N GLN C 87 " --> pdb=" O GLU C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 102 removed outlier: 3.623A pdb=" N VAL C 96 " --> pdb=" O THR C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 114 through 119 removed outlier: 3.520A pdb=" N LEU C 119 " --> pdb=" O ARG C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 140 removed outlier: 3.511A pdb=" N ASP C 130 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 139 " --> pdb=" O GLU C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 156 removed outlier: 3.560A pdb=" N GLU C 156 " --> pdb=" O MET C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 171 Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.559A pdb=" N VAL C 200 " --> pdb=" O HIS C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 209 Processing helix chain 'C' and resid 225 through 236 removed outlier: 4.023A pdb=" N LEU C 229 " --> pdb=" O ARG C 225 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 245 Processing helix chain 'C' and resid 254 through 270 removed outlier: 4.137A pdb=" N LEU C 262 " --> pdb=" O GLN C 258 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ASP C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA C 264 " --> pdb=" O ARG C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 290 removed outlier: 4.485A pdb=" N TYR C 286 " --> pdb=" O VAL C 282 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR C 288 " --> pdb=" O ALA C 284 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 294 No H-bonds generated for 'chain 'C' and resid 292 through 294' Processing helix chain 'C' and resid 295 through 318 Processing helix chain 'C' and resid 346 through 354 removed outlier: 3.740A pdb=" N MET C 350 " --> pdb=" O GLY C 346 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER C 354 " --> pdb=" O MET C 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 87 Processing helix chain 'D' and resid 92 through 102 Processing helix chain 'D' and resid 106 through 113 Processing helix chain 'D' and resid 114 through 121 removed outlier: 3.512A pdb=" N LEU D 118 " --> pdb=" O PRO D 114 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE D 121 " --> pdb=" O ASP D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 140 Processing helix chain 'D' and resid 147 through 156 removed outlier: 3.721A pdb=" N GLU D 156 " --> pdb=" O MET D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 172 Processing helix chain 'D' and resid 190 through 202 removed outlier: 3.763A pdb=" N VAL D 200 " --> pdb=" O HIS D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 209 Processing helix chain 'D' and resid 225 through 237 removed outlier: 3.957A pdb=" N LEU D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 245 Processing helix chain 'D' and resid 254 through 272 removed outlier: 3.906A pdb=" N LEU D 262 " --> pdb=" O GLN D 258 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA D 264 " --> pdb=" O ARG D 260 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU D 271 " --> pdb=" O GLN D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 290 removed outlier: 3.717A pdb=" N PHE D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 294 No H-bonds generated for 'chain 'D' and resid 292 through 294' Processing helix chain 'D' and resid 295 through 318 Processing helix chain 'D' and resid 346 through 354 removed outlier: 3.556A pdb=" N MET D 350 " --> pdb=" O GLY D 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 87 removed outlier: 3.587A pdb=" N GLN E 87 " --> pdb=" O GLU E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 102 removed outlier: 3.622A pdb=" N VAL E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 113 Processing helix chain 'E' and resid 114 through 120 removed outlier: 3.640A pdb=" N LEU E 118 " --> pdb=" O PRO E 114 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU E 119 " --> pdb=" O ARG E 115 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU E 120 " --> pdb=" O LYS E 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 114 through 120' Processing helix chain 'E' and resid 125 through 140 removed outlier: 3.519A pdb=" N LEU E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 155 Processing helix chain 'E' and resid 164 through 171 Processing helix chain 'E' and resid 190 through 202 removed outlier: 3.500A pdb=" N VAL E 200 " --> pdb=" O HIS E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 209 Processing helix chain 'E' and resid 225 through 237 removed outlier: 3.911A pdb=" N LEU E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN E 234 " --> pdb=" O VAL E 230 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 246 Processing helix chain 'E' and resid 254 through 270 removed outlier: 3.965A pdb=" N LEU E 262 " --> pdb=" O GLN E 258 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP E 263 " --> pdb=" O LEU E 259 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA E 264 " --> pdb=" O ARG E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 290 Processing helix chain 'E' and resid 292 through 294 No H-bonds generated for 'chain 'E' and resid 292 through 294' Processing helix chain 'E' and resid 295 through 318 Processing helix chain 'E' and resid 346 through 354 removed outlier: 3.523A pdb=" N MET E 350 " --> pdb=" O GLY E 346 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER E 354 " --> pdb=" O MET E 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 87 Processing helix chain 'F' and resid 92 through 102 removed outlier: 3.625A pdb=" N VAL F 96 " --> pdb=" O THR F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 113 Processing helix chain 'F' and resid 114 through 120 removed outlier: 4.031A pdb=" N LEU F 118 " --> pdb=" O PRO F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 140 removed outlier: 3.505A pdb=" N GLU F 135 " --> pdb=" O LYS F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 156 Processing helix chain 'F' and resid 164 through 172 Processing helix chain 'F' and resid 190 through 202 Processing helix chain 'F' and resid 205 through 209 Processing helix chain 'F' and resid 225 through 237 removed outlier: 3.785A pdb=" N LEU F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 246 Processing helix chain 'F' and resid 254 through 272 removed outlier: 4.007A pdb=" N LEU F 262 " --> pdb=" O GLN F 258 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASP F 263 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA F 264 " --> pdb=" O ARG F 260 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU F 271 " --> pdb=" O GLN F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 290 removed outlier: 4.403A pdb=" N TYR F 286 " --> pdb=" O VAL F 282 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR F 288 " --> pdb=" O ALA F 284 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE F 290 " --> pdb=" O TYR F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 318 Processing helix chain 'F' and resid 347 through 354 Processing helix chain 'G' and resid 124 through 137 removed outlier: 3.652A pdb=" N TYR G 129 " --> pdb=" O LYS G 125 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU G 130 " --> pdb=" O ASP G 126 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR G 131 " --> pdb=" O LEU G 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 137 Processing helix chain 'I' and resid 123 through 137 removed outlier: 3.565A pdb=" N GLU I 130 " --> pdb=" O ASP I 126 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR I 131 " --> pdb=" O LEU I 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 137 removed outlier: 3.515A pdb=" N LYS J 133 " --> pdb=" O TYR J 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 136 Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 160 Processing sheet with id=AA2, first strand: chain 'A' and resid 391 through 393 removed outlier: 6.853A pdb=" N ARG A 357 " --> pdb=" O VAL A 373 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 184 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ILE A 277 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N THR A 324 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL A 279 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU A 216 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ASP A 280 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE A 218 " --> pdb=" O ASP A 280 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 248 " --> pdb=" O CYS A 215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 327 through 329 Processing sheet with id=AA4, first strand: chain 'B' and resid 159 through 160 Processing sheet with id=AA5, first strand: chain 'B' and resid 391 through 393 removed outlier: 6.854A pdb=" N ARG B 357 " --> pdb=" O VAL B 373 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N THR B 181 " --> pdb=" O VAL B 323 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ASN B 325 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU B 183 " --> pdb=" O ASN B 325 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N SER B 275 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N VAL B 322 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE B 277 " --> pdb=" O VAL B 322 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N THR B 324 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL B 279 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LYS B 214 " --> pdb=" O PHE B 274 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU B 276 " --> pdb=" O LYS B 214 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 327 through 329 Processing sheet with id=AA7, first strand: chain 'C' and resid 159 through 160 Processing sheet with id=AA8, first strand: chain 'C' and resid 391 through 393 removed outlier: 6.637A pdb=" N ARG C 357 " --> pdb=" O VAL C 373 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N THR C 181 " --> pdb=" O VAL C 323 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASN C 325 " --> pdb=" O THR C 181 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU C 183 " --> pdb=" O ASN C 325 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N SER C 275 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N VAL C 322 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE C 277 " --> pdb=" O VAL C 322 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N THR C 324 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N VAL C 279 " --> pdb=" O THR C 324 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LYS C 214 " --> pdb=" O PHE C 274 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C 276 " --> pdb=" O LYS C 214 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 327 through 329 Processing sheet with id=AB1, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AB2, first strand: chain 'D' and resid 391 through 393 removed outlier: 6.751A pdb=" N ARG D 357 " --> pdb=" O VAL D 373 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY D 185 " --> pdb=" O ASN D 325 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA D 320 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LYS D 214 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE D 277 " --> pdb=" O LYS D 214 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU D 216 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL D 279 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE D 218 " --> pdb=" O VAL D 279 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 327 through 329 Processing sheet with id=AB4, first strand: chain 'E' and resid 159 through 160 Processing sheet with id=AB5, first strand: chain 'E' and resid 391 through 393 removed outlier: 6.758A pdb=" N ARG E 357 " --> pdb=" O VAL E 373 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N THR E 181 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASN E 325 " --> pdb=" O THR E 181 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU E 183 " --> pdb=" O ASN E 325 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N SER E 275 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL E 322 " --> pdb=" O SER E 275 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE E 277 " --> pdb=" O VAL E 322 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N THR E 324 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL E 279 " --> pdb=" O THR E 324 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N LYS E 214 " --> pdb=" O PHE E 274 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU E 276 " --> pdb=" O LYS E 214 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 327 through 329 Processing sheet with id=AB7, first strand: chain 'F' and resid 159 through 160 Processing sheet with id=AB8, first strand: chain 'F' and resid 247 through 251 removed outlier: 5.284A pdb=" N LYS F 214 " --> pdb=" O PHE F 274 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU F 276 " --> pdb=" O LYS F 214 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER F 275 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N VAL F 322 " --> pdb=" O SER F 275 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE F 277 " --> pdb=" O VAL F 322 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N THR F 324 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL F 279 " --> pdb=" O THR F 324 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ARG F 357 " --> pdb=" O VAL F 373 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 327 through 329 removed outlier: 3.540A pdb=" N VAL F 328 " --> pdb=" O LYS F 343 " (cutoff:3.500A) 796 hydrogen bonds defined for protein. 2235 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5019 1.33 - 1.45: 2127 1.45 - 1.57: 9419 1.57 - 1.69: 65 1.69 - 1.81: 168 Bond restraints: 16798 Sorted by residual: bond pdb=" C ASN J 141 " pdb=" N LYS J 142 " ideal model delta sigma weight residual 1.332 1.414 -0.082 1.35e-02 5.49e+03 3.66e+01 bond pdb=" C LYS J 142 " pdb=" N VAL J 143 " ideal model delta sigma weight residual 1.328 1.265 0.063 1.19e-02 7.06e+03 2.79e+01 bond pdb=" N LYS J 144 " pdb=" CA LYS J 144 " ideal model delta sigma weight residual 1.455 1.490 -0.034 1.09e-02 8.42e+03 9.99e+00 bond pdb=" N VAL J 147 " pdb=" CA VAL J 147 " ideal model delta sigma weight residual 1.458 1.496 -0.037 1.22e-02 6.72e+03 9.36e+00 bond pdb=" C3' DT X 9 " pdb=" C2' DT X 9 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.57e+00 ... (remaining 16793 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 22317 1.73 - 3.45: 383 3.45 - 5.18: 31 5.18 - 6.90: 4 6.90 - 8.63: 10 Bond angle restraints: 22745 Sorted by residual: angle pdb=" N LEU K 124 " pdb=" CA LEU K 124 " pdb=" C LEU K 124 " ideal model delta sigma weight residual 111.75 119.86 -8.11 1.28e+00 6.10e-01 4.02e+01 angle pdb=" N VAL J 138 " pdb=" CA VAL J 138 " pdb=" C VAL J 138 " ideal model delta sigma weight residual 108.17 115.69 -7.52 1.40e+00 5.10e-01 2.88e+01 angle pdb=" N TYR K 129 " pdb=" CA TYR K 129 " pdb=" C TYR K 129 " ideal model delta sigma weight residual 111.36 105.74 5.62 1.09e+00 8.42e-01 2.66e+01 angle pdb=" N GLN J 137 " pdb=" CA GLN J 137 " pdb=" C GLN J 137 " ideal model delta sigma weight residual 111.54 118.51 -6.97 1.36e+00 5.41e-01 2.63e+01 angle pdb=" N TYR J 136 " pdb=" CA TYR J 136 " pdb=" C TYR J 136 " ideal model delta sigma weight residual 113.61 121.12 -7.51 1.50e+00 4.44e-01 2.51e+01 ... (remaining 22740 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9290 17.97 - 35.93: 739 35.93 - 53.90: 201 53.90 - 71.86: 53 71.86 - 89.83: 18 Dihedral angle restraints: 10301 sinusoidal: 4364 harmonic: 5937 Sorted by residual: dihedral pdb=" N GLN J 137 " pdb=" C GLN J 137 " pdb=" CA GLN J 137 " pdb=" CB GLN J 137 " ideal model delta harmonic sigma weight residual 122.80 132.79 -9.99 0 2.50e+00 1.60e-01 1.60e+01 dihedral pdb=" C GLN J 137 " pdb=" N GLN J 137 " pdb=" CA GLN J 137 " pdb=" CB GLN J 137 " ideal model delta harmonic sigma weight residual -122.60 -132.37 9.77 0 2.50e+00 1.60e-01 1.53e+01 dihedral pdb=" CG ARG B 228 " pdb=" CD ARG B 228 " pdb=" NE ARG B 228 " pdb=" CZ ARG B 228 " ideal model delta sinusoidal sigma weight residual 90.00 134.85 -44.85 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 10298 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2331 0.075 - 0.151: 236 0.151 - 0.226: 10 0.226 - 0.301: 1 0.301 - 0.376: 3 Chirality restraints: 2581 Sorted by residual: chirality pdb=" CA GLN J 137 " pdb=" N GLN J 137 " pdb=" C GLN J 137 " pdb=" CB GLN J 137 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CA TYR J 136 " pdb=" N TYR J 136 " pdb=" C TYR J 136 " pdb=" CB TYR J 136 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA TYR K 129 " pdb=" N TYR K 129 " pdb=" C TYR K 129 " pdb=" CB TYR K 129 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 2578 not shown) Planarity restraints: 2873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE K 128 " 0.007 2.00e-02 2.50e+03 1.45e-02 2.10e+00 pdb=" C ILE K 128 " -0.025 2.00e-02 2.50e+03 pdb=" O ILE K 128 " 0.009 2.00e-02 2.50e+03 pdb=" N TYR K 129 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 187 " 0.006 2.00e-02 2.50e+03 1.08e-02 2.03e+00 pdb=" CG PHE C 187 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE C 187 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE C 187 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE C 187 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 187 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 187 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET D 335 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.76e+00 pdb=" C MET D 335 " -0.023 2.00e-02 2.50e+03 pdb=" O MET D 335 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA D 336 " 0.008 2.00e-02 2.50e+03 ... (remaining 2870 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 118 2.56 - 3.15: 12685 3.15 - 3.73: 24926 3.73 - 4.32: 36117 4.32 - 4.90: 59624 Nonbonded interactions: 133470 Sorted by model distance: nonbonded pdb=" OG SER B 192 " pdb="MG MG B 502 " model vdw 1.976 2.170 nonbonded pdb=" O1G ATP A 501 " pdb="MG MG A 502 " model vdw 2.006 2.170 nonbonded pdb=" OG SER D 192 " pdb="MG MG D 502 " model vdw 2.014 2.170 nonbonded pdb=" OG SER C 192 " pdb="MG MG C 502 " model vdw 2.018 2.170 nonbonded pdb=" O1G ATP D 501 " pdb="MG MG D 502 " model vdw 2.020 2.170 ... (remaining 133465 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 81 through 502) selection = chain 'B' selection = (chain 'C' and resid 81 through 502) selection = (chain 'D' and resid 81 through 502) selection = chain 'E' selection = (chain 'F' and resid 81 through 502) } ncs_group { reference = chain 'G' selection = (chain 'H' and ((resid 121 and (name N or name CA or name C or name O or name CB \ )) or resid 122 through 152)) selection = (chain 'I' and ((resid 121 and (name N or name CA or name C or name O or name CB \ )) or resid 122 through 152)) selection = (chain 'J' and ((resid 121 and (name N or name CA or name C or name O or name CB \ )) or resid 122 through 152)) selection = (chain 'K' and ((resid 121 and (name N or name CA or name C or name O or name CB \ )) or resid 122 through 152)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.140 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 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 : 0.003 0.082 16798 Z= 0.187 Angle : 0.517 8.631 22745 Z= 0.344 Chirality : 0.044 0.376 2581 Planarity : 0.003 0.033 2873 Dihedral : 14.949 89.830 6489 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.41 % Allowed : 0.41 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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: 0.67 (0.19), residues: 2063 helix: 0.67 (0.17), residues: 962 sheet: 1.28 (0.31), residues: 326 loop : -0.05 (0.24), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 188 TYR 0.014 0.001 TYR I 145 PHE 0.024 0.001 PHE C 187 HIS 0.002 0.000 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.19 (16798) covalent geometry : angle 0.51715 / 0.34 (22745) hydrogen bonds : bond 0.23908 / 15.78 ( 796) hydrogen bonds : angle 7.35199 / 5.33 ( 2235) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 178 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: B 89 ASN cc_start: 0.8913 (m110) cc_final: 0.8658 (m-40) REVERT: B 315 ASP cc_start: 0.8110 (m-30) cc_final: 0.7877 (m-30) REVERT: D 335 MET cc_start: -0.0601 (ppp) cc_final: -0.0854 (pmm) REVERT: F 89 ASN cc_start: 0.8861 (t0) cc_final: 0.8472 (t0) REVERT: G 139 ASP cc_start: 0.8147 (p0) cc_final: 0.7851 (p0) REVERT: K 127 LEU cc_start: 0.8737 (tt) cc_final: 0.8382 (tp) REVERT: K 129 TYR cc_start: 0.9023 (t80) cc_final: 0.8630 (t80) REVERT: K 139 ASP cc_start: 0.8182 (p0) cc_final: 0.7512 (p0) outliers start: 7 outliers final: 0 residues processed: 179 average time/residue: 0.6297 time to fit residues: 123.5807 Evaluate side-chains 149 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 GLN E 105 HIS F 87 GLN ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 141 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.091226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.061035 restraints weight = 38427.497| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.61 r_work: 0.2760 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 16798 Z= 0.240 Angle : 0.584 7.483 22745 Z= 0.312 Chirality : 0.045 0.154 2581 Planarity : 0.004 0.050 2873 Dihedral : 13.464 88.731 2632 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.11 % Allowed : 6.95 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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: 0.83 (0.19), residues: 2063 helix: 0.96 (0.18), residues: 944 sheet: 1.07 (0.30), residues: 328 loop : -0.05 (0.23), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 293 TYR 0.012 0.001 TYR I 145 PHE 0.016 0.001 PHE C 187 HIS 0.004 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.24 (16798) covalent geometry : angle 0.58432 / 0.31 (22745) hydrogen bonds : bond 0.05028 / 3.36 ( 796) hydrogen bonds : angle 5.17275 / 3.76 ( 2235) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.564 Fit side-chains revert: symmetry clash REVERT: B 89 ASN cc_start: 0.8970 (m110) cc_final: 0.8555 (m-40) REVERT: B 315 ASP cc_start: 0.8221 (m-30) cc_final: 0.7888 (m-30) REVERT: B 353 SER cc_start: 0.8587 (m) cc_final: 0.8348 (m) REVERT: C 335 MET cc_start: 0.0212 (OUTLIER) cc_final: -0.0690 (pmm) REVERT: D 269 MET cc_start: 0.9314 (OUTLIER) cc_final: 0.9110 (mmm) REVERT: E 108 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7981 (mt-10) REVERT: F 89 ASN cc_start: 0.8957 (t0) cc_final: 0.8535 (t0) REVERT: G 139 ASP cc_start: 0.8585 (p0) cc_final: 0.7901 (p0) REVERT: H 139 ASP cc_start: 0.7565 (t0) cc_final: 0.7299 (t0) REVERT: I 133 LYS cc_start: 0.8607 (tppp) cc_final: 0.8312 (ttmm) REVERT: I 137 GLN cc_start: 0.8468 (mp10) cc_final: 0.8222 (mp10) REVERT: K 122 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8639 (ttmt) REVERT: K 129 TYR cc_start: 0.9424 (t80) cc_final: 0.9042 (t80) REVERT: K 139 ASP cc_start: 0.8520 (p0) cc_final: 0.7805 (p0) outliers start: 19 outliers final: 7 residues processed: 167 average time/residue: 0.6172 time to fit residues: 113.8761 Evaluate side-chains 159 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain J residue 145 TYR Chi-restraints excluded: chain J residue 150 SER Chi-restraints excluded: chain K residue 122 LYS Chi-restraints excluded: chain K residue 123 SER Chi-restraints excluded: chain K residue 126 ASP Chi-restraints excluded: chain K residue 146 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 121 optimal weight: 0.0010 chunk 126 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 178 optimal weight: 7.9990 chunk 145 optimal weight: 7.9990 chunk 169 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.092578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.063319 restraints weight = 39243.095| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.46 r_work: 0.2857 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16798 Z= 0.130 Angle : 0.500 7.375 22745 Z= 0.265 Chirality : 0.041 0.151 2581 Planarity : 0.003 0.041 2873 Dihedral : 13.054 89.418 2632 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.88 % Allowed : 9.81 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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: 0.98 (0.19), residues: 2063 helix: 1.11 (0.18), residues: 962 sheet: 1.31 (0.30), residues: 316 loop : -0.09 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 260 TYR 0.018 0.001 TYR H 129 PHE 0.014 0.001 PHE E 187 HIS 0.002 0.000 HIS E 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (16798) covalent geometry : angle 0.49988 / 0.26 (22745) hydrogen bonds : bond 0.03791 / 2.56 ( 796) hydrogen bonds : angle 4.63095 / 3.37 ( 2235) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: B 89 ASN cc_start: 0.8934 (m110) cc_final: 0.8479 (m-40) REVERT: B 152 MET cc_start: 0.7940 (tmm) cc_final: 0.7705 (tmm) REVERT: B 234 GLN cc_start: 0.8611 (mt0) cc_final: 0.8001 (mt0) REVERT: B 315 ASP cc_start: 0.8220 (m-30) cc_final: 0.7906 (m-30) REVERT: B 353 SER cc_start: 0.8683 (m) cc_final: 0.8457 (m) REVERT: C 335 MET cc_start: 0.0264 (OUTLIER) cc_final: -0.0751 (pmm) REVERT: E 108 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7874 (mt-10) REVERT: F 89 ASN cc_start: 0.8970 (t0) cc_final: 0.8528 (t0) REVERT: F 152 MET cc_start: 0.8781 (mmp) cc_final: 0.8573 (mmp) REVERT: G 139 ASP cc_start: 0.8510 (p0) cc_final: 0.8147 (p0) REVERT: G 142 LYS cc_start: 0.8955 (mtmm) cc_final: 0.8687 (mppt) REVERT: I 126 ASP cc_start: 0.8980 (m-30) cc_final: 0.8767 (m-30) REVERT: I 133 LYS cc_start: 0.8616 (tppp) cc_final: 0.8321 (ttmm) REVERT: I 137 GLN cc_start: 0.8569 (mp10) cc_final: 0.8248 (mp10) REVERT: J 121 LYS cc_start: 0.9119 (mmmm) cc_final: 0.8801 (tptp) REVERT: K 122 LYS cc_start: 0.9006 (ttmt) cc_final: 0.8780 (ttmt) REVERT: K 129 TYR cc_start: 0.9442 (t80) cc_final: 0.9052 (t80) REVERT: K 139 ASP cc_start: 0.8512 (p0) cc_final: 0.7815 (p0) outliers start: 15 outliers final: 7 residues processed: 163 average time/residue: 0.6527 time to fit residues: 117.2000 Evaluate side-chains 159 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain J residue 145 TYR Chi-restraints excluded: chain K residue 123 SER Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 126 ASP Chi-restraints excluded: chain K residue 146 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 120 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 187 optimal weight: 9.9990 chunk 159 optimal weight: 10.0000 chunk 147 optimal weight: 0.1980 chunk 61 optimal weight: 4.9990 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 132 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 = 0.3565 r_free = 0.3565 target = 0.090390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.061155 restraints weight = 38858.664| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 3.41 r_work: 0.2802 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 16798 Z= 0.278 Angle : 0.592 8.317 22745 Z= 0.312 Chirality : 0.045 0.149 2581 Planarity : 0.004 0.050 2873 Dihedral : 12.901 89.621 2632 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.75 % Allowed : 10.51 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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: 0.74 (0.19), residues: 2063 helix: 1.00 (0.17), residues: 958 sheet: 0.94 (0.30), residues: 318 loop : -0.21 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 260 TYR 0.011 0.001 TYR E 217 PHE 0.013 0.002 PHE B 184 HIS 0.003 0.001 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00647 / 0.28 (16798) covalent geometry : angle 0.59245 / 0.31 (22745) hydrogen bonds : bond 0.04536 / 3.05 ( 796) hydrogen bonds : angle 4.79518 / 3.49 ( 2235) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: A 142 MET cc_start: 0.6080 (OUTLIER) cc_final: 0.5836 (mmm) REVERT: B 89 ASN cc_start: 0.9017 (m110) cc_final: 0.8584 (m-40) REVERT: B 315 ASP cc_start: 0.8262 (m-30) cc_final: 0.7960 (m-30) REVERT: B 353 SER cc_start: 0.8739 (m) cc_final: 0.8500 (m) REVERT: C 335 MET cc_start: 0.0417 (OUTLIER) cc_final: -0.0628 (pmm) REVERT: D 349 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8895 (mp) REVERT: E 108 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7985 (mt-10) REVERT: F 89 ASN cc_start: 0.8993 (t0) cc_final: 0.8586 (t0) REVERT: F 152 MET cc_start: 0.8846 (mmp) cc_final: 0.8607 (mmp) REVERT: G 139 ASP cc_start: 0.8618 (p0) cc_final: 0.7902 (p0) REVERT: H 130 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8867 (pp20) REVERT: I 133 LYS cc_start: 0.8673 (tppp) cc_final: 0.8315 (ttmm) REVERT: I 137 GLN cc_start: 0.8651 (mp10) cc_final: 0.8296 (mp10) REVERT: J 121 LYS cc_start: 0.9142 (mmmm) cc_final: 0.8916 (tptp) REVERT: J 139 ASP cc_start: 0.7643 (t0) cc_final: 0.7442 (t0) REVERT: K 122 LYS cc_start: 0.9070 (ttmt) cc_final: 0.8793 (ttpt) REVERT: K 129 TYR cc_start: 0.9454 (t80) cc_final: 0.8980 (t80) REVERT: K 130 GLU cc_start: 0.9293 (mt-10) cc_final: 0.9040 (mt-10) REVERT: K 139 ASP cc_start: 0.8418 (p0) cc_final: 0.7802 (p0) outliers start: 30 outliers final: 11 residues processed: 173 average time/residue: 0.6095 time to fit residues: 116.3866 Evaluate side-chains 162 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain G residue 152 LYS Chi-restraints excluded: chain J residue 145 TYR Chi-restraints excluded: chain K residue 123 SER Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 126 ASP Chi-restraints excluded: chain K residue 146 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 154 optimal weight: 7.9990 chunk 167 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 200 optimal weight: 0.1980 chunk 62 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 72 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 105 HIS ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.093137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.064013 restraints weight = 38610.753| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 3.44 r_work: 0.2874 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16798 Z= 0.102 Angle : 0.491 8.816 22745 Z= 0.258 Chirality : 0.041 0.147 2581 Planarity : 0.003 0.040 2873 Dihedral : 12.524 89.764 2632 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.63 % Allowed : 11.91 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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: 0.95 (0.19), residues: 2063 helix: 1.15 (0.18), residues: 970 sheet: 1.30 (0.30), residues: 304 loop : -0.20 (0.23), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 260 TYR 0.010 0.001 TYR J 129 PHE 0.015 0.001 PHE B 187 HIS 0.002 0.000 HIS E 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (16798) covalent geometry : angle 0.49050 / 0.26 (22745) hydrogen bonds : bond 0.03082 / 2.08 ( 796) hydrogen bonds : angle 4.32187 / 3.15 ( 2235) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 142 MET cc_start: 0.5996 (OUTLIER) cc_final: 0.5788 (mmm) REVERT: B 89 ASN cc_start: 0.8908 (m110) cc_final: 0.8457 (m-40) REVERT: B 152 MET cc_start: 0.7895 (tmm) cc_final: 0.7661 (tmm) REVERT: B 234 GLN cc_start: 0.8608 (mt0) cc_final: 0.7983 (mt0) REVERT: B 315 ASP cc_start: 0.8157 (m-30) cc_final: 0.7840 (m-30) REVERT: B 335 MET cc_start: 0.0279 (ppp) cc_final: -0.1875 (ttt) REVERT: B 353 SER cc_start: 0.8671 (m) cc_final: 0.8432 (m) REVERT: C 335 MET cc_start: 0.0425 (OUTLIER) cc_final: -0.0402 (pmm) REVERT: C 345 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7805 (tt) REVERT: E 108 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7748 (mt-10) REVERT: F 89 ASN cc_start: 0.8977 (t0) cc_final: 0.8521 (t0) REVERT: F 152 MET cc_start: 0.8806 (mmp) cc_final: 0.8552 (mmp) REVERT: F 302 HIS cc_start: 0.8934 (t-90) cc_final: 0.8730 (t-90) REVERT: G 139 ASP cc_start: 0.8322 (p0) cc_final: 0.8008 (p0) REVERT: I 133 LYS cc_start: 0.8665 (tppp) cc_final: 0.8307 (ttmm) REVERT: I 137 GLN cc_start: 0.8697 (mp10) cc_final: 0.8330 (mp10) REVERT: J 137 GLN cc_start: 0.8541 (mp10) cc_final: 0.8287 (mp10) REVERT: K 122 LYS cc_start: 0.9237 (ttmt) cc_final: 0.8640 (ttpp) REVERT: K 129 TYR cc_start: 0.9439 (t80) cc_final: 0.8995 (t80) REVERT: K 130 GLU cc_start: 0.9348 (mt-10) cc_final: 0.8958 (mt-10) REVERT: K 139 ASP cc_start: 0.8427 (p0) cc_final: 0.7791 (p0) outliers start: 28 outliers final: 7 residues processed: 174 average time/residue: 0.5849 time to fit residues: 112.4617 Evaluate side-chains 167 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 156 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain J residue 145 TYR Chi-restraints excluded: chain J residue 150 SER Chi-restraints excluded: chain K residue 123 SER Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 146 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 21 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 141 ASN ** K 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.090929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.061632 restraints weight = 38848.669| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.42 r_work: 0.2825 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 16798 Z= 0.238 Angle : 0.582 9.380 22745 Z= 0.302 Chirality : 0.044 0.147 2581 Planarity : 0.004 0.044 2873 Dihedral : 12.624 89.528 2632 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.46 % Allowed : 13.31 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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: 0.82 (0.19), residues: 2063 helix: 1.09 (0.18), residues: 962 sheet: 0.96 (0.30), residues: 318 loop : -0.21 (0.23), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 260 TYR 0.018 0.001 TYR H 129 PHE 0.011 0.001 PHE B 184 HIS 0.003 0.001 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.24 (16798) covalent geometry : angle 0.58180 / 0.30 (22745) hydrogen bonds : bond 0.04063 / 2.73 ( 796) hydrogen bonds : angle 4.54979 / 3.32 ( 2235) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 142 MET cc_start: 0.6020 (OUTLIER) cc_final: 0.5286 (mmt) REVERT: A 271 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8218 (tm-30) REVERT: B 89 ASN cc_start: 0.8983 (m110) cc_final: 0.8537 (m-40) REVERT: B 234 GLN cc_start: 0.8588 (mt0) cc_final: 0.7985 (mt0) REVERT: B 315 ASP cc_start: 0.8233 (m-30) cc_final: 0.7931 (m-30) REVERT: B 353 SER cc_start: 0.8808 (m) cc_final: 0.8571 (m) REVERT: C 335 MET cc_start: 0.0514 (OUTLIER) cc_final: -0.0336 (pmm) REVERT: D 301 MET cc_start: 0.8802 (tpt) cc_final: 0.8171 (tpp) REVERT: D 349 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8884 (mp) REVERT: E 108 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7926 (mt-10) REVERT: E 335 MET cc_start: 0.2186 (pmm) cc_final: -0.1629 (tmt) REVERT: F 89 ASN cc_start: 0.9002 (t0) cc_final: 0.8580 (t0) REVERT: F 152 MET cc_start: 0.8824 (mmp) cc_final: 0.8607 (mmp) REVERT: G 139 ASP cc_start: 0.8392 (p0) cc_final: 0.8090 (p0) REVERT: I 133 LYS cc_start: 0.8690 (tppp) cc_final: 0.8314 (ttmm) REVERT: I 137 GLN cc_start: 0.8695 (mp10) cc_final: 0.8318 (mp10) REVERT: I 144 LYS cc_start: 0.8851 (mttm) cc_final: 0.8578 (mttm) REVERT: J 137 GLN cc_start: 0.8688 (mp10) cc_final: 0.8401 (mp10) REVERT: K 122 LYS cc_start: 0.9254 (ttmt) cc_final: 0.8625 (tmmm) REVERT: K 129 TYR cc_start: 0.9439 (t80) cc_final: 0.9020 (t80) REVERT: K 139 ASP cc_start: 0.8405 (p0) cc_final: 0.7760 (p0) outliers start: 25 outliers final: 10 residues processed: 179 average time/residue: 0.6330 time to fit residues: 124.6975 Evaluate side-chains 174 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain I residue 135 PHE Chi-restraints excluded: chain J residue 145 TYR Chi-restraints excluded: chain K residue 123 SER Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 146 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 23 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 3 optimal weight: 0.0270 chunk 131 optimal weight: 0.7980 chunk 1 optimal weight: 20.0000 chunk 168 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 132 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 = 0.3600 r_free = 0.3600 target = 0.092414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.063271 restraints weight = 38374.316| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.39 r_work: 0.2850 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16798 Z= 0.121 Angle : 0.534 9.935 22745 Z= 0.274 Chirality : 0.041 0.147 2581 Planarity : 0.003 0.039 2873 Dihedral : 12.414 88.192 2632 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.28 % Allowed : 14.13 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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: 1.08 (0.19), residues: 2063 helix: 1.35 (0.18), residues: 942 sheet: 1.26 (0.30), residues: 304 loop : -0.17 (0.23), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 260 TYR 0.007 0.001 TYR J 129 PHE 0.012 0.001 PHE E 187 HIS 0.001 0.000 HIS E 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (16798) covalent geometry : angle 0.53384 / 0.27 (22745) hydrogen bonds : bond 0.03165 / 2.13 ( 796) hydrogen bonds : angle 4.28256 / 3.13 ( 2235) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.6025 (OUTLIER) cc_final: 0.5398 (mmt) REVERT: A 271 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8209 (tm-30) REVERT: B 89 ASN cc_start: 0.8917 (m110) cc_final: 0.8461 (m-40) REVERT: B 234 GLN cc_start: 0.8617 (mt0) cc_final: 0.8016 (mt0) REVERT: B 293 ARG cc_start: 0.8158 (ttm170) cc_final: 0.7941 (tpp-160) REVERT: B 315 ASP cc_start: 0.8149 (m-30) cc_final: 0.7844 (m-30) REVERT: B 335 MET cc_start: -0.0099 (ppp) cc_final: -0.2122 (ttt) REVERT: B 353 SER cc_start: 0.8755 (m) cc_final: 0.8513 (m) REVERT: C 335 MET cc_start: 0.0561 (OUTLIER) cc_final: -0.0256 (pmm) REVERT: E 108 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7810 (mt-10) REVERT: F 89 ASN cc_start: 0.8992 (t0) cc_final: 0.8548 (t0) REVERT: F 152 MET cc_start: 0.8806 (mmp) cc_final: 0.8571 (mmp) REVERT: F 260 ARG cc_start: 0.8498 (ttp-110) cc_final: 0.8276 (ttp-110) REVERT: F 302 HIS cc_start: 0.8986 (t-90) cc_final: 0.8765 (t-90) REVERT: G 139 ASP cc_start: 0.8494 (p0) cc_final: 0.8181 (p0) REVERT: I 133 LYS cc_start: 0.8705 (tppp) cc_final: 0.8283 (ttmm) REVERT: I 137 GLN cc_start: 0.8704 (mp10) cc_final: 0.8345 (mp10) REVERT: I 144 LYS cc_start: 0.8837 (mttm) cc_final: 0.8553 (mttm) REVERT: J 137 GLN cc_start: 0.8746 (mp10) cc_final: 0.8448 (mp10) REVERT: J 139 ASP cc_start: 0.7761 (t0) cc_final: 0.7527 (t0) REVERT: K 122 LYS cc_start: 0.9361 (ttmt) cc_final: 0.8946 (ttpp) REVERT: K 129 TYR cc_start: 0.9442 (t80) cc_final: 0.9077 (t80) REVERT: K 139 ASP cc_start: 0.8437 (p0) cc_final: 0.7845 (p0) outliers start: 22 outliers final: 10 residues processed: 181 average time/residue: 0.6171 time to fit residues: 123.2805 Evaluate side-chains 173 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain I residue 135 PHE Chi-restraints excluded: chain J residue 145 TYR Chi-restraints excluded: chain K residue 123 SER Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 146 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 138 optimal weight: 7.9990 chunk 163 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 199 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 200 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 348 ASN G 141 ASN ** K 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.092764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.063567 restraints weight = 38830.153| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.41 r_work: 0.2868 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16798 Z= 0.128 Angle : 0.557 12.826 22745 Z= 0.280 Chirality : 0.041 0.148 2581 Planarity : 0.003 0.037 2873 Dihedral : 12.262 88.414 2632 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.11 % Allowed : 15.00 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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: 1.12 (0.19), residues: 2063 helix: 1.38 (0.18), residues: 940 sheet: 1.43 (0.31), residues: 296 loop : -0.17 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 260 TYR 0.006 0.001 TYR J 129 PHE 0.011 0.001 PHE F 274 HIS 0.001 0.000 HIS C 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (16798) covalent geometry : angle 0.55694 / 0.28 (22745) hydrogen bonds : bond 0.03151 / 2.13 ( 796) hydrogen bonds : angle 4.22737 / 3.08 ( 2235) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.6113 (OUTLIER) cc_final: 0.5495 (mmt) REVERT: A 271 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8206 (tm-30) REVERT: B 89 ASN cc_start: 0.8896 (m110) cc_final: 0.8441 (m-40) REVERT: B 183 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8575 (mt) REVERT: B 234 GLN cc_start: 0.8586 (mt0) cc_final: 0.8002 (mt0) REVERT: B 315 ASP cc_start: 0.8184 (m-30) cc_final: 0.7835 (m-30) REVERT: B 335 MET cc_start: -0.0054 (ppp) cc_final: -0.2031 (ttt) REVERT: B 353 SER cc_start: 0.8800 (m) cc_final: 0.8554 (m) REVERT: C 335 MET cc_start: 0.0852 (OUTLIER) cc_final: 0.0023 (pmm) REVERT: D 349 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8821 (mp) REVERT: E 108 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7792 (mt-10) REVERT: E 335 MET cc_start: 0.1944 (pmm) cc_final: -0.1869 (tmt) REVERT: F 89 ASN cc_start: 0.9005 (t0) cc_final: 0.8576 (t0) REVERT: F 152 MET cc_start: 0.8824 (mmp) cc_final: 0.8575 (mmp) REVERT: F 302 HIS cc_start: 0.8988 (t-90) cc_final: 0.8762 (t-90) REVERT: G 139 ASP cc_start: 0.8508 (p0) cc_final: 0.8221 (p0) REVERT: I 133 LYS cc_start: 0.8703 (tppp) cc_final: 0.8288 (ttmm) REVERT: I 137 GLN cc_start: 0.8705 (mp10) cc_final: 0.8355 (mp10) REVERT: I 144 LYS cc_start: 0.8896 (mttm) cc_final: 0.8612 (mttm) REVERT: J 137 GLN cc_start: 0.8781 (mp10) cc_final: 0.8454 (mp10) REVERT: J 139 ASP cc_start: 0.7814 (t0) cc_final: 0.7595 (t0) REVERT: K 122 LYS cc_start: 0.9364 (ttmt) cc_final: 0.8777 (tmmm) REVERT: K 129 TYR cc_start: 0.9447 (t80) cc_final: 0.9086 (t80) REVERT: K 139 ASP cc_start: 0.8414 (p0) cc_final: 0.7823 (p0) outliers start: 19 outliers final: 11 residues processed: 171 average time/residue: 0.6640 time to fit residues: 125.0473 Evaluate side-chains 171 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain J residue 145 TYR Chi-restraints excluded: chain K residue 123 SER Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 146 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 102 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 163 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 151 optimal weight: 0.6980 chunk 190 optimal weight: 6.9990 chunk 181 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 174 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 141 ASN ** K 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.092931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.063995 restraints weight = 38415.072| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.38 r_work: 0.2875 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16798 Z= 0.128 Angle : 0.573 12.713 22745 Z= 0.286 Chirality : 0.041 0.148 2581 Planarity : 0.003 0.042 2873 Dihedral : 12.229 88.943 2632 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.28 % Allowed : 15.06 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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: 1.14 (0.19), residues: 2063 helix: 1.39 (0.18), residues: 940 sheet: 1.20 (0.31), residues: 308 loop : -0.09 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 260 TYR 0.021 0.001 TYR H 129 PHE 0.014 0.001 PHE F 274 HIS 0.002 0.000 HIS C 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (16798) covalent geometry : angle 0.57280 / 0.29 (22745) hydrogen bonds : bond 0.03095 / 2.10 ( 796) hydrogen bonds : angle 4.19649 / 3.06 ( 2235) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.6095 (OUTLIER) cc_final: 0.5491 (mmt) REVERT: A 271 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8199 (tm-30) REVERT: B 89 ASN cc_start: 0.8875 (m110) cc_final: 0.8418 (m-40) REVERT: B 183 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8542 (mt) REVERT: B 234 GLN cc_start: 0.8545 (mt0) cc_final: 0.7984 (mt0) REVERT: B 315 ASP cc_start: 0.8187 (m-30) cc_final: 0.7837 (m-30) REVERT: B 335 MET cc_start: -0.0068 (ppp) cc_final: -0.2036 (ttt) REVERT: B 353 SER cc_start: 0.8766 (m) cc_final: 0.8520 (m) REVERT: C 335 MET cc_start: 0.0818 (OUTLIER) cc_final: -0.0013 (pmm) REVERT: D 301 MET cc_start: 0.8648 (tpt) cc_final: 0.7968 (tpp) REVERT: D 349 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8821 (mp) REVERT: E 108 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7791 (mt-10) REVERT: E 335 MET cc_start: 0.1926 (pmm) cc_final: -0.1794 (tmt) REVERT: F 89 ASN cc_start: 0.9016 (t0) cc_final: 0.8587 (t0) REVERT: F 152 MET cc_start: 0.8818 (mmp) cc_final: 0.8569 (mmp) REVERT: F 302 HIS cc_start: 0.8982 (t-90) cc_final: 0.8752 (t-90) REVERT: G 139 ASP cc_start: 0.8506 (p0) cc_final: 0.8220 (p0) REVERT: I 133 LYS cc_start: 0.8701 (tppp) cc_final: 0.8289 (ttmm) REVERT: I 137 GLN cc_start: 0.8767 (mp10) cc_final: 0.8398 (mp10) REVERT: J 137 GLN cc_start: 0.8790 (mp10) cc_final: 0.8457 (mp10) REVERT: J 139 ASP cc_start: 0.7846 (t0) cc_final: 0.7619 (t0) REVERT: K 122 LYS cc_start: 0.9394 (ttmt) cc_final: 0.8825 (tmmm) REVERT: K 129 TYR cc_start: 0.9456 (t80) cc_final: 0.9096 (t80) REVERT: K 139 ASP cc_start: 0.8413 (p0) cc_final: 0.7825 (p0) outliers start: 22 outliers final: 12 residues processed: 171 average time/residue: 0.6710 time to fit residues: 126.4557 Evaluate side-chains 170 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain I residue 135 PHE Chi-restraints excluded: chain J residue 145 TYR Chi-restraints excluded: chain K residue 123 SER Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 146 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 104 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 46 optimal weight: 0.0470 chunk 193 optimal weight: 3.9990 chunk 160 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 99 optimal weight: 0.4980 chunk 184 optimal weight: 7.9990 overall best weight: 1.2882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 132 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 = 0.3620 r_free = 0.3620 target = 0.093400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.064259 restraints weight = 38431.847| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.42 r_work: 0.2880 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16798 Z= 0.121 Angle : 0.583 13.398 22745 Z= 0.287 Chirality : 0.041 0.148 2581 Planarity : 0.003 0.046 2873 Dihedral : 12.148 88.482 2632 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.11 % Allowed : 15.24 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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: 1.19 (0.19), residues: 2063 helix: 1.43 (0.18), residues: 938 sheet: 1.24 (0.30), residues: 312 loop : -0.07 (0.23), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 260 TYR 0.005 0.001 TYR F 286 PHE 0.016 0.001 PHE F 274 HIS 0.001 0.000 HIS E 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (16798) covalent geometry : angle 0.58282 / 0.29 (22745) hydrogen bonds : bond 0.02985 / 2.03 ( 796) hydrogen bonds : angle 4.15396 / 3.03 ( 2235) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.6045 (OUTLIER) cc_final: 0.5402 (mmt) REVERT: A 271 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8201 (tm-30) REVERT: B 89 ASN cc_start: 0.8847 (m110) cc_final: 0.8387 (m-40) REVERT: B 183 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8534 (mt) REVERT: B 234 GLN cc_start: 0.8538 (mt0) cc_final: 0.7984 (mt0) REVERT: B 315 ASP cc_start: 0.8156 (m-30) cc_final: 0.7805 (m-30) REVERT: B 335 MET cc_start: -0.0068 (ppp) cc_final: -0.1987 (ttt) REVERT: B 353 SER cc_start: 0.8768 (m) cc_final: 0.8540 (m) REVERT: C 335 MET cc_start: 0.0809 (OUTLIER) cc_final: -0.0030 (pmm) REVERT: D 283 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8391 (mtm) REVERT: D 301 MET cc_start: 0.8597 (tpt) cc_final: 0.7923 (tpp) REVERT: D 349 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8817 (mp) REVERT: E 108 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7780 (mt-10) REVERT: E 335 MET cc_start: 0.1662 (pmm) cc_final: -0.2111 (tmt) REVERT: F 89 ASN cc_start: 0.9025 (t0) cc_final: 0.8597 (t0) REVERT: F 152 MET cc_start: 0.8799 (mmp) cc_final: 0.8553 (mmp) REVERT: G 139 ASP cc_start: 0.8491 (p0) cc_final: 0.8204 (p0) REVERT: I 133 LYS cc_start: 0.8704 (tppp) cc_final: 0.8290 (ttmm) REVERT: I 137 GLN cc_start: 0.8753 (mp10) cc_final: 0.8379 (mp10) REVERT: J 137 GLN cc_start: 0.8796 (mp10) cc_final: 0.8461 (mp10) REVERT: J 139 ASP cc_start: 0.7902 (t0) cc_final: 0.7663 (t0) REVERT: K 122 LYS cc_start: 0.9399 (ttmt) cc_final: 0.9048 (ttpp) REVERT: K 129 TYR cc_start: 0.9420 (t80) cc_final: 0.9079 (t80) REVERT: K 139 ASP cc_start: 0.8459 (p0) cc_final: 0.7871 (p0) outliers start: 19 outliers final: 11 residues processed: 167 average time/residue: 0.7143 time to fit residues: 131.6195 Evaluate side-chains 168 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain I residue 135 PHE Chi-restraints excluded: chain J residue 145 TYR Chi-restraints excluded: chain K residue 123 SER Chi-restraints excluded: chain K residue 124 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 141 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 135 optimal weight: 0.0770 chunk 132 optimal weight: 4.9990 chunk 187 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 89 ASN ** K 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.093034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.063532 restraints weight = 38816.551| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.47 r_work: 0.2868 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16798 Z= 0.134 Angle : 0.587 12.504 22745 Z= 0.290 Chirality : 0.041 0.150 2581 Planarity : 0.003 0.039 2873 Dihedral : 12.133 88.048 2632 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.99 % Allowed : 15.59 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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: 1.18 (0.19), residues: 2063 helix: 1.44 (0.18), residues: 938 sheet: 1.29 (0.31), residues: 302 loop : -0.10 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 260 TYR 0.022 0.001 TYR H 129 PHE 0.014 0.001 PHE F 274 HIS 0.002 0.000 HIS C 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (16798) covalent geometry : angle 0.58673 / 0.29 (22745) hydrogen bonds : bond 0.03057 / 2.08 ( 796) hydrogen bonds : angle 4.17443 / 3.05 ( 2235) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4720.70 seconds wall clock time: 81 minutes 17.74 seconds (4877.74 seconds total)