Starting phenix.real_space_refine on Thu Sep 18 11:54:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e6n_47573/09_2025/9e6n_47573.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e6n_47573/09_2025/9e6n_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_47573/09_2025/9e6n_47573.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e6n_47573/09_2025/9e6n_47573.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e6n_47573/09_2025/9e6n_47573.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e6n_47573/09_2025/9e6n_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: 4.50, per 1000 atoms: 0.27 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: 1.44 Conformation dependent library (CDL) restraints added in 810.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.40 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: 2.93 Time building geometry restraints manager: 1.89 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=" N SER K 150 " pdb=" CA SER K 150 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.23e-02 6.61e+03 7.72e+00 ... (remaining 16793 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 22377 1.73 - 3.45: 323 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: 2342 0.075 - 0.151: 225 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: 1.070 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.710 Find NCS groups from input model: 0.440 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:9.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 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= 0.157 Angle : 0.499 8.631 22745 Z= 0.293 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 aren 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 covalent geometry : bond 0.00280 (16798) covalent geometry : angle 0.49867 (22745) hydrogen bonds : bond 0.23908 ( 796) hydrogen bonds : angle 7.35199 ( 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 : 0.516 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: 0.7114 time to fit residues: 139.4884 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 : 0.652 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3561 r_free = 0.3561 target = 0.091120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.061161 restraints weight = 38457.815| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.54 r_work: 0.2760 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 16798 Z= 0.241 Angle : 0.579 8.281 22745 Z= 0.307 Chirality : 0.044 0.156 2581 Planarity : 0.004 0.043 2873 Dihedral : 13.139 89.139 2632 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.93 % Allowed : 7.24 % Favored : 91.83 % 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 aren not related in a simple way. whole: 0.90 (0.19), residues: 2063 helix: 1.02 (0.18), residues: 948 sheet: 1.42 (0.30), residues: 312 loop : -0.13 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 260 TYR 0.012 0.001 TYR E 217 PHE 0.019 0.002 PHE C 187 HIS 0.003 0.001 HIS C 196 Details of bonding type rmsd covalent geometry : bond 0.00562 (16798) covalent geometry : angle 0.57853 (22745) hydrogen bonds : bond 0.04870 ( 796) hydrogen bonds : angle 5.10265 ( 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 177 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: B 89 ASN cc_start: 0.9015 (m110) cc_final: 0.8597 (m-40) REVERT: B 315 ASP cc_start: 0.8220 (m-30) cc_final: 0.7889 (m-30) REVERT: B 353 SER cc_start: 0.8619 (m) cc_final: 0.8378 (m) REVERT: C 335 MET cc_start: 0.0255 (OUTLIER) cc_final: -0.0761 (pmm) REVERT: E 108 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.7966 (mt-10) REVERT: F 89 ASN cc_start: 0.8969 (t0) cc_final: 0.8568 (t0) REVERT: G 139 ASP cc_start: 0.8686 (p0) cc_final: 0.7971 (p0) REVERT: H 139 ASP cc_start: 0.7665 (t0) cc_final: 0.7415 (t0) REVERT: I 133 LYS cc_start: 0.8673 (tppp) cc_final: 0.8285 (ttmm) REVERT: I 137 GLN cc_start: 0.8488 (mp10) cc_final: 0.8261 (mp10) REVERT: K 122 LYS cc_start: 0.8924 (ttmt) cc_final: 0.8678 (ttmt) REVERT: K 129 TYR cc_start: 0.9400 (t80) cc_final: 0.9043 (t80) REVERT: K 139 ASP cc_start: 0.8505 (p0) cc_final: 0.7813 (p0) outliers start: 16 outliers final: 5 residues processed: 165 average time/residue: 0.7051 time to fit residues: 127.7845 Evaluate side-chains 156 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 149 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 335 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 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: 10.0000 chunk 126 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 178 optimal weight: 6.9990 chunk 145 optimal weight: 8.9990 chunk 169 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3604 r_free = 0.3604 target = 0.092437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.063232 restraints weight = 39264.417| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.45 r_work: 0.2858 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16798 Z= 0.147 Angle : 0.506 8.452 22745 Z= 0.266 Chirality : 0.042 0.156 2581 Planarity : 0.003 0.041 2873 Dihedral : 12.626 89.823 2632 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.17 % Allowed : 9.05 % Favored : 89.78 % 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 aren not related in a simple way. whole: 0.96 (0.19), residues: 2063 helix: 1.11 (0.18), residues: 964 sheet: 1.41 (0.31), residues: 302 loop : -0.15 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 260 TYR 0.009 0.001 TYR J 129 PHE 0.015 0.001 PHE E 187 HIS 0.002 0.001 HIS E 196 Details of bonding type rmsd covalent geometry : bond 0.00340 (16798) covalent geometry : angle 0.50606 (22745) hydrogen bonds : bond 0.03627 ( 796) hydrogen bonds : angle 4.54921 ( 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 176 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: B 89 ASN cc_start: 0.8942 (m110) cc_final: 0.8501 (m-40) REVERT: B 234 GLN cc_start: 0.8586 (mt0) cc_final: 0.7953 (mt0) REVERT: B 315 ASP cc_start: 0.8209 (m-30) cc_final: 0.7910 (m-30) REVERT: B 353 SER cc_start: 0.8690 (m) cc_final: 0.8456 (m) REVERT: C 335 MET cc_start: 0.0385 (OUTLIER) cc_final: -0.0633 (pmm) REVERT: D 269 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8984 (mtt) REVERT: E 108 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7872 (mt-10) REVERT: F 89 ASN cc_start: 0.8984 (t0) cc_final: 0.8560 (t0) REVERT: G 139 ASP cc_start: 0.8652 (p0) cc_final: 0.7998 (p0) REVERT: G 142 LYS cc_start: 0.8903 (mtmm) cc_final: 0.8525 (mppt) REVERT: I 126 ASP cc_start: 0.8963 (m-30) cc_final: 0.8747 (m-30) REVERT: I 133 LYS cc_start: 0.8629 (tppp) cc_final: 0.8308 (ttmm) REVERT: I 137 GLN cc_start: 0.8618 (mp10) cc_final: 0.8274 (mp10) REVERT: J 121 LYS cc_start: 0.9129 (mmmm) cc_final: 0.8886 (tptp) REVERT: K 122 LYS cc_start: 0.9168 (ttmt) cc_final: 0.8565 (ttpp) REVERT: K 129 TYR cc_start: 0.9442 (t80) cc_final: 0.9029 (t80) REVERT: K 139 ASP cc_start: 0.8529 (p0) cc_final: 0.7912 (p0) outliers start: 20 outliers final: 8 residues processed: 162 average time/residue: 0.6948 time to fit residues: 123.3922 Evaluate side-chains 162 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 D residue 269 MET Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 120 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 190 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 201 optimal weight: 5.9990 chunk 187 optimal weight: 0.0270 chunk 159 optimal weight: 0.0970 chunk 147 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.3840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3615 r_free = 0.3615 target = 0.093124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.063953 restraints weight = 38407.388| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.42 r_work: 0.2873 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1812 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= 0.119 Angle : 0.493 8.808 22745 Z= 0.256 Chirality : 0.041 0.152 2581 Planarity : 0.003 0.036 2873 Dihedral : 12.411 89.959 2632 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.23 % Allowed : 10.74 % Favored : 88.03 % 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 aren not related in a simple way. whole: 1.03 (0.19), residues: 2063 helix: 1.19 (0.18), residues: 970 sheet: 1.15 (0.30), residues: 316 loop : -0.05 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 260 TYR 0.007 0.001 TYR J 129 PHE 0.014 0.001 PHE B 187 HIS 0.002 0.000 HIS C 196 Details of bonding type rmsd covalent geometry : bond 0.00270 (16798) covalent geometry : angle 0.49265 (22745) hydrogen bonds : bond 0.03158 ( 796) hydrogen bonds : angle 4.32499 ( 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 181 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: B 89 ASN cc_start: 0.8912 (m110) cc_final: 0.8470 (m-40) REVERT: B 152 MET cc_start: 0.7929 (tmm) cc_final: 0.7721 (tmm) REVERT: B 234 GLN cc_start: 0.8572 (mt0) cc_final: 0.7984 (mt0) REVERT: B 315 ASP cc_start: 0.8203 (m-30) cc_final: 0.7882 (m-30) REVERT: B 348 ASN cc_start: 0.8424 (m-40) cc_final: 0.8152 (m110) REVERT: B 353 SER cc_start: 0.8683 (m) cc_final: 0.8444 (m) REVERT: C 335 MET cc_start: 0.0368 (OUTLIER) cc_final: -0.0655 (pmm) REVERT: C 345 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7736 (tt) REVERT: D 345 ILE cc_start: 0.7537 (OUTLIER) cc_final: 0.7202 (tp) REVERT: E 108 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7848 (mt-10) REVERT: F 89 ASN cc_start: 0.8990 (t0) cc_final: 0.8554 (t0) REVERT: G 139 ASP cc_start: 0.8588 (p0) cc_final: 0.7757 (p0) REVERT: H 130 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8837 (pp20) REVERT: I 133 LYS cc_start: 0.8664 (tppp) cc_final: 0.8337 (ttmm) REVERT: I 137 GLN cc_start: 0.8655 (mp10) cc_final: 0.8298 (mp10) REVERT: J 146 LYS cc_start: 0.8661 (ptmm) cc_final: 0.8394 (ptpp) REVERT: K 122 LYS cc_start: 0.9241 (ttmt) cc_final: 0.9028 (ttpt) REVERT: K 129 TYR cc_start: 0.9464 (t80) cc_final: 0.9009 (t80) REVERT: K 130 GLU cc_start: 0.9331 (mt-10) cc_final: 0.9121 (mt-10) REVERT: K 139 ASP cc_start: 0.8504 (p0) cc_final: 0.7859 (p0) outliers start: 21 outliers final: 8 residues processed: 169 average time/residue: 0.7060 time to fit residues: 131.1668 Evaluate side-chains 165 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain D residue 345 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 154 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 chunk 200 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 141 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3594 r_free = 0.3594 target = 0.092087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.062863 restraints weight = 38813.256| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.43 r_work: 0.2850 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16798 Z= 0.167 Angle : 0.530 9.262 22745 Z= 0.274 Chirality : 0.042 0.152 2581 Planarity : 0.003 0.039 2873 Dihedral : 12.363 88.544 2632 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.58 % Allowed : 12.03 % Favored : 86.40 % 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 aren not related in a simple way. whole: 1.00 (0.19), residues: 2063 helix: 1.20 (0.18), residues: 968 sheet: 1.23 (0.30), residues: 308 loop : -0.14 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 260 TYR 0.019 0.001 TYR H 129 PHE 0.012 0.001 PHE B 187 HIS 0.002 0.001 HIS C 196 Details of bonding type rmsd covalent geometry : bond 0.00388 (16798) covalent geometry : angle 0.53012 (22745) hydrogen bonds : bond 0.03509 ( 796) hydrogen bonds : angle 4.36781 ( 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 185 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: B 89 ASN cc_start: 0.8911 (m110) cc_final: 0.8461 (m-40) REVERT: B 234 GLN cc_start: 0.8530 (mt0) cc_final: 0.7951 (mt0) REVERT: B 315 ASP cc_start: 0.8230 (m-30) cc_final: 0.7916 (m-30) REVERT: B 335 MET cc_start: 0.0469 (ppp) cc_final: -0.1638 (ttt) REVERT: B 348 ASN cc_start: 0.8486 (m-40) cc_final: 0.8239 (m110) REVERT: B 353 SER cc_start: 0.8773 (m) cc_final: 0.8533 (m) REVERT: C 335 MET cc_start: 0.0472 (OUTLIER) cc_final: -0.0472 (pmm) REVERT: C 345 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7779 (tt) REVERT: D 345 ILE cc_start: 0.7627 (OUTLIER) cc_final: 0.7351 (tp) REVERT: E 108 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7853 (mt-10) REVERT: F 89 ASN cc_start: 0.8994 (t0) cc_final: 0.8567 (t0) REVERT: G 125 LYS cc_start: 0.9277 (tptm) cc_final: 0.9073 (tptp) REVERT: G 139 ASP cc_start: 0.8362 (p0) cc_final: 0.7922 (p0) REVERT: H 130 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8867 (pp20) REVERT: I 133 LYS cc_start: 0.8683 (tppp) cc_final: 0.8304 (ttmm) REVERT: I 137 GLN cc_start: 0.8704 (mp10) cc_final: 0.8325 (mp10) REVERT: J 130 GLU cc_start: 0.9215 (mm-30) cc_final: 0.8850 (tm-30) REVERT: K 122 LYS cc_start: 0.9311 (ttmt) cc_final: 0.8739 (ttpp) REVERT: K 129 TYR cc_start: 0.9457 (t80) cc_final: 0.9029 (t80) REVERT: K 139 ASP cc_start: 0.8446 (p0) cc_final: 0.7800 (p0) outliers start: 27 outliers final: 11 residues processed: 177 average time/residue: 0.6695 time to fit residues: 130.3251 Evaluate side-chains 165 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 92 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 D residue 277 ILE Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain H residue 146 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 21 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 164 optimal weight: 0.7980 chunk 92 optimal weight: 7.9990 chunk 90 optimal weight: 0.0980 chunk 106 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 172 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 110 optimal weight: 0.0570 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3618 r_free = 0.3618 target = 0.093274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.064137 restraints weight = 38528.548| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.43 r_work: 0.2867 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2016 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= 0.112 Angle : 0.521 11.811 22745 Z= 0.263 Chirality : 0.041 0.149 2581 Planarity : 0.003 0.035 2873 Dihedral : 12.176 88.942 2632 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.63 % Allowed : 12.61 % Favored : 85.76 % 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 aren not related in a simple way. whole: 1.26 (0.19), residues: 2063 helix: 1.48 (0.18), residues: 942 sheet: 1.18 (0.30), residues: 316 loop : 0.02 (0.23), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 260 TYR 0.006 0.001 TYR F 286 PHE 0.011 0.001 PHE E 187 HIS 0.002 0.000 HIS F 257 Details of bonding type rmsd covalent geometry : bond 0.00252 (16798) covalent geometry : angle 0.52131 (22745) hydrogen bonds : bond 0.02949 ( 796) hydrogen bonds : angle 4.17705 ( 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 193 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 89 ASN cc_start: 0.8861 (m110) cc_final: 0.8404 (m-40) REVERT: B 117 ASP cc_start: 0.8967 (m-30) cc_final: 0.8713 (m-30) REVERT: B 234 GLN cc_start: 0.8566 (mt0) cc_final: 0.8008 (mt0) REVERT: B 315 ASP cc_start: 0.8173 (m-30) cc_final: 0.7843 (m-30) REVERT: B 348 ASN cc_start: 0.8448 (m-40) cc_final: 0.8020 (m110) REVERT: B 353 SER cc_start: 0.8682 (m) cc_final: 0.8429 (m) REVERT: C 335 MET cc_start: 0.0696 (OUTLIER) cc_final: -0.0378 (pmm) REVERT: E 108 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7835 (mt-10) REVERT: E 335 MET cc_start: 0.1947 (pmm) cc_final: -0.1729 (tmt) REVERT: F 89 ASN cc_start: 0.9007 (t0) cc_final: 0.8575 (t0) REVERT: G 139 ASP cc_start: 0.8433 (p0) cc_final: 0.8094 (p0) REVERT: H 130 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8876 (pp20) REVERT: I 133 LYS cc_start: 0.8688 (tppp) cc_final: 0.8306 (ttmm) REVERT: I 137 GLN cc_start: 0.8740 (mp10) cc_final: 0.8362 (mp10) REVERT: J 130 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8836 (tm-30) REVERT: J 146 LYS cc_start: 0.8632 (ptmm) cc_final: 0.8349 (ptpp) REVERT: K 122 LYS cc_start: 0.9387 (ttmt) cc_final: 0.9029 (ttpp) REVERT: K 128 ILE cc_start: 0.8847 (mt) cc_final: 0.8627 (mp) REVERT: K 129 TYR cc_start: 0.9473 (t80) cc_final: 0.9088 (t80) REVERT: K 139 ASP cc_start: 0.8414 (p0) cc_final: 0.7809 (p0) outliers start: 28 outliers final: 14 residues processed: 184 average time/residue: 0.7447 time to fit residues: 150.6304 Evaluate side-chains 169 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 G residue 126 ASP Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain J residue 126 ASP 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: 3.9990 chunk 89 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 131 optimal weight: 0.0670 chunk 1 optimal weight: 6.9990 chunk 168 optimal weight: 20.0000 chunk 8 optimal weight: 0.0970 chunk 83 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3632 r_free = 0.3632 target = 0.094097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.064942 restraints weight = 38254.724| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.44 r_work: 0.2894 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16798 Z= 0.101 Angle : 0.535 10.695 22745 Z= 0.267 Chirality : 0.040 0.155 2581 Planarity : 0.003 0.034 2873 Dihedral : 12.028 89.352 2632 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.28 % Allowed : 13.84 % Favored : 84.88 % 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 aren not related in a simple way. whole: 1.34 (0.19), residues: 2063 helix: 1.53 (0.18), residues: 942 sheet: 1.64 (0.31), residues: 296 loop : -0.08 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 260 TYR 0.020 0.001 TYR H 129 PHE 0.011 0.001 PHE B 144 HIS 0.001 0.000 HIS E 257 Details of bonding type rmsd covalent geometry : bond 0.00226 (16798) covalent geometry : angle 0.53483 (22745) hydrogen bonds : bond 0.02702 ( 796) hydrogen bonds : angle 4.06095 ( 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 179 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 271 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8172 (tm-30) REVERT: B 89 ASN cc_start: 0.8827 (m110) cc_final: 0.8369 (m-40) REVERT: B 117 ASP cc_start: 0.8975 (m-30) cc_final: 0.8719 (m-30) REVERT: B 234 GLN cc_start: 0.8525 (mt0) cc_final: 0.7981 (mt0) REVERT: B 293 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7698 (tpt170) REVERT: B 315 ASP cc_start: 0.8143 (m-30) cc_final: 0.7803 (m-30) REVERT: B 335 MET cc_start: -0.0062 (ppp) cc_final: -0.2005 (ttt) REVERT: B 348 ASN cc_start: 0.8299 (m-40) cc_final: 0.7910 (m110) REVERT: B 353 SER cc_start: 0.8731 (m) cc_final: 0.8489 (m) REVERT: C 335 MET cc_start: 0.0634 (OUTLIER) cc_final: -0.0447 (pmm) REVERT: C 350 MET cc_start: 0.9164 (tpt) cc_final: 0.8854 (tpt) REVERT: D 286 TYR cc_start: 0.9461 (m-80) cc_final: 0.9228 (m-80) REVERT: E 108 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7818 (mt-10) REVERT: E 350 MET cc_start: 0.8790 (tpt) cc_final: 0.8445 (mmm) REVERT: F 89 ASN cc_start: 0.9012 (t0) cc_final: 0.8583 (t0) REVERT: G 139 ASP cc_start: 0.8460 (p0) cc_final: 0.8112 (p0) REVERT: H 130 GLU cc_start: 0.9160 (mm-30) cc_final: 0.8890 (pp20) REVERT: I 133 LYS cc_start: 0.8724 (tppp) cc_final: 0.8296 (ttmm) REVERT: I 137 GLN cc_start: 0.8699 (mp10) cc_final: 0.8338 (mp10) REVERT: J 130 GLU cc_start: 0.9196 (mm-30) cc_final: 0.8818 (tm-30) REVERT: J 146 LYS cc_start: 0.8592 (ptmm) cc_final: 0.8292 (ptpp) REVERT: K 122 LYS cc_start: 0.9379 (ttmt) cc_final: 0.9015 (ttpp) REVERT: K 129 TYR cc_start: 0.9446 (t80) cc_final: 0.9046 (t80) REVERT: K 139 ASP cc_start: 0.8490 (p0) cc_final: 0.7900 (p0) outliers start: 22 outliers final: 14 residues processed: 174 average time/residue: 0.7491 time to fit residues: 142.9854 Evaluate side-chains 166 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 293 ARG 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 183 LEU 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 G residue 124 LEU 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=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: 0.9980 chunk 55 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 72 optimal weight: 0.0570 chunk 81 optimal weight: 9.9990 chunk 199 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 200 optimal weight: 0.6980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3644 r_free = 0.3644 target = 0.094650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.065514 restraints weight = 38536.611| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 3.43 r_work: 0.2911 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16798 Z= 0.099 Angle : 0.547 12.068 22745 Z= 0.270 Chirality : 0.040 0.153 2581 Planarity : 0.003 0.034 2873 Dihedral : 11.852 89.444 2632 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.52 % Allowed : 14.42 % Favored : 84.06 % 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 aren not related in a simple way. whole: 1.41 (0.19), residues: 2063 helix: 1.59 (0.18), residues: 944 sheet: 1.59 (0.31), residues: 304 loop : -0.03 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 260 TYR 0.005 0.001 TYR F 286 PHE 0.012 0.001 PHE E 187 HIS 0.003 0.000 HIS F 151 Details of bonding type rmsd covalent geometry : bond 0.00221 (16798) covalent geometry : angle 0.54659 (22745) hydrogen bonds : bond 0.02532 ( 796) hydrogen bonds : angle 3.97649 ( 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 187 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 271 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8172 (tm-30) REVERT: B 89 ASN cc_start: 0.8773 (m110) cc_final: 0.8288 (m-40) REVERT: B 117 ASP cc_start: 0.8962 (m-30) cc_final: 0.8717 (m-30) REVERT: B 234 GLN cc_start: 0.8463 (mt0) cc_final: 0.7896 (mt0) REVERT: B 293 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7873 (tpt170) REVERT: B 315 ASP cc_start: 0.8099 (m-30) cc_final: 0.7748 (m-30) REVERT: B 335 MET cc_start: -0.0017 (ppp) cc_final: -0.1968 (ttt) REVERT: B 348 ASN cc_start: 0.8215 (m-40) cc_final: 0.7878 (m110) REVERT: B 353 SER cc_start: 0.8568 (m) cc_final: 0.8321 (m) REVERT: C 335 MET cc_start: 0.0566 (OUTLIER) cc_final: 0.0056 (pmt) REVERT: C 350 MET cc_start: 0.9102 (tpt) cc_final: 0.8763 (tpt) REVERT: D 286 TYR cc_start: 0.9440 (m-80) cc_final: 0.9231 (m-80) REVERT: E 108 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7795 (mt-10) REVERT: E 335 MET cc_start: 0.1340 (pmm) cc_final: -0.2381 (tmt) REVERT: F 89 ASN cc_start: 0.9041 (t0) cc_final: 0.8658 (t0) REVERT: F 302 HIS cc_start: 0.8897 (t-90) cc_final: 0.8639 (t-90) REVERT: G 139 ASP cc_start: 0.8478 (p0) cc_final: 0.8108 (p0) REVERT: H 130 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8938 (mm-30) REVERT: I 133 LYS cc_start: 0.8710 (tppp) cc_final: 0.8288 (ttmm) REVERT: I 137 GLN cc_start: 0.8704 (mp10) cc_final: 0.8348 (mp10) REVERT: J 130 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8808 (tm-30) REVERT: J 146 LYS cc_start: 0.8555 (ptmm) cc_final: 0.8264 (ptpp) REVERT: K 122 LYS cc_start: 0.9436 (ttmt) cc_final: 0.9103 (ttpp) REVERT: K 129 TYR cc_start: 0.9452 (t80) cc_final: 0.9095 (t80) REVERT: K 139 ASP cc_start: 0.8531 (p0) cc_final: 0.7957 (p0) outliers start: 26 outliers final: 13 residues processed: 179 average time/residue: 0.7135 time to fit residues: 140.4720 Evaluate side-chains 169 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 293 ARG 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 335 MET Chi-restraints excluded: chain D residue 277 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 102 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 151 optimal weight: 0.9980 chunk 190 optimal weight: 6.9990 chunk 181 optimal weight: 9.9990 chunk 108 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 174 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 348 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 = 0.3637 r_free = 0.3637 target = 0.094199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.065075 restraints weight = 38420.377| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 3.42 r_work: 0.2903 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2262 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= 0.111 Angle : 0.567 11.367 22745 Z= 0.278 Chirality : 0.041 0.152 2581 Planarity : 0.003 0.034 2873 Dihedral : 11.829 88.892 2632 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.05 % Allowed : 15.24 % Favored : 83.71 % 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 aren not related in a simple way. whole: 1.41 (0.19), residues: 2063 helix: 1.61 (0.18), residues: 942 sheet: 1.54 (0.31), residues: 300 loop : -0.01 (0.23), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 260 TYR 0.021 0.001 TYR H 129 PHE 0.012 0.001 PHE F 274 HIS 0.002 0.000 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00257 (16798) covalent geometry : angle 0.56666 (22745) hydrogen bonds : bond 0.02700 ( 796) hydrogen bonds : angle 3.99938 ( 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 173 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 271 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8211 (tm-30) REVERT: B 89 ASN cc_start: 0.8753 (m110) cc_final: 0.8275 (m-40) REVERT: B 117 ASP cc_start: 0.8967 (m-30) cc_final: 0.8730 (m-30) REVERT: B 234 GLN cc_start: 0.8463 (mt0) cc_final: 0.7896 (mt0) REVERT: B 293 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7882 (tpt170) REVERT: B 315 ASP cc_start: 0.8151 (m-30) cc_final: 0.7777 (m-30) REVERT: B 335 MET cc_start: 0.0021 (ppp) cc_final: -0.1866 (ttt) REVERT: B 348 ASN cc_start: 0.8207 (m-40) cc_final: 0.7881 (m110) REVERT: B 353 SER cc_start: 0.8704 (m) cc_final: 0.8485 (m) REVERT: C 335 MET cc_start: 0.0532 (OUTLIER) cc_final: 0.0013 (pmt) REVERT: E 108 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7822 (mt-10) REVERT: E 335 MET cc_start: 0.1413 (pmm) cc_final: -0.2307 (tmt) REVERT: F 89 ASN cc_start: 0.9047 (t0) cc_final: 0.8665 (t0) REVERT: G 139 ASP cc_start: 0.8499 (p0) cc_final: 0.8115 (p0) REVERT: H 130 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8948 (mm-30) REVERT: I 133 LYS cc_start: 0.8728 (tppp) cc_final: 0.8294 (ttmm) REVERT: I 137 GLN cc_start: 0.8721 (mp10) cc_final: 0.8361 (mp10) REVERT: J 121 LYS cc_start: 0.8978 (tppp) cc_final: 0.8633 (tptp) REVERT: J 130 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8855 (tm-30) REVERT: J 146 LYS cc_start: 0.8577 (ptmm) cc_final: 0.8278 (ptpp) REVERT: K 122 LYS cc_start: 0.9403 (ttmt) cc_final: 0.9053 (ttpp) REVERT: K 129 TYR cc_start: 0.9454 (t80) cc_final: 0.9104 (t80) REVERT: K 139 ASP cc_start: 0.8528 (p0) cc_final: 0.7957 (p0) outliers start: 18 outliers final: 13 residues processed: 168 average time/residue: 0.7219 time to fit residues: 133.3155 Evaluate side-chains 170 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 293 ARG 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 335 MET Chi-restraints excluded: chain D residue 277 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: 0.5980 chunk 39 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 193 optimal weight: 10.0000 chunk 160 optimal weight: 10.0000 chunk 90 optimal weight: 0.3980 chunk 132 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 184 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3641 r_free = 0.3641 target = 0.094390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.065250 restraints weight = 38450.564| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.42 r_work: 0.2904 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 16798 Z= 0.108 Angle : 0.560 12.465 22745 Z= 0.275 Chirality : 0.040 0.152 2581 Planarity : 0.003 0.034 2873 Dihedral : 11.798 89.515 2632 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.11 % Allowed : 15.35 % Favored : 83.54 % 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 aren not related in a simple way. whole: 1.42 (0.19), residues: 2063 helix: 1.62 (0.18), residues: 942 sheet: 1.57 (0.31), residues: 300 loop : -0.02 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 260 TYR 0.005 0.001 TYR F 286 PHE 0.012 0.001 PHE F 274 HIS 0.001 0.000 HIS F 352 Details of bonding type rmsd covalent geometry : bond 0.00247 (16798) covalent geometry : angle 0.55960 (22745) hydrogen bonds : bond 0.02621 ( 796) hydrogen bonds : angle 3.96967 ( 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 178 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 271 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8224 (tm-30) REVERT: A 350 MET cc_start: 0.7614 (tpt) cc_final: 0.6894 (mmm) REVERT: B 89 ASN cc_start: 0.8722 (m110) cc_final: 0.8242 (m-40) REVERT: B 117 ASP cc_start: 0.8966 (m-30) cc_final: 0.8705 (m-30) REVERT: B 234 GLN cc_start: 0.8462 (mt0) cc_final: 0.7909 (mt0) REVERT: B 315 ASP cc_start: 0.8133 (m-30) cc_final: 0.7742 (m-30) REVERT: B 335 MET cc_start: 0.0073 (ppp) cc_final: -0.1857 (ttt) REVERT: B 348 ASN cc_start: 0.8100 (m-40) cc_final: 0.7810 (m110) REVERT: B 353 SER cc_start: 0.8736 (m) cc_final: 0.8482 (m) REVERT: C 335 MET cc_start: 0.0528 (OUTLIER) cc_final: 0.0002 (pmt) REVERT: C 350 MET cc_start: 0.9082 (tpt) cc_final: 0.8783 (tpt) REVERT: E 108 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7766 (mt-10) REVERT: E 335 MET cc_start: 0.1389 (pmm) cc_final: -0.2267 (tmt) REVERT: F 89 ASN cc_start: 0.9057 (t0) cc_final: 0.8675 (t0) REVERT: G 139 ASP cc_start: 0.8512 (p0) cc_final: 0.8133 (p0) REVERT: H 130 GLU cc_start: 0.9172 (mm-30) cc_final: 0.8957 (mm-30) REVERT: I 133 LYS cc_start: 0.8700 (tppp) cc_final: 0.8271 (ttmm) REVERT: I 137 GLN cc_start: 0.8739 (mp10) cc_final: 0.8362 (mp10) REVERT: J 121 LYS cc_start: 0.8964 (tppp) cc_final: 0.8712 (tptp) REVERT: J 130 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8870 (tm-30) REVERT: K 122 LYS cc_start: 0.9419 (ttmt) cc_final: 0.8991 (ttpp) REVERT: K 129 TYR cc_start: 0.9449 (t80) cc_final: 0.9085 (t80) REVERT: K 130 GLU cc_start: 0.9357 (mt-10) cc_final: 0.9001 (mt-10) REVERT: K 139 ASP cc_start: 0.8518 (p0) cc_final: 0.7925 (p0) outliers start: 19 outliers final: 14 residues processed: 173 average time/residue: 0.7573 time to fit residues: 143.6214 Evaluate side-chains 170 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 293 ARG 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 335 MET Chi-restraints excluded: chain D residue 277 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 141 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 135 optimal weight: 0.3980 chunk 132 optimal weight: 8.9990 chunk 187 optimal weight: 10.0000 chunk 108 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 82 optimal weight: 0.7980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3630 r_free = 0.3630 target = 0.093770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.064571 restraints weight = 38587.273| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 3.42 r_work: 0.2891 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16798 Z= 0.124 Angle : 0.570 11.066 22745 Z= 0.282 Chirality : 0.041 0.153 2581 Planarity : 0.003 0.034 2873 Dihedral : 11.839 88.849 2632 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.17 % Allowed : 15.24 % Favored : 83.60 % 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 aren not related in a simple way. whole: 1.41 (0.19), residues: 2063 helix: 1.60 (0.18), residues: 940 sheet: 1.57 (0.31), residues: 300 loop : -0.03 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 260 TYR 0.006 0.001 TYR I 129 PHE 0.012 0.001 PHE F 274 HIS 0.002 0.000 HIS F 352 Details of bonding type rmsd covalent geometry : bond 0.00288 (16798) covalent geometry : angle 0.56954 (22745) hydrogen bonds : bond 0.02839 ( 796) hydrogen bonds : angle 4.03521 ( 2235) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5698.09 seconds wall clock time: 97 minutes 49.67 seconds (5869.67 seconds total)