Starting phenix.real_space_refine on Sun May 18 04:38:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e6n_47573/05_2025/9e6n_47573.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e6n_47573/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9e6n_47573/05_2025/9e6n_47573.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e6n_47573/05_2025/9e6n_47573.map" model { file = "/net/cci-nas-00/data/ceres_data/9e6n_47573/05_2025/9e6n_47573.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e6n_47573/05_2025/9e6n_47573.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.71, per 1000 atoms: 0.53 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: 3.83 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.82 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: 5.34 Time building geometry restraints manager: 4.50 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 400 or resid 501 through 502)) selection = chain 'B' selection = (chain 'C' and (resid 81 through 400 or resid 501 through 502)) selection = (chain 'D' and (resid 81 through 400 or resid 501 through 502)) selection = chain 'E' selection = (chain 'F' and (resid 81 through 400 or resid 501 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: 4.770 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 35.950 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.060 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:11.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.620 ------------------------------------------------------------------------------- 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 : 4.64 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.002 0.000 HIS E 105 PHE 0.024 0.001 PHE C 187 TYR 0.014 0.001 TYR I 145 ARG 0.003 0.000 ARG B 188 Details of bonding type rmsd hydrogen bonds : bond 0.23908 ( 796) hydrogen bonds : angle 7.35199 ( 2235) covalent geometry : bond 0.00280 (16798) covalent geometry : angle 0.49867 (22745) *********************** 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 : 1.747 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: 1.4527 time to fit residues: 286.1664 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 : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 10.0000 chunk 157 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 163 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 121 optimal weight: 0.0020 chunk 188 optimal weight: 10.0000 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 GLN ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.092293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.062171 restraints weight = 38465.438| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 3.59 r_work: 0.2786 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 16798 Z= 0.169 Angle : 0.535 8.357 22745 Z= 0.284 Chirality : 0.043 0.148 2581 Planarity : 0.004 0.038 2873 Dihedral : 13.107 89.986 2632 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.93 % Allowed : 6.89 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.19), residues: 2063 helix: 1.08 (0.18), residues: 950 sheet: 1.26 (0.30), residues: 326 loop : 0.02 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 196 PHE 0.017 0.001 PHE C 187 TYR 0.010 0.001 TYR I 145 ARG 0.005 0.000 ARG E 260 Details of bonding type rmsd hydrogen bonds : bond 0.04434 ( 796) hydrogen bonds : angle 4.97736 ( 2235) covalent geometry : bond 0.00383 (16798) covalent geometry : angle 0.53509 (22745) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 1.699 Fit side-chains revert: symmetry clash REVERT: B 89 ASN cc_start: 0.8963 (m110) cc_final: 0.8529 (m-40) REVERT: B 234 GLN cc_start: 0.8620 (mt0) cc_final: 0.8102 (mt0) REVERT: B 315 ASP cc_start: 0.8185 (m-30) cc_final: 0.7871 (m-30) REVERT: B 353 SER cc_start: 0.8656 (m) cc_final: 0.8411 (m) REVERT: C 335 MET cc_start: 0.0218 (OUTLIER) cc_final: -0.0674 (pmm) REVERT: E 108 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7930 (mt-10) REVERT: F 89 ASN cc_start: 0.8962 (t0) cc_final: 0.8534 (t0) REVERT: G 139 ASP cc_start: 0.8672 (p0) cc_final: 0.7967 (p0) REVERT: H 139 ASP cc_start: 0.7581 (t0) cc_final: 0.7293 (t0) REVERT: I 133 LYS cc_start: 0.8616 (tppp) cc_final: 0.8310 (ttmm) REVERT: I 137 GLN cc_start: 0.8428 (mp10) cc_final: 0.8196 (mp10) REVERT: K 122 LYS cc_start: 0.8946 (ttmt) cc_final: 0.8692 (ttmt) REVERT: K 129 TYR cc_start: 0.9403 (t80) cc_final: 0.9041 (t80) REVERT: K 139 ASP cc_start: 0.8515 (p0) cc_final: 0.7812 (p0) outliers start: 16 outliers final: 6 residues processed: 169 average time/residue: 1.4099 time to fit residues: 263.0960 Evaluate side-chains 159 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 151 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain D residue 152 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 80 optimal weight: 0.6980 chunk 167 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 193 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 171 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 184 optimal weight: 9.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.093282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.064079 restraints weight = 38640.331| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.45 r_work: 0.2877 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16798 Z= 0.123 Angle : 0.491 8.702 22745 Z= 0.257 Chirality : 0.041 0.157 2581 Planarity : 0.003 0.036 2873 Dihedral : 12.545 89.567 2632 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.28 % Allowed : 8.99 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.19), residues: 2063 helix: 1.19 (0.18), residues: 968 sheet: 1.57 (0.31), residues: 304 loop : -0.06 (0.23), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 196 PHE 0.015 0.001 PHE C 187 TYR 0.019 0.001 TYR H 129 ARG 0.006 0.000 ARG E 260 Details of bonding type rmsd hydrogen bonds : bond 0.03382 ( 796) hydrogen bonds : angle 4.45616 ( 2235) covalent geometry : bond 0.00277 (16798) covalent geometry : angle 0.49121 (22745) *********************** 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 181 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 1.892 Fit side-chains revert: symmetry clash REVERT: B 89 ASN cc_start: 0.8908 (m110) cc_final: 0.8457 (m-40) REVERT: B 152 MET cc_start: 0.7944 (tmm) cc_final: 0.7687 (tmm) REVERT: B 234 GLN cc_start: 0.8582 (mt0) cc_final: 0.7955 (mt0) REVERT: B 315 ASP cc_start: 0.8179 (m-30) cc_final: 0.7861 (m-30) REVERT: B 353 SER cc_start: 0.8668 (m) cc_final: 0.8443 (m) REVERT: C 335 MET cc_start: 0.0231 (OUTLIER) cc_final: -0.0678 (pmm) REVERT: D 268 MET cc_start: 0.9404 (OUTLIER) cc_final: 0.8859 (mtm) REVERT: D 269 MET cc_start: 0.9250 (OUTLIER) cc_final: 0.8996 (mtt) REVERT: E 108 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7862 (mt-10) REVERT: F 89 ASN cc_start: 0.8978 (t0) cc_final: 0.8545 (t0) REVERT: G 139 ASP cc_start: 0.8633 (p0) cc_final: 0.8406 (p0) REVERT: I 133 LYS cc_start: 0.8613 (tppp) cc_final: 0.8322 (ttmm) REVERT: I 137 GLN cc_start: 0.8532 (mp10) cc_final: 0.8228 (mp10) REVERT: J 121 LYS cc_start: 0.9117 (mmmm) cc_final: 0.8825 (tptp) REVERT: K 122 LYS cc_start: 0.9194 (ttmt) cc_final: 0.8963 (ttpt) REVERT: K 129 TYR cc_start: 0.9439 (t80) cc_final: 0.9002 (t80) REVERT: K 130 GLU cc_start: 0.9276 (mt-10) cc_final: 0.9042 (mt-10) REVERT: K 139 ASP cc_start: 0.8526 (p0) cc_final: 0.7899 (p0) outliers start: 22 outliers final: 6 residues processed: 166 average time/residue: 1.4071 time to fit residues: 258.0013 Evaluate side-chains 161 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain D residue 268 MET Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain F residue 383 CYS 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 152 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 201 optimal weight: 5.9990 chunk 199 optimal weight: 6.9990 chunk 76 optimal weight: 0.0970 chunk 10 optimal weight: 2.9990 chunk 206 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 chunk 143 optimal weight: 9.9990 chunk 116 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 105 HIS E 105 HIS ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.093172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.064008 restraints weight = 38525.286| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 3.43 r_work: 0.2876 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16798 Z= 0.127 Angle : 0.495 8.473 22745 Z= 0.258 Chirality : 0.041 0.146 2581 Planarity : 0.003 0.035 2873 Dihedral : 12.342 89.755 2632 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.11 % Allowed : 10.51 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.19), residues: 2063 helix: 1.23 (0.18), residues: 970 sheet: 1.25 (0.31), residues: 316 loop : -0.03 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 196 PHE 0.013 0.001 PHE B 187 TYR 0.007 0.001 TYR J 129 ARG 0.006 0.000 ARG E 260 Details of bonding type rmsd hydrogen bonds : bond 0.03193 ( 796) hydrogen bonds : angle 4.31440 ( 2235) covalent geometry : bond 0.00289 (16798) covalent geometry : angle 0.49480 (22745) *********************** 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 180 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 2.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 89 ASN cc_start: 0.8883 (m110) cc_final: 0.8431 (m-40) REVERT: B 142 MET cc_start: 0.8509 (mmp) cc_final: 0.8307 (mmt) REVERT: B 234 GLN cc_start: 0.8579 (mt0) cc_final: 0.7993 (mt0) REVERT: B 315 ASP cc_start: 0.8175 (m-30) cc_final: 0.7861 (m-30) REVERT: B 348 ASN cc_start: 0.8437 (m-40) cc_final: 0.8181 (m110) REVERT: B 353 SER cc_start: 0.8684 (m) cc_final: 0.8453 (m) REVERT: C 335 MET cc_start: 0.0258 (OUTLIER) cc_final: -0.0767 (pmm) REVERT: C 345 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7742 (tt) REVERT: D 268 MET cc_start: 0.9401 (OUTLIER) cc_final: 0.8839 (mtm) REVERT: D 269 MET cc_start: 0.9227 (mmm) cc_final: 0.8984 (mtt) REVERT: E 108 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7883 (mt-10) REVERT: F 89 ASN cc_start: 0.8996 (t0) cc_final: 0.8552 (t0) REVERT: G 139 ASP cc_start: 0.8591 (p0) cc_final: 0.7977 (p0) REVERT: H 130 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8837 (pp20) REVERT: I 133 LYS cc_start: 0.8648 (tppp) cc_final: 0.8310 (ttmm) REVERT: I 137 GLN cc_start: 0.8651 (mp10) cc_final: 0.8291 (mp10) REVERT: J 139 ASP cc_start: 0.7618 (t0) cc_final: 0.7416 (t0) REVERT: J 146 LYS cc_start: 0.8632 (ptmm) cc_final: 0.8404 (ptpp) REVERT: K 122 LYS cc_start: 0.9244 (ttmt) cc_final: 0.8697 (ttpp) REVERT: K 129 TYR cc_start: 0.9455 (t80) cc_final: 0.8995 (t80) REVERT: K 130 GLU cc_start: 0.9347 (mt-10) cc_final: 0.8941 (mt-10) REVERT: K 139 ASP cc_start: 0.8446 (p0) cc_final: 0.7803 (p0) outliers start: 19 outliers final: 8 residues processed: 171 average time/residue: 1.4207 time to fit residues: 268.5654 Evaluate side-chains 164 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 293 ARG 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 268 MET Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain F residue 383 CYS 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 159 optimal weight: 20.0000 chunk 115 optimal weight: 5.9990 chunk 80 optimal weight: 0.0870 chunk 19 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 95 optimal weight: 6.9990 chunk 157 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.9162 ------------------------------------------------------------------------------- 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 = 0.3603 r_free = 0.3603 target = 0.092537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.063242 restraints weight = 39116.602| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.44 r_work: 0.2864 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1892 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= 0.145 Angle : 0.525 11.701 22745 Z= 0.269 Chirality : 0.041 0.146 2581 Planarity : 0.003 0.036 2873 Dihedral : 12.230 89.139 2632 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.34 % Allowed : 12.32 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.19), residues: 2063 helix: 1.23 (0.18), residues: 970 sheet: 1.14 (0.30), residues: 318 loop : 0.00 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 196 PHE 0.013 0.001 PHE B 187 TYR 0.019 0.001 TYR H 129 ARG 0.008 0.000 ARG F 260 Details of bonding type rmsd hydrogen bonds : bond 0.03275 ( 796) hydrogen bonds : angle 4.29424 ( 2235) covalent geometry : bond 0.00334 (16798) covalent geometry : angle 0.52459 (22745) *********************** 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 181 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 1.760 Fit side-chains revert: symmetry clash REVERT: B 89 ASN cc_start: 0.8875 (m110) cc_final: 0.8425 (m-40) REVERT: B 234 GLN cc_start: 0.8596 (mt0) cc_final: 0.7999 (mt0) REVERT: B 315 ASP cc_start: 0.8197 (m-30) cc_final: 0.7887 (m-30) REVERT: B 335 MET cc_start: -0.0215 (ppp) cc_final: -0.2236 (ttt) REVERT: B 348 ASN cc_start: 0.8447 (m-40) cc_final: 0.8192 (m110) REVERT: B 350 MET cc_start: 0.9110 (mmm) cc_final: 0.8900 (mmm) REVERT: B 353 SER cc_start: 0.8691 (m) cc_final: 0.8442 (m) REVERT: C 335 MET cc_start: 0.0334 (OUTLIER) cc_final: -0.0157 (pmt) REVERT: C 345 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7814 (tt) REVERT: D 268 MET cc_start: 0.9420 (OUTLIER) cc_final: 0.8863 (mtm) REVERT: D 345 ILE cc_start: 0.7617 (OUTLIER) cc_final: 0.7335 (tp) REVERT: E 108 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7887 (mt-10) REVERT: F 89 ASN cc_start: 0.9004 (t0) cc_final: 0.8572 (t0) REVERT: G 139 ASP cc_start: 0.8642 (p0) cc_final: 0.8047 (p0) REVERT: H 130 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8861 (pp20) REVERT: I 133 LYS cc_start: 0.8699 (tppp) cc_final: 0.8330 (ttmm) REVERT: I 137 GLN cc_start: 0.8699 (mp10) cc_final: 0.8322 (mp10) REVERT: J 130 GLU cc_start: 0.9215 (mm-30) cc_final: 0.8841 (tm-30) REVERT: J 137 GLN cc_start: 0.8630 (mp10) cc_final: 0.8341 (mp10) REVERT: J 146 LYS cc_start: 0.8639 (ptmm) cc_final: 0.8394 (ptpp) REVERT: K 122 LYS cc_start: 0.9321 (ttmt) cc_final: 0.9092 (ttmt) REVERT: K 129 TYR cc_start: 0.9449 (t80) cc_final: 0.9006 (t80) REVERT: K 130 GLU cc_start: 0.9399 (mt-10) cc_final: 0.9105 (mt-10) REVERT: K 139 ASP cc_start: 0.8448 (p0) cc_final: 0.7802 (p0) outliers start: 23 outliers final: 11 residues processed: 172 average time/residue: 1.3630 time to fit residues: 259.1261 Evaluate side-chains 167 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 1.855 ------------------------------------------------------------------------------- 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 183 LEU Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain D residue 268 MET Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain F residue 383 CYS Chi-restraints excluded: chain G residue 150 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 88 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 84 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 169 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 330 GLN G 141 ASN ** K 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.090890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.061633 restraints weight = 38977.633| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 3.41 r_work: 0.2823 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 16798 Z= 0.240 Angle : 0.596 9.935 22745 Z= 0.306 Chirality : 0.044 0.147 2581 Planarity : 0.004 0.044 2873 Dihedral : 12.433 86.785 2632 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.22 % Allowed : 12.20 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.19), residues: 2063 helix: 1.13 (0.18), residues: 962 sheet: 1.11 (0.30), residues: 318 loop : -0.10 (0.23), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 196 PHE 0.011 0.001 PHE B 144 TYR 0.008 0.001 TYR K 136 ARG 0.008 0.000 ARG E 260 Details of bonding type rmsd hydrogen bonds : bond 0.04089 ( 796) hydrogen bonds : angle 4.52968 ( 2235) covalent geometry : bond 0.00562 (16798) covalent geometry : angle 0.59643 (22745) *********************** 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 194 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 156 time to evaluate : 1.818 Fit side-chains revert: symmetry clash REVERT: B 89 ASN cc_start: 0.8968 (m110) cc_final: 0.8524 (m-40) REVERT: B 234 GLN cc_start: 0.8601 (mt0) cc_final: 0.7971 (mt0) REVERT: B 293 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7739 (mmt90) REVERT: B 315 ASP cc_start: 0.8237 (m-30) cc_final: 0.7918 (m-30) REVERT: B 350 MET cc_start: 0.9185 (mmm) cc_final: 0.8909 (mmm) REVERT: B 353 SER cc_start: 0.8793 (m) cc_final: 0.8549 (m) REVERT: C 335 MET cc_start: 0.0710 (OUTLIER) cc_final: -0.0111 (pmm) REVERT: D 301 MET cc_start: 0.8759 (tpt) cc_final: 0.8168 (tpp) REVERT: E 108 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7966 (mt-10) REVERT: E 335 MET cc_start: 0.2138 (pmm) cc_final: -0.1656 (tmt) REVERT: F 89 ASN cc_start: 0.9010 (t0) cc_final: 0.8595 (t0) REVERT: G 139 ASP cc_start: 0.8687 (p0) cc_final: 0.7912 (p0) REVERT: H 130 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8887 (pp20) REVERT: I 137 GLN cc_start: 0.8703 (mp10) cc_final: 0.8362 (mp10) REVERT: J 137 GLN cc_start: 0.8763 (mp10) cc_final: 0.8442 (mp10) REVERT: J 139 ASP cc_start: 0.7844 (t0) cc_final: 0.7622 (t0) REVERT: K 122 LYS cc_start: 0.9328 (ttmt) cc_final: 0.8952 (ttpp) REVERT: K 129 TYR cc_start: 0.9442 (t80) cc_final: 0.8995 (t80) REVERT: K 130 GLU cc_start: 0.9391 (mt-10) cc_final: 0.9046 (mt-10) REVERT: K 139 ASP cc_start: 0.8421 (p0) cc_final: 0.7746 (p0) outliers start: 38 outliers final: 11 residues processed: 183 average time/residue: 1.3487 time to fit residues: 273.0069 Evaluate side-chains 162 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 293 ARG Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain F residue 383 CYS Chi-restraints excluded: chain G residue 150 SER Chi-restraints excluded: chain I residue 127 LEU Chi-restraints excluded: chain I residue 135 PHE Chi-restraints excluded: chain J residue 145 TYR Chi-restraints excluded: chain K residue 123 SER Chi-restraints excluded: chain K residue 124 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 71 optimal weight: 0.8980 chunk 156 optimal weight: 0.0570 chunk 195 optimal weight: 5.9990 chunk 100 optimal weight: 0.5980 chunk 162 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.093703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.064544 restraints weight = 38714.581| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.41 r_work: 0.2889 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16798 Z= 0.103 Angle : 0.532 10.049 22745 Z= 0.268 Chirality : 0.040 0.152 2581 Planarity : 0.003 0.037 2873 Dihedral : 12.091 89.117 2632 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.23 % Allowed : 13.72 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.19), residues: 2063 helix: 1.28 (0.18), residues: 968 sheet: 1.42 (0.30), residues: 304 loop : -0.12 (0.23), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 257 PHE 0.011 0.001 PHE E 187 TYR 0.006 0.001 TYR I 145 ARG 0.008 0.000 ARG E 260 Details of bonding type rmsd hydrogen bonds : bond 0.02755 ( 796) hydrogen bonds : angle 4.12974 ( 2235) covalent geometry : bond 0.00228 (16798) covalent geometry : angle 0.53226 (22745) *********************** 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 180 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 1.992 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 271 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8195 (tm-30) REVERT: B 89 ASN cc_start: 0.8873 (m110) cc_final: 0.8415 (m-40) REVERT: B 234 GLN cc_start: 0.8562 (mt0) cc_final: 0.7997 (mt0) REVERT: B 315 ASP cc_start: 0.8148 (m-30) cc_final: 0.7828 (m-30) REVERT: B 335 MET cc_start: 0.0062 (ppp) cc_final: -0.1891 (ttt) REVERT: B 348 ASN cc_start: 0.8419 (m-40) cc_final: 0.8008 (m110) REVERT: B 350 MET cc_start: 0.9017 (mmm) cc_final: 0.8756 (mmm) REVERT: B 353 SER cc_start: 0.8732 (m) cc_final: 0.8485 (m) REVERT: C 335 MET cc_start: 0.0705 (OUTLIER) cc_final: -0.0159 (pmm) REVERT: E 108 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7668 (mt-10) REVERT: F 89 ASN cc_start: 0.9017 (t0) cc_final: 0.8568 (t0) REVERT: G 139 ASP cc_start: 0.8443 (p0) cc_final: 0.8152 (p0) REVERT: H 130 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8923 (mm-30) REVERT: I 133 LYS cc_start: 0.8746 (tppp) cc_final: 0.8267 (ttmm) REVERT: I 137 GLN cc_start: 0.8737 (mp10) cc_final: 0.8378 (mp10) REVERT: J 137 GLN cc_start: 0.8805 (mp10) cc_final: 0.8479 (mp10) REVERT: J 139 ASP cc_start: 0.7938 (t0) cc_final: 0.7698 (t0) REVERT: K 122 LYS cc_start: 0.9383 (ttmt) cc_final: 0.9140 (ttpt) REVERT: K 129 TYR cc_start: 0.9469 (t80) cc_final: 0.9052 (t80) REVERT: K 130 GLU cc_start: 0.9399 (mt-10) cc_final: 0.9052 (mt-10) REVERT: K 139 ASP cc_start: 0.8458 (p0) cc_final: 0.7843 (p0) outliers start: 21 outliers final: 12 residues processed: 174 average time/residue: 1.4479 time to fit residues: 278.2393 Evaluate side-chains 166 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain B residue 293 ARG Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain F residue 383 CYS Chi-restraints excluded: chain G residue 150 SER Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain I residue 135 PHE Chi-restraints excluded: chain J residue 145 TYR Chi-restraints excluded: chain K residue 123 SER Chi-restraints excluded: chain K residue 124 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 198 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 145 optimal weight: 9.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 = 0.3588 r_free = 0.3588 target = 0.091593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.062293 restraints weight = 38787.938| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.41 r_work: 0.2842 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 16798 Z= 0.192 Angle : 0.595 11.777 22745 Z= 0.298 Chirality : 0.042 0.152 2581 Planarity : 0.003 0.041 2873 Dihedral : 12.229 89.548 2632 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.46 % Allowed : 14.19 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.19), residues: 2063 helix: 1.18 (0.18), residues: 968 sheet: 1.00 (0.30), residues: 320 loop : -0.06 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 196 PHE 0.011 0.001 PHE F 274 TYR 0.020 0.001 TYR H 129 ARG 0.008 0.000 ARG E 260 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 796) hydrogen bonds : angle 4.32326 ( 2235) covalent geometry : bond 0.00451 (16798) covalent geometry : angle 0.59476 (22745) *********************** 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 179 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 271 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8233 (tm-30) REVERT: B 89 ASN cc_start: 0.8922 (m110) cc_final: 0.8473 (m-40) REVERT: B 234 GLN cc_start: 0.8555 (mt0) cc_final: 0.7970 (mt0) REVERT: B 315 ASP cc_start: 0.8181 (m-30) cc_final: 0.7875 (m-30) REVERT: B 335 MET cc_start: 0.0125 (ppp) cc_final: -0.1782 (ttt) REVERT: B 348 ASN cc_start: 0.8517 (m-40) cc_final: 0.8268 (m110) REVERT: B 353 SER cc_start: 0.8760 (m) cc_final: 0.8518 (m) REVERT: D 301 MET cc_start: 0.8729 (tpt) cc_final: 0.8062 (tpp) REVERT: E 108 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7871 (mt-10) REVERT: E 335 MET cc_start: 0.1498 (pmm) cc_final: -0.2334 (tmt) REVERT: F 89 ASN cc_start: 0.9020 (t0) cc_final: 0.8598 (t0) REVERT: G 139 ASP cc_start: 0.8556 (p0) cc_final: 0.7706 (p0) REVERT: H 130 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8892 (pp20) REVERT: I 133 LYS cc_start: 0.8623 (tppp) cc_final: 0.8201 (ttmm) REVERT: I 137 GLN cc_start: 0.8748 (mp10) cc_final: 0.8387 (mp10) REVERT: J 121 LYS cc_start: 0.9093 (tppp) cc_final: 0.8743 (tptp) REVERT: J 137 GLN cc_start: 0.8809 (mp10) cc_final: 0.8467 (mp10) REVERT: J 139 ASP cc_start: 0.7886 (t0) cc_final: 0.7652 (t0) REVERT: K 122 LYS cc_start: 0.9407 (ttmt) cc_final: 0.9104 (ttmt) REVERT: K 129 TYR cc_start: 0.9427 (t80) cc_final: 0.9087 (t80) REVERT: K 130 GLU cc_start: 0.9404 (mt-10) cc_final: 0.9085 (mt-10) REVERT: K 139 ASP cc_start: 0.8433 (p0) cc_final: 0.7844 (p0) outliers start: 25 outliers final: 18 residues processed: 172 average time/residue: 1.4338 time to fit residues: 272.0858 Evaluate side-chains 169 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain B residue 293 ARG Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain F residue 383 CYS Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 150 SER Chi-restraints excluded: chain G residue 152 LYS Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain I residue 127 LEU Chi-restraints excluded: chain I residue 135 PHE Chi-restraints excluded: chain J residue 145 TYR Chi-restraints excluded: chain K residue 123 SER Chi-restraints excluded: chain K residue 124 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 176 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 36 optimal weight: 0.0040 chunk 192 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 95 optimal weight: 0.1980 chunk 59 optimal weight: 0.9990 overall best weight: 1.0398 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.093608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.064441 restraints weight = 38501.381| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.43 r_work: 0.2887 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16798 Z= 0.111 Angle : 0.563 11.725 22745 Z= 0.278 Chirality : 0.041 0.145 2581 Planarity : 0.003 0.035 2873 Dihedral : 12.020 88.415 2632 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.28 % Allowed : 14.48 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.19), residues: 2063 helix: 1.49 (0.18), residues: 940 sheet: 1.31 (0.31), residues: 308 loop : -0.02 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 257 PHE 0.014 0.001 PHE F 274 TYR 0.006 0.001 TYR I 145 ARG 0.008 0.000 ARG E 260 Details of bonding type rmsd hydrogen bonds : bond 0.02799 ( 796) hydrogen bonds : angle 4.09206 ( 2235) covalent geometry : bond 0.00253 (16798) covalent geometry : angle 0.56296 (22745) *********************** 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 177 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 1.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 271 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8199 (tm-30) REVERT: B 89 ASN cc_start: 0.8861 (m110) cc_final: 0.8404 (m-40) REVERT: B 234 GLN cc_start: 0.8539 (mt0) cc_final: 0.7964 (mt0) REVERT: B 315 ASP cc_start: 0.8163 (m-30) cc_final: 0.7834 (m-30) REVERT: B 335 MET cc_start: 0.0166 (ppp) cc_final: -0.1736 (ttt) REVERT: B 348 ASN cc_start: 0.8365 (m-40) cc_final: 0.7982 (m110) REVERT: B 353 SER cc_start: 0.8730 (m) cc_final: 0.8492 (m) REVERT: C 335 MET cc_start: 0.0906 (pp-130) cc_final: 0.0340 (ppp) REVERT: C 350 MET cc_start: 0.9194 (tpt) cc_final: 0.8868 (tpt) REVERT: D 301 MET cc_start: 0.8639 (tpt) cc_final: 0.7984 (tpp) REVERT: E 108 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7820 (mt-10) REVERT: E 335 MET cc_start: 0.1499 (pmm) cc_final: -0.2249 (tmt) REVERT: E 350 MET cc_start: 0.8594 (tpt) cc_final: 0.8386 (mmm) REVERT: F 89 ASN cc_start: 0.9065 (t0) cc_final: 0.8680 (t0) REVERT: G 139 ASP cc_start: 0.8421 (p0) cc_final: 0.7833 (p0) REVERT: H 130 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8944 (mm-30) REVERT: I 133 LYS cc_start: 0.8667 (tppp) cc_final: 0.8266 (ttmm) REVERT: I 137 GLN cc_start: 0.8745 (mp10) cc_final: 0.8373 (mp10) REVERT: J 121 LYS cc_start: 0.8994 (tppp) cc_final: 0.8762 (tptp) REVERT: J 137 GLN cc_start: 0.8831 (mp10) cc_final: 0.8543 (mp10) REVERT: J 139 ASP cc_start: 0.7923 (t0) cc_final: 0.7671 (t0) REVERT: K 129 TYR cc_start: 0.9436 (t80) cc_final: 0.9027 (t80) REVERT: K 130 GLU cc_start: 0.9413 (mt-10) cc_final: 0.9091 (mt-10) REVERT: K 139 ASP cc_start: 0.8450 (p0) cc_final: 0.7828 (p0) outliers start: 22 outliers final: 15 residues processed: 171 average time/residue: 1.4422 time to fit residues: 272.5641 Evaluate side-chains 168 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 1.963 ------------------------------------------------------------------------------- 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 293 ARG Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain F residue 383 CYS Chi-restraints excluded: chain G residue 150 SER Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain I residue 135 PHE Chi-restraints excluded: chain J residue 145 TYR Chi-restraints excluded: chain K residue 123 SER Chi-restraints excluded: chain K residue 124 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 116 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 130 optimal weight: 0.3980 chunk 95 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 330 GLN ** 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 = 0.3609 r_free = 0.3609 target = 0.092555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.063430 restraints weight = 38735.435| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.37 r_work: 0.2863 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2152 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= 0.155 Angle : 0.592 12.338 22745 Z= 0.293 Chirality : 0.042 0.150 2581 Planarity : 0.003 0.037 2873 Dihedral : 12.068 87.793 2632 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.99 % Allowed : 15.00 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.19), residues: 2063 helix: 1.43 (0.18), residues: 940 sheet: 1.15 (0.31), residues: 314 loop : 0.02 (0.23), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 196 PHE 0.013 0.001 PHE F 274 TYR 0.006 0.001 TYR K 136 ARG 0.008 0.000 ARG E 260 Details of bonding type rmsd hydrogen bonds : bond 0.03242 ( 796) hydrogen bonds : angle 4.19289 ( 2235) covalent geometry : bond 0.00362 (16798) covalent geometry : angle 0.59173 (22745) ********************** 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 170 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 2.056 Fit side-chains revert: symmetry clash REVERT: A 271 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8226 (tm-30) REVERT: B 89 ASN cc_start: 0.8886 (m110) cc_final: 0.8434 (m-40) REVERT: B 183 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8558 (mt) REVERT: B 234 GLN cc_start: 0.8567 (mt0) cc_final: 0.8008 (mt0) REVERT: B 293 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7702 (mmt90) REVERT: B 315 ASP cc_start: 0.8157 (m-30) cc_final: 0.7846 (m-30) REVERT: B 335 MET cc_start: 0.0063 (ppp) cc_final: -0.1897 (ttt) REVERT: B 348 ASN cc_start: 0.8474 (m-40) cc_final: 0.8058 (m110) REVERT: B 353 SER cc_start: 0.8719 (m) cc_final: 0.8491 (m) REVERT: C 350 MET cc_start: 0.9172 (tpt) cc_final: 0.8862 (tpt) REVERT: D 301 MET cc_start: 0.8737 (tpt) cc_final: 0.8103 (tpp) REVERT: E 108 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7811 (mt-10) REVERT: E 335 MET cc_start: 0.1511 (pmm) cc_final: -0.2198 (tmt) REVERT: E 350 MET cc_start: 0.8719 (tpt) cc_final: 0.8475 (mmm) REVERT: F 89 ASN cc_start: 0.9076 (t0) cc_final: 0.8708 (t0) REVERT: G 139 ASP cc_start: 0.8519 (p0) cc_final: 0.7913 (p0) REVERT: H 130 GLU cc_start: 0.9167 (mm-30) cc_final: 0.8955 (mm-30) REVERT: I 133 LYS cc_start: 0.8666 (tppp) cc_final: 0.8257 (ttmm) REVERT: I 137 GLN cc_start: 0.8749 (mp10) cc_final: 0.8374 (mp10) REVERT: J 121 LYS cc_start: 0.8972 (tppp) cc_final: 0.8743 (tptt) REVERT: J 130 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8864 (tm-30) REVERT: J 137 GLN cc_start: 0.8850 (mp10) cc_final: 0.8505 (mp10) REVERT: J 139 ASP cc_start: 0.7956 (t0) cc_final: 0.7710 (t0) REVERT: K 122 LYS cc_start: 0.9401 (ttpt) cc_final: 0.9143 (ttpp) REVERT: K 129 TYR cc_start: 0.9434 (t80) cc_final: 0.9053 (t80) REVERT: K 130 GLU cc_start: 0.9453 (mt-10) cc_final: 0.9127 (mt-10) REVERT: K 139 ASP cc_start: 0.8416 (p0) cc_final: 0.7823 (p0) outliers start: 17 outliers final: 12 residues processed: 165 average time/residue: 1.4438 time to fit residues: 265.6679 Evaluate side-chains 166 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 1.962 ------------------------------------------------------------------------------- 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 293 ARG Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain F residue 383 CYS Chi-restraints excluded: chain G residue 150 SER Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain I residue 135 PHE Chi-restraints excluded: chain J residue 145 TYR Chi-restraints excluded: chain K residue 123 SER Chi-restraints excluded: chain K residue 124 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 105 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 167 optimal weight: 6.9990 chunk 193 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 330 GLN ** 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 = 0.3616 r_free = 0.3616 target = 0.093057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.063896 restraints weight = 38618.208| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.41 r_work: 0.2858 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2191 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= 0.131 Angle : 0.575 13.385 22745 Z= 0.284 Chirality : 0.041 0.152 2581 Planarity : 0.003 0.037 2873 Dihedral : 12.015 88.150 2632 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.17 % Allowed : 14.89 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.19), residues: 2063 helix: 1.46 (0.18), residues: 940 sheet: 1.27 (0.31), residues: 310 loop : -0.02 (0.23), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 352 PHE 0.013 0.001 PHE F 274 TYR 0.021 0.001 TYR H 129 ARG 0.008 0.000 ARG E 260 Details of bonding type rmsd hydrogen bonds : bond 0.03002 ( 796) hydrogen bonds : angle 4.13124 ( 2235) covalent geometry : bond 0.00305 (16798) covalent geometry : angle 0.57480 (22745) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10682.82 seconds wall clock time: 185 minutes 14.42 seconds (11114.42 seconds total)