Starting phenix.real_space_refine on Wed Jul 30 04:23:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6djn_7937/07_2025/6djn_7937.cif Found real_map, /net/cci-nas-00/data/ceres_data/6djn_7937/07_2025/6djn_7937.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6djn_7937/07_2025/6djn_7937.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6djn_7937/07_2025/6djn_7937.map" model { file = "/net/cci-nas-00/data/ceres_data/6djn_7937/07_2025/6djn_7937.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6djn_7937/07_2025/6djn_7937.cif" } resolution = 3.1 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= 0.000 sd= 0.002 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 12 5.49 5 Mg 4 5.21 5 S 84 5.16 5 C 7408 2.51 5 N 1980 2.21 5 O 2280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11768 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.28, per 1000 atoms: 0.62 Number of scatterers: 11768 At special positions: 0 Unit cell: (100.32, 76.285, 165.11, 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 84 16.00 P 12 15.00 Mg 4 11.99 O 2280 8.00 N 1980 7.00 C 7408 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.83 Conformation dependent library (CDL) restraints added in 1.5 seconds 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 24 sheets defined 44.2% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 91 removed outlier: 3.902A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.838A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.785A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.879A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.996A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 275 through 283 Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.813A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 309 through 318 removed outlier: 3.514A pdb=" N GLN A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS A 315 " --> pdb=" O ASP A 311 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR A 318 " --> pdb=" O GLN A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 347 Processing helix chain 'A' and resid 351 through 355 removed outlier: 4.266A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 removed outlier: 3.862A pdb=" N GLU A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.944A pdb=" N SER A 368 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 369 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HIS A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 371' Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 91 removed outlier: 3.901A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.838A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.785A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.879A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.996A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 275 through 283 Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.813A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 309 through 318 removed outlier: 3.513A pdb=" N GLN B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS B 315 " --> pdb=" O ASP B 311 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR B 318 " --> pdb=" O GLN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 351 through 355 removed outlier: 4.266A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 364 removed outlier: 3.863A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.944A pdb=" N SER B 368 " --> pdb=" O ALA B 365 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE B 369 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N HIS B 371 " --> pdb=" O SER B 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 371' Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 93 removed outlier: 3.901A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.837A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.785A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.879A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS C 215 " --> pdb=" O ASP C 211 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.995A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 275 through 283 Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.813A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 309 through 318 removed outlier: 3.514A pdb=" N GLN C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS C 315 " --> pdb=" O ASP C 311 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR C 318 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 351 through 355 removed outlier: 4.266A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 364 removed outlier: 3.862A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.945A pdb=" N SER C 368 " --> pdb=" O ALA C 365 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE C 369 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HIS C 371 " --> pdb=" O SER C 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 371' Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 91 removed outlier: 3.901A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.838A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.785A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.880A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS D 215 " --> pdb=" O ASP D 211 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 230 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.996A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 275 through 283 Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.814A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 309 through 318 removed outlier: 3.513A pdb=" N GLN D 314 " --> pdb=" O ALA D 310 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS D 315 " --> pdb=" O ASP D 311 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR D 318 " --> pdb=" O GLN D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 351 through 355 removed outlier: 4.266A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 364 removed outlier: 3.863A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 371 removed outlier: 3.945A pdb=" N SER D 368 " --> pdb=" O ALA D 365 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE D 369 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N HIS D 371 " --> pdb=" O SER D 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 365 through 371' Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.557A pdb=" N PHE A 31 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.534A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.185A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.556A pdb=" N PHE B 31 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.535A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.185A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.557A pdb=" N PHE C 31 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.535A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.185A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.557A pdb=" N PHE D 31 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.534A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.184A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 450 hydrogen bonds defined for protein. 1110 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: 3.60 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3420 1.33 - 1.45: 1833 1.45 - 1.57: 6607 1.57 - 1.68: 12 1.68 - 1.80: 148 Bond restraints: 12020 Sorted by residual: bond pdb=" O3 PO4 B 803 " pdb=" P PO4 B 803 " ideal model delta sigma weight residual 1.569 1.494 0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" O3 PO4 D 803 " pdb=" P PO4 D 803 " ideal model delta sigma weight residual 1.569 1.496 0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" O2 PO4 A 803 " pdb=" P PO4 A 803 " ideal model delta sigma weight residual 1.567 1.496 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" O3 PO4 C 803 " pdb=" P PO4 C 803 " ideal model delta sigma weight residual 1.569 1.498 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" O3 PO4 A 803 " pdb=" P PO4 A 803 " ideal model delta sigma weight residual 1.569 1.501 0.068 2.00e-02 2.50e+03 1.17e+01 ... (remaining 12015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 15421 1.92 - 3.83: 775 3.83 - 5.75: 88 5.75 - 7.66: 24 7.66 - 9.58: 8 Bond angle restraints: 16316 Sorted by residual: angle pdb=" C GLY A 46 " pdb=" N MET A 47 " pdb=" CA MET A 47 " ideal model delta sigma weight residual 122.08 127.89 -5.81 1.47e+00 4.63e-01 1.56e+01 angle pdb=" C GLY C 46 " pdb=" N MET C 47 " pdb=" CA MET C 47 " ideal model delta sigma weight residual 122.08 127.85 -5.77 1.47e+00 4.63e-01 1.54e+01 angle pdb=" C GLY D 46 " pdb=" N MET D 47 " pdb=" CA MET D 47 " ideal model delta sigma weight residual 122.08 127.84 -5.76 1.47e+00 4.63e-01 1.54e+01 angle pdb=" C GLY B 46 " pdb=" N MET B 47 " pdb=" CA MET B 47 " ideal model delta sigma weight residual 122.08 127.84 -5.76 1.47e+00 4.63e-01 1.53e+01 angle pdb=" N HIC B 73 " pdb=" CA HIC B 73 " pdb=" CB HIC B 73 " ideal model delta sigma weight residual 110.50 116.45 -5.95 1.70e+00 3.46e-01 1.23e+01 ... (remaining 16311 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.63: 7035 23.63 - 47.26: 177 47.26 - 70.89: 0 70.89 - 94.53: 4 94.53 - 118.16: 4 Dihedral angle restraints: 7220 sinusoidal: 2920 harmonic: 4300 Sorted by residual: dihedral pdb=" C5' ADP B 802 " pdb=" O5' ADP B 802 " pdb=" PA ADP B 802 " pdb=" O2A ADP B 802 " ideal model delta sinusoidal sigma weight residual -60.00 58.16 -118.16 1 2.00e+01 2.50e-03 3.53e+01 dihedral pdb=" C5' ADP A 802 " pdb=" O5' ADP A 802 " pdb=" PA ADP A 802 " pdb=" O2A ADP A 802 " ideal model delta sinusoidal sigma weight residual -60.00 53.64 -113.63 1 2.00e+01 2.50e-03 3.36e+01 dihedral pdb=" C5' ADP C 802 " pdb=" O5' ADP C 802 " pdb=" PA ADP C 802 " pdb=" O2A ADP C 802 " ideal model delta sinusoidal sigma weight residual -60.00 48.00 -108.00 1 2.00e+01 2.50e-03 3.14e+01 ... (remaining 7217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1193 0.057 - 0.114: 530 0.114 - 0.171: 61 0.171 - 0.228: 12 0.228 - 0.285: 12 Chirality restraints: 1808 Sorted by residual: chirality pdb=" CB ILE B 151 " pdb=" CA ILE B 151 " pdb=" CG1 ILE B 151 " pdb=" CG2 ILE B 151 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB ILE A 151 " pdb=" CA ILE A 151 " pdb=" CG1 ILE A 151 " pdb=" CG2 ILE A 151 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CB ILE D 151 " pdb=" CA ILE D 151 " pdb=" CG1 ILE D 151 " pdb=" CG2 ILE D 151 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 1805 not shown) Planarity restraints: 2084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 332 " 0.057 5.00e-02 4.00e+02 8.69e-02 1.21e+01 pdb=" N PRO A 333 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 333 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 333 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 332 " -0.057 5.00e-02 4.00e+02 8.69e-02 1.21e+01 pdb=" N PRO D 333 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO D 333 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 333 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 332 " 0.057 5.00e-02 4.00e+02 8.69e-02 1.21e+01 pdb=" N PRO C 333 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO C 333 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 333 " 0.048 5.00e-02 4.00e+02 ... (remaining 2081 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 240 2.66 - 3.22: 10485 3.22 - 3.78: 18286 3.78 - 4.34: 26213 4.34 - 4.90: 43418 Nonbonded interactions: 98642 Sorted by model distance: nonbonded pdb="MG MG A 801 " pdb=" O1B ADP A 802 " model vdw 2.106 2.170 nonbonded pdb="MG MG D 801 " pdb=" O1B ADP D 802 " model vdw 2.106 2.170 nonbonded pdb="MG MG B 801 " pdb=" O1B ADP B 802 " model vdw 2.117 2.170 nonbonded pdb="MG MG C 801 " pdb=" O1B ADP C 802 " model vdw 2.131 2.170 nonbonded pdb="MG MG A 801 " pdb=" O4 PO4 A 803 " model vdw 2.146 2.170 ... (remaining 98637 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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: 0.010 Normalize map: mean=0, sd=1: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.230 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 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 : 0.011 0.075 12020 Z= 0.458 Angle : 0.950 9.577 16316 Z= 0.495 Chirality : 0.062 0.285 1808 Planarity : 0.008 0.087 2084 Dihedral : 10.671 118.157 4468 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -4.61 (0.16), residues: 1468 helix: -4.20 (0.10), residues: 600 sheet: -2.19 (0.29), residues: 244 loop : -1.95 (0.20), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.005 TRP C 340 HIS 0.011 0.003 HIS A 40 PHE 0.019 0.003 PHE A 31 TYR 0.015 0.002 TYR B 169 ARG 0.013 0.002 ARG D 147 Details of bonding type rmsd hydrogen bonds : bond 0.28869 ( 442) hydrogen bonds : angle 10.03799 ( 1110) covalent geometry : bond 0.01062 (12020) covalent geometry : angle 0.95015 (16316) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 1.265 Fit side-chains REVERT: A 157 ASP cc_start: 0.7962 (t0) cc_final: 0.7663 (t0) REVERT: A 202 THR cc_start: 0.9037 (p) cc_final: 0.8632 (p) REVERT: A 205 GLU cc_start: 0.8141 (mp0) cc_final: 0.7772 (mp0) REVERT: B 51 ASP cc_start: 0.7591 (t70) cc_final: 0.7314 (p0) REVERT: B 82 MET cc_start: 0.9160 (tpt) cc_final: 0.8745 (tpt) REVERT: B 184 ASP cc_start: 0.8012 (m-30) cc_final: 0.7804 (m-30) REVERT: B 191 LYS cc_start: 0.8445 (ttpt) cc_final: 0.7877 (tttm) REVERT: B 194 THR cc_start: 0.8884 (m) cc_final: 0.8616 (p) REVERT: B 314 GLN cc_start: 0.8305 (tm-30) cc_final: 0.8049 (tt0) REVERT: C 92 ASN cc_start: 0.8420 (m110) cc_final: 0.8161 (m-40) REVERT: C 191 LYS cc_start: 0.8254 (ttpt) cc_final: 0.7972 (tttm) REVERT: D 92 ASN cc_start: 0.8298 (m110) cc_final: 0.8061 (m-40) REVERT: D 191 LYS cc_start: 0.8465 (ttpt) cc_final: 0.8121 (ttmm) REVERT: D 225 ASN cc_start: 0.8181 (m-40) cc_final: 0.7795 (m-40) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.2993 time to fit residues: 98.6896 Evaluate side-chains 114 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 GLN A 78 ASN A 137 GLN A 161 HIS A 162 ASN A 263 GLN B 12 ASN B 59 GLN B 78 ASN B 161 HIS B 162 ASN C 59 GLN C 121 GLN C 161 HIS C 162 ASN C 246 GLN D 12 ASN D 161 HIS D 162 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.094702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.080594 restraints weight = 19159.865| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.02 r_work: 0.2878 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12020 Z= 0.142 Angle : 0.627 6.685 16316 Z= 0.311 Chirality : 0.046 0.150 1808 Planarity : 0.006 0.066 2084 Dihedral : 7.819 98.369 1672 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.96 % Allowed : 7.48 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -3.09 (0.19), residues: 1468 helix: -2.76 (0.16), residues: 624 sheet: -1.67 (0.29), residues: 236 loop : -1.11 (0.22), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 340 HIS 0.004 0.001 HIS C 40 PHE 0.009 0.001 PHE D 262 TYR 0.010 0.001 TYR C 143 ARG 0.004 0.001 ARG C 95 Details of bonding type rmsd hydrogen bonds : bond 0.03636 ( 442) hydrogen bonds : angle 5.16365 ( 1110) covalent geometry : bond 0.00322 (12020) covalent geometry : angle 0.62672 (16316) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 1.432 Fit side-chains revert: symmetry clash REVERT: A 12 ASN cc_start: 0.8546 (p0) cc_final: 0.8291 (p0) REVERT: A 191 LYS cc_start: 0.8900 (ttpt) cc_final: 0.8512 (ttmt) REVERT: A 291 LYS cc_start: 0.9062 (tmtt) cc_final: 0.8816 (tptt) REVERT: A 305 MET cc_start: 0.9127 (mmm) cc_final: 0.8879 (mmt) REVERT: B 51 ASP cc_start: 0.8095 (t70) cc_final: 0.7662 (p0) REVERT: B 82 MET cc_start: 0.9375 (tpt) cc_final: 0.8970 (tpt) REVERT: B 191 LYS cc_start: 0.8645 (ttpt) cc_final: 0.8286 (tttm) REVERT: B 227 MET cc_start: 0.8792 (tpt) cc_final: 0.8589 (tpt) REVERT: D 176 MET cc_start: 0.9191 (mmm) cc_final: 0.8914 (mmm) REVERT: D 283 MET cc_start: 0.8790 (mmm) cc_final: 0.8502 (mmt) REVERT: D 325 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.7250 (ptp) outliers start: 12 outliers final: 6 residues processed: 145 average time/residue: 0.2488 time to fit residues: 52.6449 Evaluate side-chains 107 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 106 optimal weight: 0.2980 chunk 80 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 110 optimal weight: 0.0070 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.093957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.079567 restraints weight = 19421.714| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.05 r_work: 0.2877 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12020 Z= 0.148 Angle : 0.590 7.126 16316 Z= 0.287 Chirality : 0.046 0.190 1808 Planarity : 0.005 0.059 2084 Dihedral : 7.285 93.249 1672 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.80 % Allowed : 9.08 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.91 (0.21), residues: 1468 helix: -1.68 (0.19), residues: 616 sheet: -1.16 (0.31), residues: 236 loop : -0.59 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 340 HIS 0.005 0.001 HIS B 40 PHE 0.008 0.001 PHE D 262 TYR 0.008 0.001 TYR C 91 ARG 0.005 0.001 ARG D 206 Details of bonding type rmsd hydrogen bonds : bond 0.02954 ( 442) hydrogen bonds : angle 4.50986 ( 1110) covalent geometry : bond 0.00340 (12020) covalent geometry : angle 0.58990 (16316) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 1.426 Fit side-chains revert: symmetry clash REVERT: A 12 ASN cc_start: 0.8537 (p0) cc_final: 0.8257 (p0) REVERT: A 305 MET cc_start: 0.9127 (mmm) cc_final: 0.8901 (mmt) REVERT: A 325 MET cc_start: 0.8146 (ppp) cc_final: 0.7346 (ppp) REVERT: B 82 MET cc_start: 0.9373 (tpt) cc_final: 0.9094 (tpt) REVERT: B 227 MET cc_start: 0.8840 (tpt) cc_final: 0.8640 (tpt) REVERT: B 276 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8160 (mt-10) REVERT: C 355 MET cc_start: 0.8809 (mtm) cc_final: 0.8407 (mtm) REVERT: D 176 MET cc_start: 0.9260 (mmm) cc_final: 0.8978 (mmm) REVERT: D 325 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7803 (ptp) outliers start: 10 outliers final: 8 residues processed: 129 average time/residue: 0.2207 time to fit residues: 43.5612 Evaluate side-chains 104 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN D 12 ASN D 173 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.093174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.078961 restraints weight = 19177.934| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.01 r_work: 0.2848 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 12020 Z= 0.237 Angle : 0.645 7.678 16316 Z= 0.315 Chirality : 0.048 0.201 1808 Planarity : 0.005 0.056 2084 Dihedral : 7.686 104.851 1672 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.91 % Allowed : 8.52 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.42 (0.21), residues: 1468 helix: -1.23 (0.20), residues: 608 sheet: -1.02 (0.31), residues: 236 loop : -0.33 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 340 HIS 0.007 0.001 HIS B 40 PHE 0.011 0.002 PHE D 262 TYR 0.009 0.001 TYR C 69 ARG 0.004 0.001 ARG A 206 Details of bonding type rmsd hydrogen bonds : bond 0.03247 ( 442) hydrogen bonds : angle 4.47006 ( 1110) covalent geometry : bond 0.00551 (12020) covalent geometry : angle 0.64546 (16316) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 1.450 Fit side-chains REVERT: A 12 ASN cc_start: 0.8608 (p0) cc_final: 0.8342 (p0) REVERT: A 291 LYS cc_start: 0.9187 (tmtt) cc_final: 0.8856 (tptt) REVERT: A 325 MET cc_start: 0.8271 (ppp) cc_final: 0.7532 (ppp) REVERT: B 82 MET cc_start: 0.9344 (tpt) cc_final: 0.9044 (tpt) REVERT: B 276 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8189 (mt-10) REVERT: B 325 MET cc_start: 0.8043 (ppp) cc_final: 0.7131 (ppp) REVERT: C 84 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8923 (mttt) REVERT: C 132 MET cc_start: 0.8936 (ppp) cc_final: 0.8676 (ptm) REVERT: D 176 MET cc_start: 0.9346 (mmm) cc_final: 0.9059 (mmm) outliers start: 24 outliers final: 14 residues processed: 118 average time/residue: 0.2190 time to fit residues: 38.8523 Evaluate side-chains 110 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 43 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 0.0060 chunk 38 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN D 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.092863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.078674 restraints weight = 19184.507| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.02 r_work: 0.2843 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 12020 Z= 0.162 Angle : 0.588 7.065 16316 Z= 0.283 Chirality : 0.046 0.184 1808 Planarity : 0.004 0.054 2084 Dihedral : 7.219 99.516 1672 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.35 % Allowed : 9.32 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 (0.22), residues: 1468 helix: -0.98 (0.21), residues: 628 sheet: -0.80 (0.32), residues: 236 loop : -0.15 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 340 HIS 0.004 0.001 HIS B 40 PHE 0.008 0.001 PHE A 127 TYR 0.008 0.001 TYR B 169 ARG 0.004 0.000 ARG C 335 Details of bonding type rmsd hydrogen bonds : bond 0.02716 ( 442) hydrogen bonds : angle 4.28167 ( 1110) covalent geometry : bond 0.00377 (12020) covalent geometry : angle 0.58820 (16316) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 1.330 Fit side-chains REVERT: A 12 ASN cc_start: 0.8609 (p0) cc_final: 0.8364 (p0) REVERT: A 157 ASP cc_start: 0.8376 (t0) cc_final: 0.7861 (m-30) REVERT: A 325 MET cc_start: 0.8300 (ppp) cc_final: 0.7715 (ppp) REVERT: B 276 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8214 (mt-10) REVERT: B 325 MET cc_start: 0.8219 (ppp) cc_final: 0.7235 (ppp) REVERT: C 84 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8734 (mtmt) REVERT: D 176 MET cc_start: 0.9309 (mmm) cc_final: 0.8983 (mmm) outliers start: 17 outliers final: 12 residues processed: 116 average time/residue: 0.2068 time to fit residues: 37.1835 Evaluate side-chains 114 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 104 optimal weight: 0.0980 chunk 100 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 115 optimal weight: 0.0270 chunk 7 optimal weight: 3.9990 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.094575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.080262 restraints weight = 19128.427| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.05 r_work: 0.2871 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12020 Z= 0.156 Angle : 0.584 6.944 16316 Z= 0.280 Chirality : 0.046 0.179 1808 Planarity : 0.004 0.052 2084 Dihedral : 6.988 93.170 1672 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.43 % Allowed : 9.55 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.22), residues: 1468 helix: -0.51 (0.22), residues: 600 sheet: -0.82 (0.31), residues: 256 loop : 0.09 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 340 HIS 0.005 0.001 HIS A 40 PHE 0.007 0.001 PHE D 127 TYR 0.006 0.001 TYR C 91 ARG 0.005 0.000 ARG C 335 Details of bonding type rmsd hydrogen bonds : bond 0.02672 ( 442) hydrogen bonds : angle 4.21729 ( 1110) covalent geometry : bond 0.00363 (12020) covalent geometry : angle 0.58372 (16316) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 1.382 Fit side-chains REVERT: A 12 ASN cc_start: 0.8531 (p0) cc_final: 0.8286 (p0) REVERT: A 157 ASP cc_start: 0.8361 (t0) cc_final: 0.7834 (m-30) REVERT: A 325 MET cc_start: 0.8298 (ppp) cc_final: 0.7753 (ppp) REVERT: B 276 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8250 (mt-10) REVERT: B 325 MET cc_start: 0.8211 (ppp) cc_final: 0.7287 (ppp) REVERT: C 84 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8858 (mtmt) REVERT: D 176 MET cc_start: 0.9366 (mmm) cc_final: 0.9064 (mmm) outliers start: 18 outliers final: 14 residues processed: 128 average time/residue: 0.2172 time to fit residues: 42.1631 Evaluate side-chains 118 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 19 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 23 optimal weight: 0.3980 chunk 114 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 121 GLN A 360 GLN D 353 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.095135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.080985 restraints weight = 19211.797| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.05 r_work: 0.2882 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12020 Z= 0.132 Angle : 0.568 6.674 16316 Z= 0.270 Chirality : 0.045 0.168 1808 Planarity : 0.004 0.032 2084 Dihedral : 6.711 91.211 1672 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.35 % Allowed : 10.03 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.55 (0.22), residues: 1468 helix: -0.33 (0.22), residues: 608 sheet: -0.76 (0.32), residues: 256 loop : 0.06 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 340 HIS 0.004 0.001 HIS A 161 PHE 0.007 0.001 PHE A 127 TYR 0.006 0.001 TYR C 91 ARG 0.006 0.000 ARG C 335 Details of bonding type rmsd hydrogen bonds : bond 0.02507 ( 442) hydrogen bonds : angle 4.15216 ( 1110) covalent geometry : bond 0.00309 (12020) covalent geometry : angle 0.56764 (16316) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 1.306 Fit side-chains REVERT: A 12 ASN cc_start: 0.8506 (p0) cc_final: 0.8295 (p0) REVERT: A 157 ASP cc_start: 0.8358 (t0) cc_final: 0.7894 (m-30) REVERT: A 325 MET cc_start: 0.8226 (ppp) cc_final: 0.7753 (ppp) REVERT: B 205 GLU cc_start: 0.8512 (mp0) cc_final: 0.8283 (mp0) REVERT: B 276 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8242 (mt-10) REVERT: B 325 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7286 (ppp) REVERT: C 84 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8787 (mtmt) REVERT: D 176 MET cc_start: 0.9365 (mmm) cc_final: 0.9070 (mmm) outliers start: 17 outliers final: 12 residues processed: 126 average time/residue: 0.2026 time to fit residues: 39.5448 Evaluate side-chains 118 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 115 optimal weight: 0.0070 chunk 20 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 263 GLN A 360 GLN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.095991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.082434 restraints weight = 19179.624| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.98 r_work: 0.2902 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12020 Z= 0.114 Angle : 0.554 6.368 16316 Z= 0.263 Chirality : 0.044 0.158 1808 Planarity : 0.003 0.032 2084 Dihedral : 6.391 86.024 1672 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.59 % Allowed : 10.51 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.30 (0.23), residues: 1468 helix: -0.11 (0.22), residues: 608 sheet: -0.70 (0.32), residues: 256 loop : 0.21 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 79 HIS 0.003 0.001 HIS A 161 PHE 0.006 0.001 PHE A 127 TYR 0.007 0.001 TYR C 91 ARG 0.005 0.000 ARG C 335 Details of bonding type rmsd hydrogen bonds : bond 0.02396 ( 442) hydrogen bonds : angle 4.08667 ( 1110) covalent geometry : bond 0.00265 (12020) covalent geometry : angle 0.55383 (16316) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 1.368 Fit side-chains REVERT: A 12 ASN cc_start: 0.8459 (p0) cc_final: 0.8198 (p0) REVERT: A 103 THR cc_start: 0.9355 (m) cc_final: 0.9123 (p) REVERT: A 325 MET cc_start: 0.8213 (ppp) cc_final: 0.7790 (ppp) REVERT: B 205 GLU cc_start: 0.8516 (mp0) cc_final: 0.8293 (mp0) REVERT: B 325 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7312 (ppp) REVERT: C 84 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8855 (mtpp) REVERT: C 328 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8669 (tptp) outliers start: 20 outliers final: 14 residues processed: 133 average time/residue: 0.1937 time to fit residues: 40.1684 Evaluate side-chains 121 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 21 optimal weight: 1.9990 chunk 120 optimal weight: 0.4980 chunk 36 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 137 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 133 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN A 246 GLN ** D 115 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 = 0.3247 r_free = 0.3247 target = 0.095624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.081479 restraints weight = 19064.682| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.04 r_work: 0.2895 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12020 Z= 0.124 Angle : 0.562 6.449 16316 Z= 0.268 Chirality : 0.045 0.160 1808 Planarity : 0.003 0.032 2084 Dihedral : 6.378 87.358 1672 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.43 % Allowed : 11.15 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.21 (0.23), residues: 1468 helix: -0.04 (0.22), residues: 608 sheet: -0.65 (0.32), residues: 256 loop : 0.27 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 79 HIS 0.003 0.001 HIS B 40 PHE 0.007 0.001 PHE A 127 TYR 0.006 0.001 TYR C 91 ARG 0.005 0.000 ARG C 335 Details of bonding type rmsd hydrogen bonds : bond 0.02433 ( 442) hydrogen bonds : angle 4.07218 ( 1110) covalent geometry : bond 0.00288 (12020) covalent geometry : angle 0.56177 (16316) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 1.314 Fit side-chains REVERT: A 12 ASN cc_start: 0.8455 (p0) cc_final: 0.8182 (p0) REVERT: A 103 THR cc_start: 0.9390 (m) cc_final: 0.9143 (p) REVERT: A 157 ASP cc_start: 0.8298 (t0) cc_final: 0.7811 (m-30) REVERT: A 325 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7742 (ppp) REVERT: B 205 GLU cc_start: 0.8551 (mp0) cc_final: 0.8299 (mp0) REVERT: B 325 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7322 (ppp) REVERT: C 84 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8848 (mtpp) REVERT: C 328 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8649 (tptp) outliers start: 18 outliers final: 12 residues processed: 123 average time/residue: 0.1952 time to fit residues: 37.4038 Evaluate side-chains 124 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 40 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 127 optimal weight: 0.5980 chunk 135 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.095171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.081062 restraints weight = 18939.255| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.03 r_work: 0.2887 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12020 Z= 0.138 Angle : 0.574 6.601 16316 Z= 0.275 Chirality : 0.045 0.163 1808 Planarity : 0.003 0.032 2084 Dihedral : 6.486 90.060 1672 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.35 % Allowed : 11.31 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.18 (0.23), residues: 1468 helix: -0.02 (0.22), residues: 608 sheet: -0.65 (0.32), residues: 256 loop : 0.30 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 79 HIS 0.004 0.001 HIS B 40 PHE 0.007 0.001 PHE A 127 TYR 0.007 0.001 TYR C 91 ARG 0.005 0.000 ARG C 335 Details of bonding type rmsd hydrogen bonds : bond 0.02518 ( 442) hydrogen bonds : angle 4.09161 ( 1110) covalent geometry : bond 0.00323 (12020) covalent geometry : angle 0.57381 (16316) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 1.378 Fit side-chains REVERT: A 12 ASN cc_start: 0.8472 (p0) cc_final: 0.8203 (p0) REVERT: A 103 THR cc_start: 0.9400 (m) cc_final: 0.9164 (p) REVERT: A 157 ASP cc_start: 0.8296 (t0) cc_final: 0.7798 (m-30) REVERT: A 325 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7733 (ppp) REVERT: B 205 GLU cc_start: 0.8571 (mp0) cc_final: 0.8315 (mp0) REVERT: B 325 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7277 (ppp) REVERT: C 84 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8797 (mtmt) REVERT: C 132 MET cc_start: 0.8935 (ppp) cc_final: 0.8690 (ptm) REVERT: C 328 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8640 (tptp) outliers start: 17 outliers final: 12 residues processed: 121 average time/residue: 0.2011 time to fit residues: 37.9408 Evaluate side-chains 125 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 80 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 36 optimal weight: 0.0670 chunk 145 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 69 optimal weight: 0.0570 chunk 112 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 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 = 0.3260 r_free = 0.3260 target = 0.096356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.082380 restraints weight = 18992.142| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.02 r_work: 0.2913 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12020 Z= 0.108 Angle : 0.552 6.171 16316 Z= 0.264 Chirality : 0.044 0.157 1808 Planarity : 0.003 0.032 2084 Dihedral : 6.125 81.716 1672 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.59 % Allowed : 11.15 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.04 (0.23), residues: 1468 helix: 0.11 (0.22), residues: 608 sheet: -0.64 (0.32), residues: 256 loop : 0.38 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 356 HIS 0.003 0.001 HIS A 161 PHE 0.006 0.001 PHE A 127 TYR 0.007 0.001 TYR D 294 ARG 0.005 0.000 ARG C 335 Details of bonding type rmsd hydrogen bonds : bond 0.02326 ( 442) hydrogen bonds : angle 4.01942 ( 1110) covalent geometry : bond 0.00250 (12020) covalent geometry : angle 0.55219 (16316) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5445.82 seconds wall clock time: 94 minutes 14.58 seconds (5654.58 seconds total)