Starting phenix.real_space_refine on Fri Sep 11 22:09:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6djo_7938/09_2026/6djo_7938.cif Found real_map, /net/cci-nas-00/data/ceres_data/6djo_7938/09_2026/6djo_7938.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6djo_7938/09_2026/6djo_7938.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6djo_7938/09_2026/6djo_7938.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6djo_7938/09_2026/6djo_7938.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6djo_7938/09_2026/6djo_7938.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6djo_7938/09_2026/6djo_7938.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6djo_7938/09_2026/6djo_7938.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 8 5.49 5 Mg 4 5.21 5 S 84 5.16 5 C 7408 2.51 5 N 1980 2.21 5 O 2264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11748 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.62, per 1000 atoms: 0.22 Number of scatterers: 11748 At special positions: 0 Unit cell: (100.32, 76.285, 166.155, 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 8 15.00 Mg 4 11.99 O 2264 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: 0.96 Conformation dependent library (CDL) restraints added in 527.1 milliseconds 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 40.9% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 78 through 91 removed outlier: 3.534A pdb=" N GLU A 83 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR A 91 " --> pdb=" O HIS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.817A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 146 removed outlier: 3.961A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 175 removed outlier: 3.836A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.688A pdb=" N TYR A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.569A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 228 Processing helix chain 'A' and resid 229 through 232 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.738A pdb=" N TYR A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.716A pdb=" N THR A 304 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 318 removed outlier: 3.942A pdb=" N ARG A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 3.822A 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 359 through 366 removed outlier: 3.753A pdb=" N GLU A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 370 removed outlier: 3.765A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 370' Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 78 through 91 removed outlier: 3.534A pdb=" N GLU B 83 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR B 91 " --> pdb=" O HIS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.816A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU B 117 " --> pdb=" O LYS B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 146 removed outlier: 3.960A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 175 removed outlier: 3.836A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 193 removed outlier: 3.688A pdb=" N TYR B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.569A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 228 Processing helix chain 'B' and resid 229 through 232 Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 278 through 283 Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.739A pdb=" N TYR B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.717A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 318 removed outlier: 3.942A pdb=" N ARG B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) removed outlier: 3.823A 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 359 through 366 removed outlier: 3.753A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 365 " --> pdb=" O GLU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 370 removed outlier: 3.766A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 367 through 370' Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 78 through 91 removed outlier: 3.534A pdb=" N GLU C 83 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 91 " --> pdb=" O HIS C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.816A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 146 removed outlier: 3.961A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 175 removed outlier: 3.837A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 193 removed outlier: 3.688A pdb=" N TYR C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.569A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS C 215 " --> pdb=" O ASP C 211 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 228 Processing helix chain 'C' and resid 229 through 232 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 278 through 283 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.738A pdb=" N TYR C 294 " --> pdb=" O ARG C 290 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 removed outlier: 3.717A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 318 removed outlier: 3.942A pdb=" N ARG C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 3.823A 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 359 through 366 removed outlier: 3.753A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 370 removed outlier: 3.765A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 367 through 370' Processing helix chain 'D' and resid 56 through 61 Processing helix chain 'D' and resid 78 through 91 removed outlier: 3.535A pdb=" N GLU D 83 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR D 91 " --> pdb=" O HIS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.816A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU D 117 " --> pdb=" O LYS D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 146 removed outlier: 3.961A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 175 removed outlier: 3.836A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 193 removed outlier: 3.688A pdb=" N TYR D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.568A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS D 215 " --> pdb=" O ASP D 211 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 228 Processing helix chain 'D' and resid 229 through 232 Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.738A pdb=" N TYR D 294 " --> pdb=" O ARG D 290 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 removed outlier: 3.717A pdb=" N THR D 304 " --> pdb=" O GLY D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 318 removed outlier: 3.942A pdb=" N ARG D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN D 314 " --> pdb=" O ALA D 310 " (cutoff:3.500A) removed outlier: 3.823A 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 359 through 366 removed outlier: 3.753A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA D 365 " --> pdb=" O GLU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 370 removed outlier: 3.765A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 367 through 370' Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 12 removed outlier: 3.539A pdb=" N VAL A 9 " --> pdb=" O GLY A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 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 103 through 107 removed outlier: 6.756A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 176 through 178 removed outlier: 3.934A pdb=" N HIS A 161 " --> pdb=" O ASP A 154 " (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 8 through 12 removed outlier: 3.539A pdb=" N VAL B 9 " --> pdb=" O GLY B 20 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 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 103 through 107 removed outlier: 6.756A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.935A pdb=" N HIS B 161 " --> pdb=" O ASP B 154 " (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 8 through 12 removed outlier: 3.540A pdb=" N VAL C 9 " --> pdb=" O GLY C 20 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 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 103 through 107 removed outlier: 6.757A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 176 through 178 removed outlier: 3.934A pdb=" N HIS C 161 " --> pdb=" O ASP C 154 " (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 8 through 12 removed outlier: 3.539A pdb=" N VAL D 9 " --> pdb=" O GLY D 20 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 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 103 through 107 removed outlier: 6.756A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 176 through 178 removed outlier: 3.935A pdb=" N HIS D 161 " --> pdb=" O ASP D 154 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 372 hydrogen bonds defined for protein. 936 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: 1.96 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3792 1.34 - 1.46: 2374 1.46 - 1.57: 5678 1.57 - 1.69: 12 1.69 - 1.81: 148 Bond restraints: 12004 Sorted by residual: bond pdb=" C VAL D 370 " pdb=" N HIS D 371 " ideal model delta sigma weight residual 1.334 1.399 -0.065 1.46e-02 4.69e+03 1.99e+01 bond pdb=" C VAL B 370 " pdb=" N HIS B 371 " ideal model delta sigma weight residual 1.334 1.387 -0.053 1.46e-02 4.69e+03 1.32e+01 bond pdb=" C VAL C 370 " pdb=" N HIS C 371 " ideal model delta sigma weight residual 1.334 1.382 -0.047 1.46e-02 4.69e+03 1.04e+01 bond pdb=" C VAL A 370 " pdb=" N HIS A 371 " ideal model delta sigma weight residual 1.334 1.381 -0.046 1.46e-02 4.69e+03 1.00e+01 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.90e+00 ... (remaining 11999 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 14972 1.52 - 3.03: 1051 3.03 - 4.55: 190 4.55 - 6.06: 50 6.06 - 7.58: 29 Bond angle restraints: 16292 Sorted by residual: angle pdb=" N HIC C 73 " pdb=" CA HIC C 73 " pdb=" CB HIC C 73 " ideal model delta sigma weight residual 110.50 116.90 -6.40 1.70e+00 3.46e-01 1.42e+01 angle pdb=" N HIC B 73 " pdb=" CA HIC B 73 " pdb=" CB HIC B 73 " ideal model delta sigma weight residual 110.50 116.90 -6.40 1.70e+00 3.46e-01 1.42e+01 angle pdb=" N HIC D 73 " pdb=" CA HIC D 73 " pdb=" CB HIC D 73 " ideal model delta sigma weight residual 110.50 116.88 -6.38 1.70e+00 3.46e-01 1.41e+01 angle pdb=" N HIC A 73 " pdb=" CA HIC A 73 " pdb=" CB HIC A 73 " ideal model delta sigma weight residual 110.50 116.86 -6.36 1.70e+00 3.46e-01 1.40e+01 angle pdb=" C HIC C 73 " pdb=" CA HIC C 73 " pdb=" CB HIC C 73 " ideal model delta sigma weight residual 110.10 103.38 6.72 1.90e+00 2.77e-01 1.25e+01 ... (remaining 16287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.77: 6829 16.77 - 33.54: 297 33.54 - 50.31: 85 50.31 - 67.08: 6 67.08 - 83.85: 3 Dihedral angle restraints: 7220 sinusoidal: 2920 harmonic: 4300 Sorted by residual: dihedral pdb=" C5' ADP D 802 " pdb=" O5' ADP D 802 " pdb=" PA ADP D 802 " pdb=" O2A ADP D 802 " ideal model delta sinusoidal sigma weight residual -60.00 23.86 -83.85 1 2.00e+01 2.50e-03 2.14e+01 dihedral pdb=" CA MET A 325 " pdb=" C MET A 325 " pdb=" N LYS A 326 " pdb=" CA LYS A 326 " ideal model delta harmonic sigma weight residual 180.00 -157.23 -22.77 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA MET D 325 " pdb=" C MET D 325 " pdb=" N LYS D 326 " pdb=" CA LYS D 326 " ideal model delta harmonic sigma weight residual -180.00 -157.28 -22.72 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 7217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1126 0.052 - 0.103: 579 0.103 - 0.155: 75 0.155 - 0.206: 12 0.206 - 0.258: 16 Chirality restraints: 1808 Sorted by residual: chirality pdb=" CA CYS C 257 " pdb=" N CYS C 257 " pdb=" C CYS C 257 " pdb=" CB CYS C 257 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA CYS A 257 " pdb=" N CYS A 257 " pdb=" C CYS A 257 " pdb=" CB CYS A 257 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA CYS D 257 " pdb=" N CYS D 257 " pdb=" C CYS D 257 " pdb=" CB CYS D 257 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 1805 not shown) Planarity restraints: 2084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 372 " 0.260 9.50e-02 1.11e+02 1.16e-01 8.31e+00 pdb=" NE ARG D 372 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG D 372 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG D 372 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 372 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 372 " 0.260 9.50e-02 1.11e+02 1.16e-01 8.30e+00 pdb=" NE ARG C 372 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG C 372 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG C 372 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 372 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 372 " 0.259 9.50e-02 1.11e+02 1.16e-01 8.28e+00 pdb=" NE ARG B 372 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG B 372 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 372 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 372 " 0.009 2.00e-02 2.50e+03 ... (remaining 2081 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 163 2.62 - 3.19: 9991 3.19 - 3.76: 17230 3.76 - 4.33: 25357 4.33 - 4.90: 41589 Nonbonded interactions: 94330 Sorted by model distance: nonbonded pdb="MG MG A 801 " pdb=" O1B ADP A 802 " model vdw 2.053 2.170 nonbonded pdb="MG MG D 801 " pdb=" O1B ADP D 802 " model vdw 2.077 2.170 nonbonded pdb="MG MG C 801 " pdb=" O1B ADP C 802 " model vdw 2.082 2.170 nonbonded pdb="MG MG B 801 " pdb=" O1B ADP B 802 " model vdw 2.092 2.170 nonbonded pdb="MG MG D 801 " pdb=" O3B ADP D 802 " model vdw 2.122 2.170 ... (remaining 94325 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.000 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 11.870 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 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 : 0.009 0.072 12004 Z= 0.404 Angle : 0.943 7.580 16292 Z= 0.502 Chirality : 0.060 0.258 1808 Planarity : 0.008 0.116 2084 Dihedral : 10.850 83.855 4468 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.96 % Allowed : 3.18 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.76 (0.17), residues: 1468 helix: -4.43 (0.10), residues: 556 sheet: -2.45 (0.41), residues: 132 loop : -2.24 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 177 TYR 0.016 0.002 TYR B 169 PHE 0.018 0.002 PHE B 31 TRP 0.029 0.004 TRP C 340 HIS 0.008 0.003 HIS D 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00909 / 0.40 (12004) covalent geometry : angle 0.94313 / 0.50 (16292) hydrogen bonds : bond 0.30802 / 20.83 ( 372) hydrogen bonds : angle 10.27367 / 7.21 ( 936) *********************** 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 302 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 290 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8798 (ppp) cc_final: 0.8583 (ppp) REVERT: A 283 MET cc_start: 0.7802 (mmt) cc_final: 0.7519 (mmm) REVERT: B 153 LEU cc_start: 0.9050 (tp) cc_final: 0.8796 (tp) REVERT: B 296 ASN cc_start: 0.8378 (m-40) cc_final: 0.8085 (m-40) REVERT: B 367 PRO cc_start: 0.8662 (Cg_endo) cc_final: 0.8430 (Cg_exo) REVERT: C 123 MET cc_start: 0.8834 (mmm) cc_final: 0.8616 (mmt) REVERT: C 244 ASP cc_start: 0.7895 (p0) cc_final: 0.7681 (p0) REVERT: D 10 CYS cc_start: 0.8303 (t) cc_final: 0.8086 (t) REVERT: D 44 MET cc_start: 0.7523 (mmp) cc_final: 0.7092 (mmt) REVERT: D 132 MET cc_start: 0.8660 (ppp) cc_final: 0.8459 (ttp) REVERT: D 154 ASP cc_start: 0.8395 (t0) cc_final: 0.8095 (t0) REVERT: D 162 ASN cc_start: 0.8664 (m110) cc_final: 0.8432 (m110) REVERT: D 191 LYS cc_start: 0.8766 (ttpt) cc_final: 0.8495 (tttm) REVERT: D 326 LYS cc_start: 0.8062 (pmtt) cc_final: 0.7776 (ptmt) outliers start: 12 outliers final: 9 residues processed: 301 average time/residue: 0.1243 time to fit residues: 52.1172 Evaluate side-chains 159 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 373 LYS Chi-restraints excluded: chain D residue 375 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 ASN B 111 ASN B 162 ASN B 246 GLN C 12 ASN C 128 ASN C 137 GLN C 162 ASN D 78 ASN D 162 ASN D 246 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.088893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.075768 restraints weight = 24379.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.078443 restraints weight = 12630.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.080288 restraints weight = 7946.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.081540 restraints weight = 5622.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.082428 restraints weight = 4355.288| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12004 Z= 0.150 Angle : 0.667 6.658 16292 Z= 0.332 Chirality : 0.048 0.185 1808 Planarity : 0.005 0.037 2084 Dihedral : 8.268 78.171 1702 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.07 % Allowed : 8.28 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.79 (0.18), residues: 1468 helix: -3.31 (0.14), residues: 584 sheet: -2.85 (0.35), residues: 164 loop : -1.56 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 312 TYR 0.009 0.001 TYR A 169 PHE 0.013 0.001 PHE B 375 TRP 0.016 0.002 TRP C 340 HIS 0.004 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (12004) covalent geometry : angle 0.66658 / 0.33 (16292) hydrogen bonds : bond 0.04431 / 3.06 ( 372) hydrogen bonds : angle 6.43859 / 4.47 ( 936) *********************** 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 203 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7481 (mmm) cc_final: 0.5860 (mpp) REVERT: B 41 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7689 (mp10) REVERT: B 82 MET cc_start: 0.8596 (tpt) cc_final: 0.8379 (tpt) REVERT: B 367 PRO cc_start: 0.8600 (Cg_endo) cc_final: 0.8371 (Cg_exo) REVERT: C 113 LYS cc_start: 0.6845 (mmtt) cc_final: 0.6238 (mmtt) REVERT: C 123 MET cc_start: 0.8700 (mmm) cc_final: 0.8222 (mmm) REVERT: C 202 THR cc_start: 0.8912 (p) cc_final: 0.8570 (t) REVERT: C 205 GLU cc_start: 0.7245 (mp0) cc_final: 0.7034 (mt-10) REVERT: C 314 GLN cc_start: 0.8487 (tm-30) cc_final: 0.8139 (tm-30) REVERT: D 10 CYS cc_start: 0.8281 (t) cc_final: 0.8024 (t) REVERT: D 132 MET cc_start: 0.8316 (ppp) cc_final: 0.8013 (ttp) REVERT: D 142 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8688 (mt) REVERT: D 154 ASP cc_start: 0.8394 (t0) cc_final: 0.7896 (t0) REVERT: D 191 LYS cc_start: 0.8763 (ttpt) cc_final: 0.8543 (tttm) REVERT: D 205 GLU cc_start: 0.7530 (mp0) cc_final: 0.7325 (mp0) outliers start: 26 outliers final: 9 residues processed: 200 average time/residue: 0.0966 time to fit residues: 29.0684 Evaluate side-chains 142 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 373 LYS Chi-restraints excluded: chain D residue 375 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 101 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 100 optimal weight: 0.0270 chunk 25 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN B 111 ASN C 12 ASN C 246 GLN D 78 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.089618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.076375 restraints weight = 24126.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.079116 restraints weight = 12510.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.080985 restraints weight = 7807.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.082231 restraints weight = 5512.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.083160 restraints weight = 4294.011| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12004 Z= 0.126 Angle : 0.600 6.235 16292 Z= 0.294 Chirality : 0.047 0.193 1808 Planarity : 0.004 0.034 2084 Dihedral : 7.389 74.027 1682 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.91 % Allowed : 10.59 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.04 (0.20), residues: 1468 helix: -2.59 (0.17), residues: 596 sheet: -2.55 (0.36), residues: 180 loop : -1.10 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 95 TYR 0.007 0.001 TYR A 169 PHE 0.014 0.001 PHE B 223 TRP 0.011 0.001 TRP C 340 HIS 0.005 0.001 HIS D 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (12004) covalent geometry : angle 0.60043 / 0.29 (16292) hydrogen bonds : bond 0.03656 / 2.54 ( 372) hydrogen bonds : angle 5.82953 / 4.05 ( 936) *********************** 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 167 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7480 (mmm) cc_final: 0.5812 (mpp) REVERT: A 137 GLN cc_start: 0.8389 (mt0) cc_final: 0.8048 (mt0) REVERT: A 176 MET cc_start: 0.8281 (mmm) cc_final: 0.8060 (mmt) REVERT: B 41 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7854 (mp10) REVERT: B 44 MET cc_start: 0.6298 (mmm) cc_final: 0.4304 (mpp) REVERT: B 367 PRO cc_start: 0.8604 (Cg_endo) cc_final: 0.8369 (Cg_exo) REVERT: C 113 LYS cc_start: 0.6844 (mmtt) cc_final: 0.6283 (mmtt) REVERT: C 132 MET cc_start: 0.8256 (ppp) cc_final: 0.7913 (ppp) REVERT: C 202 THR cc_start: 0.8922 (p) cc_final: 0.8546 (t) REVERT: C 205 GLU cc_start: 0.7312 (mp0) cc_final: 0.7098 (mt-10) REVERT: D 132 MET cc_start: 0.8262 (ppp) cc_final: 0.7889 (ttp) REVERT: D 142 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8638 (mt) REVERT: D 154 ASP cc_start: 0.8322 (t0) cc_final: 0.7923 (t0) REVERT: D 191 LYS cc_start: 0.8781 (ttpt) cc_final: 0.8549 (tttm) REVERT: D 201 VAL cc_start: 0.8494 (OUTLIER) cc_final: 0.8194 (p) REVERT: D 205 GLU cc_start: 0.7504 (mp0) cc_final: 0.7173 (mp0) outliers start: 24 outliers final: 10 residues processed: 163 average time/residue: 0.0953 time to fit residues: 24.0539 Evaluate side-chains 136 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 375 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 10 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 125 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.088003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.074625 restraints weight = 24230.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.077319 restraints weight = 12575.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.079181 restraints weight = 7886.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.080472 restraints weight = 5588.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.081295 restraints weight = 4314.296| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 12004 Z= 0.168 Angle : 0.611 6.381 16292 Z= 0.298 Chirality : 0.048 0.161 1808 Planarity : 0.004 0.031 2084 Dihedral : 7.108 73.113 1678 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.07 % Allowed : 10.99 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.21), residues: 1468 helix: -2.11 (0.20), residues: 572 sheet: -2.34 (0.44), residues: 124 loop : -0.75 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 206 TYR 0.008 0.001 TYR D 306 PHE 0.015 0.001 PHE B 223 TRP 0.011 0.002 TRP C 340 HIS 0.010 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (12004) covalent geometry : angle 0.61113 / 0.30 (16292) hydrogen bonds : bond 0.03494 / 2.44 ( 372) hydrogen bonds : angle 5.54127 / 3.86 ( 936) *********************** 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 146 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7507 (mmm) cc_final: 0.5836 (mpp) REVERT: A 121 GLN cc_start: 0.8665 (tm-30) cc_final: 0.8327 (tm-30) REVERT: A 137 GLN cc_start: 0.8370 (mt0) cc_final: 0.8021 (mt0) REVERT: A 176 MET cc_start: 0.8227 (mmm) cc_final: 0.7986 (mmt) REVERT: B 41 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7900 (mp10) REVERT: B 44 MET cc_start: 0.6391 (mmm) cc_final: 0.4372 (mpp) REVERT: B 292 ASP cc_start: 0.8227 (t0) cc_final: 0.7856 (t0) REVERT: B 367 PRO cc_start: 0.8738 (Cg_endo) cc_final: 0.8508 (Cg_exo) REVERT: C 113 LYS cc_start: 0.6876 (mmtt) cc_final: 0.6278 (mmtt) REVERT: C 132 MET cc_start: 0.8222 (ppp) cc_final: 0.7869 (ppp) REVERT: C 202 THR cc_start: 0.8923 (p) cc_final: 0.8582 (t) REVERT: C 269 MET cc_start: 0.7007 (OUTLIER) cc_final: 0.6772 (mtp) REVERT: D 132 MET cc_start: 0.8416 (ppp) cc_final: 0.8020 (ttp) REVERT: D 142 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8693 (mt) REVERT: D 154 ASP cc_start: 0.8358 (t0) cc_final: 0.7973 (t0) REVERT: D 201 VAL cc_start: 0.8556 (OUTLIER) cc_final: 0.8224 (p) REVERT: D 205 GLU cc_start: 0.7470 (mp0) cc_final: 0.7076 (mp0) outliers start: 26 outliers final: 14 residues processed: 139 average time/residue: 0.0868 time to fit residues: 19.4130 Evaluate side-chains 132 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 72 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN C 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.084976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.071929 restraints weight = 24644.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.074531 restraints weight = 12860.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.076333 restraints weight = 8087.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.077589 restraints weight = 5747.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.078383 restraints weight = 4437.361| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 12004 Z= 0.271 Angle : 0.678 6.591 16292 Z= 0.336 Chirality : 0.051 0.159 1808 Planarity : 0.004 0.031 2084 Dihedral : 7.284 77.159 1674 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.07 % Allowed : 11.70 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.21), residues: 1468 helix: -2.04 (0.20), residues: 572 sheet: -2.31 (0.38), residues: 172 loop : -0.66 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 312 TYR 0.013 0.001 TYR D 143 PHE 0.012 0.002 PHE B 375 TRP 0.015 0.002 TRP C 340 HIS 0.008 0.002 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.27 (12004) covalent geometry : angle 0.67807 / 0.34 (16292) hydrogen bonds : bond 0.03824 / 2.67 ( 372) hydrogen bonds : angle 5.63387 / 3.92 ( 936) *********************** 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 147 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7481 (mmm) cc_final: 0.5808 (mpp) REVERT: A 121 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8530 (tm-30) REVERT: A 137 GLN cc_start: 0.8357 (mt0) cc_final: 0.8023 (mt0) REVERT: A 325 MET cc_start: 0.8055 (ppp) cc_final: 0.7041 (ppp) REVERT: B 44 MET cc_start: 0.6413 (mmm) cc_final: 0.4395 (mpp) REVERT: B 292 ASP cc_start: 0.8239 (t0) cc_final: 0.7884 (t0) REVERT: B 367 PRO cc_start: 0.8630 (Cg_endo) cc_final: 0.8428 (Cg_exo) REVERT: C 113 LYS cc_start: 0.6850 (mmtt) cc_final: 0.6196 (mmtt) REVERT: C 132 MET cc_start: 0.8205 (ppp) cc_final: 0.7876 (ppp) REVERT: C 269 MET cc_start: 0.7046 (mtp) cc_final: 0.6782 (mtp) REVERT: D 132 MET cc_start: 0.8613 (ppp) cc_final: 0.8136 (ttp) REVERT: D 142 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8819 (mt) REVERT: D 154 ASP cc_start: 0.8381 (t0) cc_final: 0.7969 (t0) REVERT: D 201 VAL cc_start: 0.8652 (OUTLIER) cc_final: 0.8287 (p) REVERT: D 205 GLU cc_start: 0.7417 (mp0) cc_final: 0.7158 (mp0) outliers start: 26 outliers final: 16 residues processed: 139 average time/residue: 0.0846 time to fit residues: 18.8716 Evaluate side-chains 133 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 201 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 112 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 100 optimal weight: 0.0770 chunk 60 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 297 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 = 0.3227 r_free = 0.3227 target = 0.088489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.075055 restraints weight = 24232.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.077832 restraints weight = 12504.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.079755 restraints weight = 7840.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.081039 restraints weight = 5550.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.081930 restraints weight = 4291.300| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12004 Z= 0.116 Angle : 0.581 6.701 16292 Z= 0.280 Chirality : 0.046 0.163 1808 Planarity : 0.003 0.030 2084 Dihedral : 6.827 68.266 1674 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.19 % Allowed : 12.42 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.22), residues: 1468 helix: -1.74 (0.21), residues: 572 sheet: -2.09 (0.37), residues: 172 loop : -0.42 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 206 TYR 0.006 0.001 TYR D 306 PHE 0.015 0.001 PHE B 223 TRP 0.014 0.001 TRP C 340 HIS 0.003 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (12004) covalent geometry : angle 0.58081 / 0.28 (16292) hydrogen bonds : bond 0.03181 / 2.23 ( 372) hydrogen bonds : angle 5.28286 / 3.67 ( 936) *********************** 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 141 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.486 Fit side-chains REVERT: A 44 MET cc_start: 0.7569 (mmm) cc_final: 0.5820 (mpp) REVERT: A 325 MET cc_start: 0.7860 (ppp) cc_final: 0.7032 (ppp) REVERT: B 44 MET cc_start: 0.6273 (mmm) cc_final: 0.4288 (mpp) REVERT: B 292 ASP cc_start: 0.8096 (t0) cc_final: 0.7787 (t0) REVERT: C 113 LYS cc_start: 0.6909 (mmtt) cc_final: 0.6295 (mmtt) REVERT: C 132 MET cc_start: 0.8170 (ppp) cc_final: 0.7825 (ppp) REVERT: C 202 THR cc_start: 0.8810 (p) cc_final: 0.8496 (t) REVERT: C 325 MET cc_start: 0.8203 (ppp) cc_final: 0.7628 (ppp) REVERT: D 132 MET cc_start: 0.8426 (ppp) cc_final: 0.7969 (ttp) REVERT: D 142 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8713 (mt) REVERT: D 154 ASP cc_start: 0.8306 (t0) cc_final: 0.7910 (t0) REVERT: D 162 ASN cc_start: 0.8440 (m-40) cc_final: 0.8162 (m-40) REVERT: D 201 VAL cc_start: 0.8543 (OUTLIER) cc_final: 0.8181 (p) REVERT: D 205 GLU cc_start: 0.7404 (mp0) cc_final: 0.7156 (mp0) outliers start: 15 outliers final: 8 residues processed: 136 average time/residue: 0.0831 time to fit residues: 18.3133 Evaluate side-chains 124 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 121 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 41 optimal weight: 0.0370 chunk 62 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN ** D 297 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 = 0.3227 r_free = 0.3227 target = 0.088444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.075157 restraints weight = 24208.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.077946 restraints weight = 12443.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.079870 restraints weight = 7736.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.081165 restraints weight = 5436.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.082045 restraints weight = 4191.463| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12004 Z= 0.122 Angle : 0.579 6.349 16292 Z= 0.280 Chirality : 0.046 0.155 1808 Planarity : 0.003 0.032 2084 Dihedral : 6.613 66.287 1674 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.19 % Allowed : 13.30 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.22), residues: 1468 helix: -1.55 (0.21), residues: 572 sheet: -1.94 (0.37), residues: 172 loop : -0.30 (0.25), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 312 TYR 0.007 0.001 TYR B 279 PHE 0.009 0.001 PHE B 223 TRP 0.012 0.001 TRP C 340 HIS 0.004 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (12004) covalent geometry : angle 0.57874 / 0.28 (16292) hydrogen bonds : bond 0.03139 / 2.20 ( 372) hydrogen bonds : angle 5.12924 / 3.55 ( 936) *********************** 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 134 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.442 Fit side-chains REVERT: A 44 MET cc_start: 0.7502 (mmm) cc_final: 0.5646 (mpp) REVERT: A 325 MET cc_start: 0.7771 (ppp) cc_final: 0.7274 (ppp) REVERT: B 44 MET cc_start: 0.6139 (mmm) cc_final: 0.4134 (mpp) REVERT: B 292 ASP cc_start: 0.8074 (t0) cc_final: 0.7791 (t0) REVERT: C 113 LYS cc_start: 0.6879 (mmtt) cc_final: 0.6294 (mmtt) REVERT: C 132 MET cc_start: 0.8188 (ppp) cc_final: 0.7866 (ppp) REVERT: C 202 THR cc_start: 0.8522 (p) cc_final: 0.8219 (t) REVERT: C 325 MET cc_start: 0.8163 (ppp) cc_final: 0.7637 (ppp) REVERT: D 132 MET cc_start: 0.8419 (ppp) cc_final: 0.8010 (ttp) REVERT: D 142 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8674 (mt) REVERT: D 154 ASP cc_start: 0.8299 (t0) cc_final: 0.7928 (t0) REVERT: D 162 ASN cc_start: 0.8370 (m-40) cc_final: 0.7951 (m-40) REVERT: D 205 GLU cc_start: 0.7339 (mp0) cc_final: 0.7104 (mp0) outliers start: 15 outliers final: 13 residues processed: 130 average time/residue: 0.0845 time to fit residues: 17.8723 Evaluate side-chains 126 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 70 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 21 optimal weight: 0.0270 chunk 109 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 95 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.088582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.075240 restraints weight = 24309.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.078018 restraints weight = 12533.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.079944 restraints weight = 7835.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.081098 restraints weight = 5534.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.082107 restraints weight = 4343.902| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12004 Z= 0.123 Angle : 0.574 7.211 16292 Z= 0.277 Chirality : 0.046 0.152 1808 Planarity : 0.003 0.029 2084 Dihedral : 6.444 65.177 1674 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.43 % Allowed : 13.38 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.22), residues: 1468 helix: -1.37 (0.22), residues: 568 sheet: -1.86 (0.37), residues: 172 loop : -0.17 (0.25), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 312 TYR 0.009 0.001 TYR B 279 PHE 0.012 0.001 PHE B 223 TRP 0.011 0.001 TRP C 340 HIS 0.003 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (12004) covalent geometry : angle 0.57447 / 0.28 (16292) hydrogen bonds : bond 0.03090 / 2.18 ( 372) hydrogen bonds : angle 5.06509 / 3.51 ( 936) *********************** 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: 18 poor density : 119 time to evaluate : 0.490 Fit side-chains REVERT: A 44 MET cc_start: 0.7491 (mmm) cc_final: 0.5638 (mpp) REVERT: A 269 MET cc_start: 0.7350 (mtp) cc_final: 0.6925 (ttm) REVERT: A 325 MET cc_start: 0.7714 (ppp) cc_final: 0.7176 (ppp) REVERT: B 44 MET cc_start: 0.6106 (mmm) cc_final: 0.4155 (mpp) REVERT: B 82 MET cc_start: 0.8882 (tpp) cc_final: 0.8494 (mmm) REVERT: B 292 ASP cc_start: 0.8073 (t0) cc_final: 0.7809 (t0) REVERT: C 113 LYS cc_start: 0.6878 (mmtt) cc_final: 0.6316 (mmtt) REVERT: C 132 MET cc_start: 0.8204 (ppp) cc_final: 0.7861 (ppp) REVERT: C 325 MET cc_start: 0.8125 (ppp) cc_final: 0.7600 (ppp) REVERT: D 132 MET cc_start: 0.8402 (ppp) cc_final: 0.7664 (ttp) REVERT: D 142 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8665 (mt) REVERT: D 154 ASP cc_start: 0.8218 (t0) cc_final: 0.7981 (t70) REVERT: D 162 ASN cc_start: 0.8370 (m-40) cc_final: 0.8028 (m-40) REVERT: D 205 GLU cc_start: 0.7338 (mp0) cc_final: 0.7087 (mp0) outliers start: 18 outliers final: 16 residues processed: 132 average time/residue: 0.0817 time to fit residues: 17.5916 Evaluate side-chains 129 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 132 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.085967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.072715 restraints weight = 24429.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.075364 restraints weight = 12847.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.077243 restraints weight = 8171.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.078529 restraints weight = 5796.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.079400 restraints weight = 4484.704| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 12004 Z= 0.243 Angle : 0.655 7.061 16292 Z= 0.323 Chirality : 0.050 0.166 1808 Planarity : 0.004 0.028 2084 Dihedral : 6.741 68.540 1674 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.59 % Allowed : 13.93 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.22), residues: 1468 helix: -1.46 (0.21), residues: 572 sheet: -1.91 (0.37), residues: 172 loop : -0.27 (0.25), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 312 TYR 0.010 0.001 TYR D 143 PHE 0.011 0.001 PHE B 375 TRP 0.011 0.002 TRP C 340 HIS 0.006 0.002 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.24 (12004) covalent geometry : angle 0.65480 / 0.32 (16292) hydrogen bonds : bond 0.03603 / 2.55 ( 372) hydrogen bonds : angle 5.27395 / 3.67 ( 936) *********************** 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 141 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.446 Fit side-chains REVERT: A 44 MET cc_start: 0.7520 (mmm) cc_final: 0.5834 (mpp) REVERT: A 325 MET cc_start: 0.7758 (ppp) cc_final: 0.6982 (ppp) REVERT: B 44 MET cc_start: 0.6205 (mmm) cc_final: 0.4218 (mpp) REVERT: B 292 ASP cc_start: 0.8139 (t0) cc_final: 0.7789 (t0) REVERT: C 113 LYS cc_start: 0.6933 (mmtt) cc_final: 0.6248 (mmtt) REVERT: C 119 MET cc_start: 0.8381 (ttm) cc_final: 0.8118 (ttm) REVERT: C 132 MET cc_start: 0.8231 (ppp) cc_final: 0.7874 (ppp) REVERT: C 325 MET cc_start: 0.8114 (ppp) cc_final: 0.7659 (ppp) REVERT: D 132 MET cc_start: 0.8544 (ppp) cc_final: 0.7954 (ptm) REVERT: D 142 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8704 (mm) REVERT: D 154 ASP cc_start: 0.8335 (t0) cc_final: 0.7956 (t0) REVERT: D 162 ASN cc_start: 0.8459 (m-40) cc_final: 0.8151 (m-40) REVERT: D 205 GLU cc_start: 0.7345 (mp0) cc_final: 0.7097 (mp0) outliers start: 20 outliers final: 18 residues processed: 133 average time/residue: 0.0864 time to fit residues: 18.3287 Evaluate side-chains 139 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 65 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 12 optimal weight: 0.0980 chunk 78 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 83 optimal weight: 0.4980 chunk 115 optimal weight: 7.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN ** D 297 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 = 0.3234 r_free = 0.3234 target = 0.088855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.075486 restraints weight = 24292.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.078305 restraints weight = 12509.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.080244 restraints weight = 7784.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.081546 restraints weight = 5463.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.082476 restraints weight = 4201.810| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12004 Z= 0.113 Angle : 0.580 7.097 16292 Z= 0.281 Chirality : 0.046 0.159 1808 Planarity : 0.003 0.028 2084 Dihedral : 6.362 64.863 1674 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.51 % Allowed : 14.49 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.23), residues: 1468 helix: -1.16 (0.22), residues: 556 sheet: -1.71 (0.33), residues: 228 loop : -0.09 (0.26), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 312 TYR 0.008 0.001 TYR B 279 PHE 0.011 0.001 PHE B 223 TRP 0.013 0.001 TRP C 340 HIS 0.003 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (12004) covalent geometry : angle 0.57982 / 0.28 (16292) hydrogen bonds : bond 0.03065 / 2.17 ( 372) hydrogen bonds : angle 5.04700 / 3.50 ( 936) ********************** 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 141 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.7501 (mmm) cc_final: 0.5665 (mpp) REVERT: A 325 MET cc_start: 0.7723 (ppp) cc_final: 0.6900 (ppp) REVERT: B 44 MET cc_start: 0.6202 (mmm) cc_final: 0.4216 (mpp) REVERT: B 292 ASP cc_start: 0.8092 (t0) cc_final: 0.7861 (t0) REVERT: C 113 LYS cc_start: 0.6899 (mmtt) cc_final: 0.6283 (mmtt) REVERT: C 132 MET cc_start: 0.8189 (ppp) cc_final: 0.7844 (ppp) REVERT: C 325 MET cc_start: 0.8057 (ppp) cc_final: 0.7580 (ppp) REVERT: D 132 MET cc_start: 0.8425 (ppp) cc_final: 0.7959 (ttp) REVERT: D 142 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8686 (mt) REVERT: D 154 ASP cc_start: 0.8229 (t0) cc_final: 0.7994 (t70) REVERT: D 162 ASN cc_start: 0.8360 (m-40) cc_final: 0.8051 (m-40) REVERT: D 205 GLU cc_start: 0.7274 (mp0) cc_final: 0.7029 (mp0) REVERT: D 325 MET cc_start: 0.7955 (pmm) cc_final: 0.6973 (ptp) outliers start: 19 outliers final: 16 residues processed: 134 average time/residue: 0.0812 time to fit residues: 17.6604 Evaluate side-chains 134 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 130 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 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 = 0.3230 r_free = 0.3230 target = 0.088541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.075147 restraints weight = 24307.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.077938 restraints weight = 12641.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.079835 restraints weight = 7912.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.081181 restraints weight = 5608.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.081990 restraints weight = 4304.569| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12004 Z= 0.134 Angle : 0.589 6.839 16292 Z= 0.286 Chirality : 0.046 0.148 1808 Planarity : 0.003 0.027 2084 Dihedral : 6.298 63.496 1674 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.27 % Allowed : 14.89 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.23), residues: 1468 helix: -1.06 (0.22), residues: 556 sheet: -1.72 (0.37), residues: 172 loop : -0.02 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 312 TYR 0.011 0.001 TYR B 279 PHE 0.016 0.001 PHE B 223 TRP 0.012 0.001 TRP C 340 HIS 0.003 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (12004) covalent geometry : angle 0.58871 / 0.29 (16292) hydrogen bonds : bond 0.03181 / 2.26 ( 372) hydrogen bonds : angle 5.00746 / 3.47 ( 936) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1769.05 seconds wall clock time: 31 minutes 39.00 seconds (1899.00 seconds total)