Starting phenix.real_space_refine on Wed Jul 30 03:10:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6djo_7938/07_2025/6djo_7938.cif Found real_map, /net/cci-nas-00/data/ceres_data/6djo_7938/07_2025/6djo_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6djo_7938/07_2025/6djo_7938.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6djo_7938/07_2025/6djo_7938.map" model { file = "/net/cci-nas-00/data/ceres_data/6djo_7938/07_2025/6djo_7938.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6djo_7938/07_2025/6djo_7938.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.31, per 1000 atoms: 0.62 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: 2.67 Conformation dependent library (CDL) restraints added in 1.4 seconds 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 24 sheets defined 40.9% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 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: 3.40 Time building geometry restraints manager: 3.20 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 28.830 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.76 (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 TRP 0.029 0.004 TRP C 340 HIS 0.008 0.003 HIS D 40 PHE 0.018 0.002 PHE B 31 TYR 0.016 0.002 TYR B 169 ARG 0.012 0.001 ARG D 177 Details of bonding type rmsd hydrogen bonds : bond 0.30802 ( 372) hydrogen bonds : angle 10.27367 ( 936) covalent geometry : bond 0.00909 (12004) covalent geometry : angle 0.94313 (16292) *********************** 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 : 1.423 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: 0.7518 (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: 0.8663 (Cg_endo) cc_final: 0.8430 (Cg_exo) REVERT: C 123 MET cc_start: 0.8833 (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: 0.8304 (t) cc_final: 0.8087 (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: 0.8496 (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: 0.2891 time to fit residues: 119.4617 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 : 1.281 ------------------------------------------------------------------------------- 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 124 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 86 optimal weight: 0.0980 chunk 134 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3246 r_free = 0.3246 target = 0.089556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.076408 restraints weight = 24087.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.079110 restraints weight = 12555.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.080958 restraints weight = 7880.229| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12004 Z= 0.132 Angle : 0.659 6.518 16292 Z= 0.328 Chirality : 0.048 0.179 1808 Planarity : 0.005 0.037 2084 Dihedral : 8.243 78.211 1702 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.99 % Allowed : 8.12 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.18), residues: 1468 helix: -3.32 (0.14), residues: 584 sheet: -2.86 (0.35), residues: 164 loop : -1.56 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 340 HIS 0.003 0.001 HIS C 40 PHE 0.013 0.001 PHE B 375 TYR 0.009 0.001 TYR A 169 ARG 0.005 0.001 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.04458 ( 372) hydrogen bonds : angle 6.44286 ( 936) covalent geometry : bond 0.00297 (12004) covalent geometry : angle 0.65917 (16292) *********************** 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: 25 poor density : 178 time to evaluate : 1.509 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.7603 (mmm) cc_final: 0.5953 (mpp) REVERT: B 41 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7725 (mp10) REVERT: B 82 MET cc_start: 0.8538 (tpt) cc_final: 0.8330 (tpt) REVERT: B 367 PRO cc_start: 0.8641 (Cg_endo) cc_final: 0.8414 (Cg_exo) REVERT: C 113 LYS cc_start: 0.6841 (mmtt) cc_final: 0.6236 (mmtt) REVERT: C 202 THR cc_start: 0.8931 (p) cc_final: 0.8578 (t) REVERT: C 205 GLU cc_start: 0.7286 (mp0) cc_final: 0.7067 (mt-10) REVERT: D 10 CYS cc_start: 0.8291 (t) cc_final: 0.8025 (t) REVERT: D 132 MET cc_start: 0.8295 (ppp) cc_final: 0.7980 (ttp) REVERT: D 142 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8677 (mt) REVERT: D 154 ASP cc_start: 0.8368 (t0) cc_final: 0.7867 (t0) REVERT: D 191 LYS cc_start: 0.8747 (ttpt) cc_final: 0.8518 (tttm) REVERT: D 205 GLU cc_start: 0.7536 (mp0) cc_final: 0.7335 (mp0) outliers start: 25 outliers final: 7 residues processed: 200 average time/residue: 0.2618 time to fit residues: 78.1511 Evaluate side-chains 140 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 1.532 ------------------------------------------------------------------------------- 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 202 THR 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 76 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 118 optimal weight: 0.0670 chunk 6 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN B 111 ASN B 162 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 = 0.3231 r_free = 0.3231 target = 0.088821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.075536 restraints weight = 24245.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.078268 restraints weight = 12556.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.080137 restraints weight = 7853.920| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12004 Z= 0.153 Angle : 0.614 6.330 16292 Z= 0.301 Chirality : 0.048 0.192 1808 Planarity : 0.004 0.032 2084 Dihedral : 7.416 74.586 1682 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.07 % Allowed : 10.19 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.20), residues: 1468 helix: -2.57 (0.17), residues: 596 sheet: -2.52 (0.36), residues: 180 loop : -1.12 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 340 HIS 0.004 0.001 HIS C 40 PHE 0.010 0.001 PHE B 223 TYR 0.009 0.001 TYR D 143 ARG 0.003 0.000 ARG C 206 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 372) hydrogen bonds : angle 5.82223 ( 936) covalent geometry : bond 0.00351 (12004) covalent geometry : angle 0.61376 (16292) *********************** 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 160 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7571 (mmm) cc_final: 0.5866 (mpp) REVERT: A 137 GLN cc_start: 0.8441 (mt0) cc_final: 0.8087 (mt0) REVERT: A 176 MET cc_start: 0.8315 (mmm) cc_final: 0.8096 (mmt) REVERT: B 41 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7842 (mp10) REVERT: B 44 MET cc_start: 0.6395 (mmm) cc_final: 0.4353 (mpp) REVERT: B 292 ASP cc_start: 0.8200 (t0) cc_final: 0.7794 (t0) REVERT: B 367 PRO cc_start: 0.8736 (Cg_endo) cc_final: 0.8486 (Cg_exo) REVERT: C 113 LYS cc_start: 0.6876 (mmtt) cc_final: 0.6291 (mmtt) REVERT: C 132 MET cc_start: 0.8321 (ppp) cc_final: 0.7972 (ppp) REVERT: C 202 THR cc_start: 0.8945 (p) cc_final: 0.8567 (t) REVERT: C 205 GLU cc_start: 0.7380 (mp0) cc_final: 0.7169 (mt-10) REVERT: C 325 MET cc_start: 0.8501 (ppp) cc_final: 0.7667 (ppp) REVERT: D 132 MET cc_start: 0.8402 (ppp) cc_final: 0.8047 (ttp) REVERT: D 142 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8639 (mt) REVERT: D 154 ASP cc_start: 0.8316 (t0) cc_final: 0.7921 (t0) REVERT: D 191 LYS cc_start: 0.8785 (ttpt) cc_final: 0.8551 (tttm) REVERT: D 201 VAL cc_start: 0.8544 (OUTLIER) cc_final: 0.8243 (p) REVERT: D 205 GLU cc_start: 0.7571 (mp0) cc_final: 0.7210 (mp0) outliers start: 26 outliers final: 13 residues processed: 156 average time/residue: 0.2315 time to fit residues: 55.4955 Evaluate side-chains 133 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 373 LYS 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 202 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 375 PHE 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 34 optimal weight: 0.0370 chunk 135 optimal weight: 3.9990 chunk 107 optimal weight: 0.3980 chunk 82 optimal weight: 3.9990 chunk 83 optimal weight: 0.0870 chunk 130 optimal weight: 0.2980 chunk 137 optimal weight: 0.0060 chunk 40 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.1652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.092104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.078668 restraints weight = 23693.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.081507 restraints weight = 12168.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.083483 restraints weight = 7595.730| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12004 Z= 0.088 Angle : 0.559 6.096 16292 Z= 0.269 Chirality : 0.045 0.164 1808 Planarity : 0.004 0.033 2084 Dihedral : 6.778 68.932 1678 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.59 % Allowed : 10.67 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.21), residues: 1468 helix: -2.12 (0.19), residues: 596 sheet: -2.49 (0.35), residues: 180 loop : -0.78 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 340 HIS 0.007 0.001 HIS B 275 PHE 0.016 0.001 PHE B 223 TYR 0.007 0.001 TYR B 279 ARG 0.003 0.000 ARG D 312 Details of bonding type rmsd hydrogen bonds : bond 0.03082 ( 372) hydrogen bonds : angle 5.38467 ( 936) covalent geometry : bond 0.00192 (12004) covalent geometry : angle 0.55853 (16292) *********************** 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 157 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 1.439 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.7677 (mmm) cc_final: 0.5837 (mpp) REVERT: A 121 GLN cc_start: 0.8582 (tm-30) cc_final: 0.8141 (tm-30) REVERT: A 137 GLN cc_start: 0.8330 (mt0) cc_final: 0.8042 (mt0) REVERT: A 176 MET cc_start: 0.8198 (mmm) cc_final: 0.7946 (mmt) REVERT: A 325 MET cc_start: 0.8137 (ppp) cc_final: 0.7067 (ppp) REVERT: B 41 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7898 (mp10) REVERT: B 44 MET cc_start: 0.6262 (mmm) cc_final: 0.4271 (mpp) REVERT: B 292 ASP cc_start: 0.8136 (t0) cc_final: 0.7763 (t0) REVERT: B 367 PRO cc_start: 0.8639 (Cg_endo) cc_final: 0.8421 (Cg_exo) REVERT: C 113 LYS cc_start: 0.6884 (mmtt) cc_final: 0.6348 (mmtt) REVERT: C 132 MET cc_start: 0.8213 (ppp) cc_final: 0.7885 (ppp) REVERT: C 202 THR cc_start: 0.8867 (p) cc_final: 0.8531 (t) REVERT: C 325 MET cc_start: 0.8366 (ppp) cc_final: 0.7444 (ppp) REVERT: D 132 MET cc_start: 0.8273 (ppp) cc_final: 0.7639 (ttp) REVERT: D 154 ASP cc_start: 0.8336 (t0) cc_final: 0.7953 (t0) REVERT: D 191 LYS cc_start: 0.8708 (ttpt) cc_final: 0.8442 (tttm) REVERT: D 201 VAL cc_start: 0.8445 (OUTLIER) cc_final: 0.8117 (p) REVERT: D 205 GLU cc_start: 0.7426 (mp0) cc_final: 0.7060 (mp0) outliers start: 20 outliers final: 9 residues processed: 155 average time/residue: 0.1960 time to fit residues: 46.8281 Evaluate side-chains 131 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 C residue 167 GLU Chi-restraints excluded: chain C residue 201 VAL 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 110 optimal weight: 0.2980 chunk 123 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 12 optimal weight: 0.0970 chunk 24 optimal weight: 0.9980 chunk 143 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 162 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 = 0.3265 r_free = 0.3265 target = 0.090573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.077173 restraints weight = 24023.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.080001 restraints weight = 12432.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.081956 restraints weight = 7797.282| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3275 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= 0.117 Angle : 0.562 6.021 16292 Z= 0.271 Chirality : 0.045 0.157 1808 Planarity : 0.003 0.031 2084 Dihedral : 6.448 67.589 1674 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.35 % Allowed : 11.54 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.21), residues: 1468 helix: -1.73 (0.21), residues: 572 sheet: -2.30 (0.42), residues: 124 loop : -0.53 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 340 HIS 0.011 0.001 HIS A 275 PHE 0.031 0.001 PHE C 223 TYR 0.006 0.001 TYR A 166 ARG 0.003 0.000 ARG A 312 Details of bonding type rmsd hydrogen bonds : bond 0.03109 ( 372) hydrogen bonds : angle 5.21909 ( 936) covalent geometry : bond 0.00268 (12004) covalent geometry : angle 0.56244 (16292) *********************** 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 144 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 1.438 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.7737 (mmm) cc_final: 0.5895 (mpp) REVERT: A 121 GLN cc_start: 0.8618 (tm-30) cc_final: 0.8314 (tm-30) REVERT: A 137 GLN cc_start: 0.8296 (mt0) cc_final: 0.8010 (mt0) REVERT: A 176 MET cc_start: 0.8233 (mmm) cc_final: 0.8009 (mmt) REVERT: A 269 MET cc_start: 0.7452 (mtp) cc_final: 0.6993 (ttm) REVERT: A 325 MET cc_start: 0.8199 (ppp) cc_final: 0.7402 (ppp) REVERT: B 41 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7982 (mp10) REVERT: B 44 MET cc_start: 0.6345 (mmm) cc_final: 0.4337 (mpp) REVERT: B 162 ASN cc_start: 0.7988 (m110) cc_final: 0.7697 (m110) REVERT: B 292 ASP cc_start: 0.8132 (t0) cc_final: 0.7798 (t0) REVERT: B 367 PRO cc_start: 0.8664 (Cg_endo) cc_final: 0.8460 (Cg_exo) REVERT: C 113 LYS cc_start: 0.6882 (mmtt) cc_final: 0.6328 (mmtt) REVERT: C 123 MET cc_start: 0.8635 (mmm) cc_final: 0.8351 (mmm) REVERT: C 132 MET cc_start: 0.8202 (ppp) cc_final: 0.7890 (ppp) REVERT: C 227 MET cc_start: 0.8773 (tpp) cc_final: 0.8477 (mpp) REVERT: C 325 MET cc_start: 0.8247 (ppp) cc_final: 0.7380 (ppp) REVERT: D 132 MET cc_start: 0.8287 (ppp) cc_final: 0.7642 (ttp) REVERT: D 142 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8573 (mt) REVERT: D 154 ASP cc_start: 0.8354 (t0) cc_final: 0.7972 (t0) REVERT: D 205 GLU cc_start: 0.7426 (mp0) cc_final: 0.6875 (mp0) outliers start: 17 outliers final: 10 residues processed: 142 average time/residue: 0.1906 time to fit residues: 42.6641 Evaluate side-chains 128 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 C residue 201 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 137 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 26 optimal weight: 0.0270 chunk 67 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 overall best weight: 0.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 162 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 = 0.3238 r_free = 0.3238 target = 0.089182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.075753 restraints weight = 24224.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.078531 restraints weight = 12569.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.080490 restraints weight = 7921.057| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12004 Z= 0.140 Angle : 0.568 6.031 16292 Z= 0.275 Chirality : 0.046 0.154 1808 Planarity : 0.003 0.032 2084 Dihedral : 6.355 67.460 1674 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.43 % Allowed : 12.02 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.22), residues: 1468 helix: -1.49 (0.21), residues: 560 sheet: -2.08 (0.36), residues: 172 loop : -0.27 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 340 HIS 0.004 0.001 HIS C 40 PHE 0.014 0.001 PHE C 223 TYR 0.007 0.001 TYR D 306 ARG 0.002 0.000 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.03153 ( 372) hydrogen bonds : angle 5.15103 ( 936) covalent geometry : bond 0.00325 (12004) covalent geometry : angle 0.56775 (16292) *********************** 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 138 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 1.244 Fit side-chains REVERT: A 44 MET cc_start: 0.7738 (mmm) cc_final: 0.5896 (mpp) REVERT: A 121 GLN cc_start: 0.8699 (tm-30) cc_final: 0.8440 (tm-30) REVERT: A 137 GLN cc_start: 0.8263 (mt0) cc_final: 0.7903 (mt0) REVERT: A 269 MET cc_start: 0.7487 (mtp) cc_final: 0.7006 (ttm) REVERT: A 325 MET cc_start: 0.8112 (ppp) cc_final: 0.7425 (ppp) REVERT: B 41 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7994 (mp10) REVERT: B 44 MET cc_start: 0.6376 (mmm) cc_final: 0.4344 (mpp) REVERT: B 162 ASN cc_start: 0.7994 (m110) cc_final: 0.7751 (m-40) REVERT: B 292 ASP cc_start: 0.8139 (t0) cc_final: 0.7806 (t0) REVERT: B 367 PRO cc_start: 0.8677 (Cg_endo) cc_final: 0.8454 (Cg_exo) REVERT: C 113 LYS cc_start: 0.6923 (mmtt) cc_final: 0.6325 (mmtt) REVERT: C 123 MET cc_start: 0.8689 (mmm) cc_final: 0.8344 (mmm) REVERT: C 132 MET cc_start: 0.8223 (ppp) cc_final: 0.7901 (ppp) REVERT: C 227 MET cc_start: 0.8698 (tpp) cc_final: 0.8483 (mpp) REVERT: C 325 MET cc_start: 0.8280 (ppp) cc_final: 0.7528 (ppp) REVERT: D 132 MET cc_start: 0.8339 (ppp) cc_final: 0.7660 (ttp) REVERT: D 142 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8638 (mt) REVERT: D 154 ASP cc_start: 0.8348 (t0) cc_final: 0.7967 (t0) REVERT: D 162 ASN cc_start: 0.8345 (m-40) cc_final: 0.8029 (m-40) outliers start: 18 outliers final: 12 residues processed: 134 average time/residue: 0.1844 time to fit residues: 39.0391 Evaluate side-chains 128 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 167 GLU Chi-restraints excluded: chain C residue 282 ILE 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 76 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 ASN D 12 ASN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.089146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.075725 restraints weight = 24216.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.078542 restraints weight = 12580.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.080494 restraints weight = 7869.981| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3487 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= 0.135 Angle : 0.570 6.585 16292 Z= 0.275 Chirality : 0.046 0.154 1808 Planarity : 0.003 0.030 2084 Dihedral : 6.241 66.898 1674 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.51 % Allowed : 12.42 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.22), residues: 1468 helix: -1.35 (0.21), residues: 564 sheet: -1.99 (0.36), residues: 172 loop : -0.12 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 340 HIS 0.004 0.001 HIS C 40 PHE 0.014 0.001 PHE B 223 TYR 0.007 0.001 TYR D 306 ARG 0.002 0.000 ARG D 335 Details of bonding type rmsd hydrogen bonds : bond 0.03109 ( 372) hydrogen bonds : angle 5.06765 ( 936) covalent geometry : bond 0.00314 (12004) covalent geometry : angle 0.56968 (16292) *********************** 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 144 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 1.358 Fit side-chains REVERT: A 44 MET cc_start: 0.7703 (mmm) cc_final: 0.5772 (mpp) REVERT: A 121 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8538 (tm-30) REVERT: A 137 GLN cc_start: 0.8203 (mt0) cc_final: 0.7832 (mt0) REVERT: A 269 MET cc_start: 0.7469 (mtp) cc_final: 0.6987 (ttm) REVERT: A 283 MET cc_start: 0.8202 (mmt) cc_final: 0.7953 (mmt) REVERT: A 325 MET cc_start: 0.7962 (ppp) cc_final: 0.7297 (ppp) REVERT: B 44 MET cc_start: 0.6310 (mmm) cc_final: 0.4291 (mpp) REVERT: B 162 ASN cc_start: 0.8032 (m110) cc_final: 0.7764 (m-40) REVERT: B 292 ASP cc_start: 0.8047 (t0) cc_final: 0.7743 (t0) REVERT: B 313 MET cc_start: 0.7812 (tpp) cc_final: 0.7610 (tpp) REVERT: B 367 PRO cc_start: 0.8661 (Cg_endo) cc_final: 0.8435 (Cg_exo) REVERT: C 113 LYS cc_start: 0.6921 (mmtt) cc_final: 0.6326 (mmtt) REVERT: C 132 MET cc_start: 0.8238 (ppp) cc_final: 0.7875 (ppp) REVERT: C 325 MET cc_start: 0.8114 (ppp) cc_final: 0.7389 (ppp) REVERT: D 132 MET cc_start: 0.8355 (ppp) cc_final: 0.7972 (ttp) REVERT: D 142 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8656 (mt) REVERT: D 154 ASP cc_start: 0.8339 (t0) cc_final: 0.7932 (t0) REVERT: D 162 ASN cc_start: 0.8297 (m-40) cc_final: 0.8056 (m-40) REVERT: D 201 VAL cc_start: 0.8556 (OUTLIER) cc_final: 0.8213 (p) outliers start: 19 outliers final: 14 residues processed: 139 average time/residue: 0.1822 time to fit residues: 40.9771 Evaluate side-chains 128 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 1.211 ------------------------------------------------------------------------------- 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 B residue 142 LEU 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 355 MET Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 282 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 201 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 73 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 ASN D 12 ASN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.086584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.073232 restraints weight = 24475.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.075915 restraints weight = 12785.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.077800 restraints weight = 8100.443| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12004 Z= 0.235 Angle : 0.645 7.355 16292 Z= 0.317 Chirality : 0.049 0.159 1808 Planarity : 0.004 0.031 2084 Dihedral : 6.516 71.507 1672 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.83 % Allowed : 12.58 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.22), residues: 1468 helix: -1.45 (0.21), residues: 568 sheet: -1.92 (0.33), residues: 228 loop : -0.24 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 340 HIS 0.006 0.002 HIS C 40 PHE 0.026 0.002 PHE C 223 TYR 0.011 0.001 TYR D 143 ARG 0.006 0.001 ARG C 206 Details of bonding type rmsd hydrogen bonds : bond 0.03573 ( 372) hydrogen bonds : angle 5.26521 ( 936) covalent geometry : bond 0.00545 (12004) covalent geometry : angle 0.64514 (16292) *********************** 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 143 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 1.342 Fit side-chains REVERT: A 44 MET cc_start: 0.7685 (mmm) cc_final: 0.5826 (mpp) REVERT: A 283 MET cc_start: 0.8267 (mmt) cc_final: 0.8000 (mmt) REVERT: A 325 MET cc_start: 0.7970 (ppp) cc_final: 0.7294 (ppp) REVERT: B 44 MET cc_start: 0.6450 (mmm) cc_final: 0.4471 (mpp) REVERT: B 292 ASP cc_start: 0.8106 (t0) cc_final: 0.7806 (t0) REVERT: C 113 LYS cc_start: 0.6865 (mmtt) cc_final: 0.6232 (mmtt) REVERT: C 132 MET cc_start: 0.8256 (ppp) cc_final: 0.7895 (ppp) REVERT: C 227 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8373 (mpp) REVERT: C 325 MET cc_start: 0.8187 (ppp) cc_final: 0.7482 (ppp) REVERT: D 132 MET cc_start: 0.8569 (ppp) cc_final: 0.8112 (ttp) REVERT: D 142 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8640 (mm) REVERT: D 154 ASP cc_start: 0.8332 (t0) cc_final: 0.7933 (t0) REVERT: D 162 ASN cc_start: 0.8373 (m-40) cc_final: 0.8056 (m-40) outliers start: 23 outliers final: 19 residues processed: 134 average time/residue: 0.1780 time to fit residues: 38.4555 Evaluate side-chains 137 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 1.385 ------------------------------------------------------------------------------- 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 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 355 MET Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 324 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 21 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 17 optimal weight: 0.0970 chunk 143 optimal weight: 0.8980 chunk 100 optimal weight: 0.4980 chunk 105 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 41 optimal weight: 0.0050 chunk 30 optimal weight: 0.9980 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN D 12 ASN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.089703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.076300 restraints weight = 23900.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.079135 restraints weight = 12377.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.081085 restraints weight = 7710.497| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 12004 Z= 0.104 Angle : 0.574 7.279 16292 Z= 0.277 Chirality : 0.045 0.154 1808 Planarity : 0.003 0.045 2084 Dihedral : 6.146 58.870 1672 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.27 % Allowed : 13.69 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.23), residues: 1468 helix: -1.18 (0.22), residues: 568 sheet: -1.82 (0.32), residues: 228 loop : -0.14 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 340 HIS 0.002 0.001 HIS B 275 PHE 0.018 0.001 PHE C 223 TYR 0.009 0.001 TYR B 279 ARG 0.002 0.000 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.03137 ( 372) hydrogen bonds : angle 5.03490 ( 936) covalent geometry : bond 0.00239 (12004) covalent geometry : angle 0.57366 (16292) *********************** 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 140 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 1.282 Fit side-chains REVERT: A 44 MET cc_start: 0.7612 (mmm) cc_final: 0.5499 (mtm) REVERT: A 269 MET cc_start: 0.7295 (mtp) cc_final: 0.7018 (ttm) REVERT: A 283 MET cc_start: 0.8193 (mmt) cc_final: 0.7944 (mmt) REVERT: A 325 MET cc_start: 0.7905 (ppp) cc_final: 0.7232 (ppp) REVERT: B 44 MET cc_start: 0.6158 (mmm) cc_final: 0.4116 (mpp) REVERT: B 162 ASN cc_start: 0.7991 (m110) cc_final: 0.7677 (m-40) REVERT: B 292 ASP cc_start: 0.8018 (t0) cc_final: 0.7768 (t0) REVERT: C 113 LYS cc_start: 0.6962 (mmtt) cc_final: 0.6329 (mmtt) REVERT: C 119 MET cc_start: 0.8234 (ttm) cc_final: 0.8022 (ttm) REVERT: C 132 MET cc_start: 0.8238 (ppp) cc_final: 0.7879 (ppp) REVERT: C 227 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8369 (mpp) REVERT: C 325 MET cc_start: 0.7989 (ppp) cc_final: 0.7312 (ppp) REVERT: D 132 MET cc_start: 0.8368 (ppp) cc_final: 0.7933 (ttp) REVERT: D 142 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8662 (mt) REVERT: D 154 ASP cc_start: 0.8256 (t0) cc_final: 0.8016 (t70) REVERT: D 162 ASN cc_start: 0.8239 (m-40) cc_final: 0.7932 (m-40) REVERT: D 201 VAL cc_start: 0.8537 (OUTLIER) cc_final: 0.8119 (p) REVERT: D 202 THR cc_start: 0.8692 (p) cc_final: 0.8490 (p) outliers start: 16 outliers final: 11 residues processed: 135 average time/residue: 0.1763 time to fit residues: 38.2317 Evaluate side-chains 128 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 142 LEU 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 C residue 167 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 282 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 201 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 2 optimal weight: 0.3980 chunk 147 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 121 optimal weight: 0.0000 chunk 51 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 162 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 = 0.088436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.075289 restraints weight = 23875.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.077975 restraints weight = 12777.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.079852 restraints weight = 8143.057| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12004 Z= 0.140 Angle : 0.585 7.338 16292 Z= 0.284 Chirality : 0.046 0.150 1808 Planarity : 0.003 0.033 2084 Dihedral : 6.073 57.857 1672 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.35 % Allowed : 13.93 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.23), residues: 1468 helix: -0.97 (0.22), residues: 552 sheet: -1.85 (0.32), residues: 236 loop : 0.04 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 340 HIS 0.003 0.001 HIS C 40 PHE 0.017 0.001 PHE C 223 TYR 0.009 0.001 TYR B 279 ARG 0.003 0.000 ARG C 147 Details of bonding type rmsd hydrogen bonds : bond 0.03205 ( 372) hydrogen bonds : angle 4.99012 ( 936) covalent geometry : bond 0.00326 (12004) covalent geometry : angle 0.58499 (16292) ********************** 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 135 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 1.314 Fit side-chains REVERT: A 44 MET cc_start: 0.7553 (mmm) cc_final: 0.5457 (mtm) REVERT: A 269 MET cc_start: 0.7233 (mtp) cc_final: 0.6956 (ttm) REVERT: A 283 MET cc_start: 0.8195 (mmt) cc_final: 0.7914 (mmt) REVERT: A 325 MET cc_start: 0.7918 (ppp) cc_final: 0.7296 (ppp) REVERT: B 44 MET cc_start: 0.6150 (mmm) cc_final: 0.4131 (mpp) REVERT: B 162 ASN cc_start: 0.8010 (m110) cc_final: 0.7737 (m-40) REVERT: B 292 ASP cc_start: 0.8000 (t0) cc_final: 0.7784 (t0) REVERT: C 113 LYS cc_start: 0.6867 (mmtt) cc_final: 0.6282 (mmtt) REVERT: C 119 MET cc_start: 0.8248 (ttm) cc_final: 0.7983 (ttm) REVERT: C 132 MET cc_start: 0.8210 (ppp) cc_final: 0.7865 (ppp) REVERT: C 227 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8309 (mpp) REVERT: C 325 MET cc_start: 0.7972 (ppp) cc_final: 0.7339 (ppp) REVERT: D 132 MET cc_start: 0.8355 (ppp) cc_final: 0.7893 (ttp) REVERT: D 142 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8758 (mt) REVERT: D 154 ASP cc_start: 0.8165 (t0) cc_final: 0.7932 (t70) REVERT: D 162 ASN cc_start: 0.8277 (m-40) cc_final: 0.7988 (m-40) outliers start: 17 outliers final: 14 residues processed: 130 average time/residue: 0.1843 time to fit residues: 38.6462 Evaluate side-chains 132 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 1.357 ------------------------------------------------------------------------------- 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 282 ILE Chi-restraints excluded: chain B residue 142 LEU 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 355 MET Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 282 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 143 optimal weight: 0.0470 chunk 12 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 128 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 overall best weight: 1.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 162 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 = 0.3191 r_free = 0.3191 target = 0.086351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.073214 restraints weight = 24387.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.075813 restraints weight = 13172.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.077660 restraints weight = 8457.482| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3745 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= 0.239 Angle : 0.657 7.936 16292 Z= 0.324 Chirality : 0.050 0.204 1808 Planarity : 0.004 0.030 2084 Dihedral : 6.420 62.541 1672 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.59 % Allowed : 13.69 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.23), residues: 1468 helix: -1.06 (0.22), residues: 548 sheet: -1.76 (0.32), residues: 252 loop : 0.01 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 340 HIS 0.006 0.001 HIS C 40 PHE 0.016 0.002 PHE C 223 TYR 0.011 0.001 TYR D 143 ARG 0.005 0.001 ARG C 206 Details of bonding type rmsd hydrogen bonds : bond 0.03507 ( 372) hydrogen bonds : angle 5.19803 ( 936) covalent geometry : bond 0.00553 (12004) covalent geometry : angle 0.65668 (16292) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3295.33 seconds wall clock time: 58 minutes 30.23 seconds (3510.23 seconds total)