Starting phenix.real_space_refine on Fri Jul 3 04:03:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dnf_27565/07_2026/8dnf_27565.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dnf_27565/07_2026/8dnf_27565.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8dnf_27565/07_2026/8dnf_27565.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dnf_27565/07_2026/8dnf_27565.cif" model { file = "/net/cci-nas-00/data/ceres_data/8dnf_27565/07_2026/8dnf_27565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dnf_27565/07_2026/8dnf_27565.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dnf_27565/07_2026/8dnf_27565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dnf_27565/07_2026/8dnf_27565.map" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.095 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 88 5.16 5 C 7448 2.51 5 N 1980 2.21 5 O 2284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11812 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2925 Unusual residues: {'ACE': 1} Classifications: {'peptide': 374, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 19, 'TRANS': 354} 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: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2925 Unusual residues: {'ACE': 1} Classifications: {'peptide': 374, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 19, 'TRANS': 354} 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: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2925 Unusual residues: {'ACE': 1} Classifications: {'peptide': 374, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 19, 'TRANS': 354} 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: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2925 Unusual residues: {'ACE': 1} Classifications: {'peptide': 374, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 19, 'TRANS': 354} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.38, per 1000 atoms: 0.20 Number of scatterers: 11812 At special positions: 0 Unit cell: (80.19, 125.631, 171.072, 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 88 16.00 P 8 15.00 Mg 4 11.99 O 2284 8.00 N 1980 7.00 C 7448 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 524.1 milliseconds 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2768 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 20 sheets defined 50.0% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 54 through 60 removed outlier: 3.622A pdb=" N GLN A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 92 removed outlier: 3.684A pdb=" N LYS A 83 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TRP A 85 " --> pdb=" O MET A 81 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR A 90 " --> pdb=" O HIS A 86 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 125 removed outlier: 3.746A pdb=" N LYS A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 145 removed outlier: 3.704A pdb=" N LEU A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR A 142 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.574A pdb=" N ALA A 173 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE A 174 " --> pdb=" O PRO A 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 170 through 174' Processing helix chain 'A' and resid 180 through 193 removed outlier: 3.699A pdb=" N THR A 193 " --> pdb=" O MET A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 201 through 216 removed outlier: 3.940A pdb=" N GLU A 206 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A 213 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 232 removed outlier: 3.568A pdb=" N MET A 226 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.627A pdb=" N ARG A 255 " --> pdb=" O ASN A 251 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N CYS A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 256' Processing helix chain 'A' and resid 257 through 261 Processing helix chain 'A' and resid 262 through 267 Processing helix chain 'A' and resid 272 through 283 removed outlier: 3.691A pdb=" N THR A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 294 removed outlier: 3.655A pdb=" N ALA A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 305 removed outlier: 3.913A pdb=" N TYR A 305 " --> pdb=" O THR A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 320 removed outlier: 3.767A pdb=" N ARG A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 335 No H-bonds generated for 'chain 'A' and resid 333 through 335' Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 348 through 352 removed outlier: 3.597A pdb=" N PHE A 351 " --> pdb=" O LEU A 348 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN A 352 " --> pdb=" O SER A 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 348 through 352' Processing helix chain 'A' and resid 358 through 373 removed outlier: 3.678A pdb=" N ASP A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU A 363 " --> pdb=" O GLN A 359 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) Proline residue: A 366 - end of helix removed outlier: 4.374A pdb=" N VAL A 369 " --> pdb=" O GLY A 365 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N HIS A 370 " --> pdb=" O PRO A 366 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG A 371 " --> pdb=" O SER A 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 60 removed outlier: 3.621A pdb=" N GLN B 58 " --> pdb=" O GLY B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.685A pdb=" N LYS B 83 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP B 85 " --> pdb=" O MET B 81 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR B 90 " --> pdb=" O HIS B 86 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU B 92 " --> pdb=" O THR B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 125 removed outlier: 3.746A pdb=" N LYS B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 145 removed outlier: 3.704A pdb=" N LEU B 141 " --> pdb=" O ALA B 137 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR B 142 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.574A pdb=" N ALA B 173 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE B 174 " --> pdb=" O PRO B 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 170 through 174' Processing helix chain 'B' and resid 180 through 193 removed outlier: 3.699A pdb=" N THR B 193 " --> pdb=" O MET B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 201 through 216 removed outlier: 3.939A pdb=" N GLU B 206 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU B 213 " --> pdb=" O ARG B 209 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS B 214 " --> pdb=" O ASP B 210 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 232 removed outlier: 3.569A pdb=" N MET B 226 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA B 227 " --> pdb=" O GLU B 223 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 256 removed outlier: 3.627A pdb=" N ARG B 255 " --> pdb=" O ASN B 251 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N CYS B 256 " --> pdb=" O GLU B 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 251 through 256' Processing helix chain 'B' and resid 257 through 261 Processing helix chain 'B' and resid 262 through 267 Processing helix chain 'B' and resid 272 through 283 removed outlier: 3.691A pdb=" N THR B 277 " --> pdb=" O ILE B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 294 removed outlier: 3.655A pdb=" N ALA B 294 " --> pdb=" O LYS B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 305 removed outlier: 3.913A pdb=" N TYR B 305 " --> pdb=" O THR B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 320 removed outlier: 3.767A pdb=" N ARG B 311 " --> pdb=" O GLY B 307 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 319 " --> pdb=" O GLU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 335 No H-bonds generated for 'chain 'B' and resid 333 through 335' Processing helix chain 'B' and resid 336 through 347 Processing helix chain 'B' and resid 348 through 352 removed outlier: 3.597A pdb=" N PHE B 351 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN B 352 " --> pdb=" O SER B 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 348 through 352' Processing helix chain 'B' and resid 358 through 373 removed outlier: 3.679A pdb=" N ASP B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU B 363 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER B 364 " --> pdb=" O GLU B 360 " (cutoff:3.500A) Proline residue: B 366 - end of helix removed outlier: 4.374A pdb=" N VAL B 369 " --> pdb=" O GLY B 365 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N HIS B 370 " --> pdb=" O PRO B 366 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG B 371 " --> pdb=" O SER B 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 60 removed outlier: 3.622A pdb=" N GLN C 58 " --> pdb=" O GLY C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.684A pdb=" N LYS C 83 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP C 85 " --> pdb=" O MET C 81 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR C 90 " --> pdb=" O HIS C 86 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU C 92 " --> pdb=" O THR C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 125 removed outlier: 3.746A pdb=" N LYS C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 145 removed outlier: 3.704A pdb=" N LEU C 141 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR C 142 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA C 143 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 174 removed outlier: 3.574A pdb=" N ALA C 173 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE C 174 " --> pdb=" O PRO C 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 170 through 174' Processing helix chain 'C' and resid 180 through 193 removed outlier: 3.699A pdb=" N THR C 193 " --> pdb=" O MET C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 201 through 216 removed outlier: 3.940A pdb=" N GLU C 206 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU C 213 " --> pdb=" O ARG C 209 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS C 214 " --> pdb=" O ASP C 210 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 232 removed outlier: 3.569A pdb=" N MET C 226 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER C 231 " --> pdb=" O ALA C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 256 removed outlier: 3.626A pdb=" N ARG C 255 " --> pdb=" O ASN C 251 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N CYS C 256 " --> pdb=" O GLU C 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 251 through 256' Processing helix chain 'C' and resid 257 through 261 Processing helix chain 'C' and resid 262 through 267 Processing helix chain 'C' and resid 272 through 283 removed outlier: 3.690A pdb=" N THR C 277 " --> pdb=" O ILE C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 294 removed outlier: 3.655A pdb=" N ALA C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 305 removed outlier: 3.912A pdb=" N TYR C 305 " --> pdb=" O THR C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 320 removed outlier: 3.766A pdb=" N ARG C 311 " --> pdb=" O GLY C 307 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C 319 " --> pdb=" O GLU C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 335 No H-bonds generated for 'chain 'C' and resid 333 through 335' Processing helix chain 'C' and resid 336 through 347 Processing helix chain 'C' and resid 348 through 352 removed outlier: 3.597A pdb=" N PHE C 351 " --> pdb=" O LEU C 348 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN C 352 " --> pdb=" O SER C 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 348 through 352' Processing helix chain 'C' and resid 358 through 373 removed outlier: 3.678A pdb=" N ASP C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU C 363 " --> pdb=" O GLN C 359 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER C 364 " --> pdb=" O GLU C 360 " (cutoff:3.500A) Proline residue: C 366 - end of helix removed outlier: 4.374A pdb=" N VAL C 369 " --> pdb=" O GLY C 365 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N HIS C 370 " --> pdb=" O PRO C 366 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG C 371 " --> pdb=" O SER C 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 60 removed outlier: 3.622A pdb=" N GLN D 58 " --> pdb=" O GLY D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.684A pdb=" N LYS D 83 " --> pdb=" O ASP D 79 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP D 85 " --> pdb=" O MET D 81 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR D 90 " --> pdb=" O HIS D 86 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU D 92 " --> pdb=" O THR D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 125 removed outlier: 3.746A pdb=" N LYS D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 145 removed outlier: 3.704A pdb=" N LEU D 141 " --> pdb=" O ALA D 137 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR D 142 " --> pdb=" O VAL D 138 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 174 removed outlier: 3.574A pdb=" N ALA D 173 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE D 174 " --> pdb=" O PRO D 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 170 through 174' Processing helix chain 'D' and resid 180 through 193 removed outlier: 3.699A pdb=" N THR D 193 " --> pdb=" O MET D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 201 through 216 removed outlier: 3.940A pdb=" N GLU D 206 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE D 207 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU D 213 " --> pdb=" O ARG D 209 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS D 214 " --> pdb=" O ASP D 210 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 232 removed outlier: 3.570A pdb=" N MET D 226 " --> pdb=" O PHE D 222 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER D 231 " --> pdb=" O ALA D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 256 removed outlier: 3.627A pdb=" N ARG D 255 " --> pdb=" O ASN D 251 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N CYS D 256 " --> pdb=" O GLU D 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 251 through 256' Processing helix chain 'D' and resid 257 through 261 Processing helix chain 'D' and resid 262 through 267 Processing helix chain 'D' and resid 272 through 283 removed outlier: 3.691A pdb=" N THR D 277 " --> pdb=" O ILE D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 294 removed outlier: 3.656A pdb=" N ALA D 294 " --> pdb=" O LYS D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 305 removed outlier: 3.912A pdb=" N TYR D 305 " --> pdb=" O THR D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 320 removed outlier: 3.767A pdb=" N ARG D 311 " --> pdb=" O GLY D 307 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU D 319 " --> pdb=" O GLU D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 335 No H-bonds generated for 'chain 'D' and resid 333 through 335' Processing helix chain 'D' and resid 336 through 347 Processing helix chain 'D' and resid 348 through 352 removed outlier: 3.597A pdb=" N PHE D 351 " --> pdb=" O LEU D 348 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN D 352 " --> pdb=" O SER D 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 348 through 352' Processing helix chain 'D' and resid 358 through 373 removed outlier: 3.678A pdb=" N ASP D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU D 363 " --> pdb=" O GLN D 359 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER D 364 " --> pdb=" O GLU D 360 " (cutoff:3.500A) Proline residue: D 366 - end of helix removed outlier: 4.374A pdb=" N VAL D 369 " --> pdb=" O GLY D 365 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N HIS D 370 " --> pdb=" O PRO D 366 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG D 371 " --> pdb=" O SER D 367 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.998A pdb=" N THR A 105 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET A 131 " --> pdb=" O ILE A 356 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 53 removed outlier: 3.584A pdb=" N ARG A 36 " --> pdb=" O THR A 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 70 through 71 Processing sheet with id=AA4, first strand: chain 'A' and resid 175 through 177 removed outlier: 3.563A pdb=" N LEU A 175 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR A 161 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 162 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 151 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 164 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 154 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N THR A 296 " --> pdb=" O ILE A 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 237 through 240 removed outlier: 3.639A pdb=" N LYS A 237 " --> pdb=" O ILE A 249 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.998A pdb=" N THR B 105 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET B 131 " --> pdb=" O ILE B 356 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 52 through 53 removed outlier: 3.585A pdb=" N ARG B 36 " --> pdb=" O THR B 65 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AA9, first strand: chain 'B' and resid 175 through 177 removed outlier: 3.563A pdb=" N LEU B 175 " --> pdb=" O THR B 161 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR B 161 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 162 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL B 151 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 164 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER B 154 " --> pdb=" O SER B 299 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N THR B 296 " --> pdb=" O ILE B 329 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 237 through 240 removed outlier: 3.638A pdb=" N LYS B 237 " --> pdb=" O ILE B 249 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.998A pdb=" N THR C 105 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET C 131 " --> pdb=" O ILE C 356 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 52 through 53 removed outlier: 3.585A pdb=" N ARG C 36 " --> pdb=" O THR C 65 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 70 through 71 Processing sheet with id=AB5, first strand: chain 'C' and resid 175 through 177 removed outlier: 3.563A pdb=" N LEU C 175 " --> pdb=" O THR C 161 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR C 161 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 162 " --> pdb=" O VAL C 151 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL C 151 " --> pdb=" O VAL C 162 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE C 164 " --> pdb=" O GLY C 149 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER C 154 " --> pdb=" O SER C 299 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N THR C 296 " --> pdb=" O ILE C 329 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 237 through 240 removed outlier: 3.639A pdb=" N LYS C 237 " --> pdb=" O ILE C 249 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 28 through 31 removed outlier: 4.031A pdb=" N THR D 105 " --> pdb=" O ILE D 9 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET D 131 " --> pdb=" O ILE D 356 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 52 through 53 removed outlier: 3.585A pdb=" N ARG D 36 " --> pdb=" O THR D 65 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 70 through 71 Processing sheet with id=AC1, first strand: chain 'D' and resid 175 through 177 removed outlier: 3.563A pdb=" N LEU D 175 " --> pdb=" O THR D 161 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR D 161 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL D 162 " --> pdb=" O VAL D 151 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL D 151 " --> pdb=" O VAL D 162 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE D 164 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER D 154 " --> pdb=" O SER D 299 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N THR D 296 " --> pdb=" O ILE D 329 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 237 through 240 removed outlier: 3.638A pdb=" N LYS D 237 " --> pdb=" O ILE D 249 " (cutoff:3.500A) 434 hydrogen bonds defined for protein. 1122 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.62 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1977 1.31 - 1.44: 3135 1.44 - 1.56: 6792 1.56 - 1.68: 12 1.68 - 1.81: 152 Bond restraints: 12068 Sorted by residual: bond pdb=" C HIC C 72 " pdb=" O HIC C 72 " ideal model delta sigma weight residual 1.231 1.359 -0.128 2.00e-02 2.50e+03 4.07e+01 bond pdb=" C HIC A 72 " pdb=" O HIC A 72 " ideal model delta sigma weight residual 1.231 1.358 -0.127 2.00e-02 2.50e+03 4.05e+01 bond pdb=" C HIC D 72 " pdb=" O HIC D 72 " ideal model delta sigma weight residual 1.231 1.358 -0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" C HIC B 72 " pdb=" O HIC B 72 " ideal model delta sigma weight residual 1.231 1.358 -0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" C4 ADP A 401 " pdb=" C5 ADP A 401 " ideal model delta sigma weight residual 1.490 1.377 0.113 2.00e-02 2.50e+03 3.17e+01 ... (remaining 12063 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 15930 1.85 - 3.71: 352 3.71 - 5.56: 60 5.56 - 7.41: 16 7.41 - 9.26: 10 Bond angle restraints: 16368 Sorted by residual: angle pdb=" CA HIC C 72 " pdb=" C HIC C 72 " pdb=" O HIC C 72 " ideal model delta sigma weight residual 120.80 113.59 7.21 1.70e+00 3.46e-01 1.80e+01 angle pdb=" CA HIC D 72 " pdb=" C HIC D 72 " pdb=" O HIC D 72 " ideal model delta sigma weight residual 120.80 113.59 7.21 1.70e+00 3.46e-01 1.80e+01 angle pdb=" CA HIC B 72 " pdb=" C HIC B 72 " pdb=" O HIC B 72 " ideal model delta sigma weight residual 120.80 113.64 7.16 1.70e+00 3.46e-01 1.77e+01 angle pdb=" CA HIC A 72 " pdb=" C HIC A 72 " pdb=" O HIC A 72 " ideal model delta sigma weight residual 120.80 113.64 7.16 1.70e+00 3.46e-01 1.77e+01 angle pdb=" C GLU D 3 " pdb=" N ILE D 4 " pdb=" CA ILE D 4 " ideal model delta sigma weight residual 122.93 118.41 4.52 1.31e+00 5.83e-01 1.19e+01 ... (remaining 16363 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 7043 35.96 - 71.92: 215 71.92 - 107.89: 8 107.89 - 143.85: 1 143.85 - 179.81: 1 Dihedral angle restraints: 7268 sinusoidal: 2948 harmonic: 4320 Sorted by residual: dihedral pdb=" CH3 ACE A 0 " pdb=" C ACE A 0 " pdb=" N GLU A 1 " pdb=" CA GLU A 1 " ideal model delta sinusoidal sigma weight residual -180.00 -0.19 -179.81 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" CH3 ACE B 0 " pdb=" C ACE B 0 " pdb=" N GLU B 1 " pdb=" CA GLU B 1 " ideal model delta sinusoidal sigma weight residual 180.00 94.37 85.63 1 5.00e+00 4.00e-02 3.55e+02 dihedral pdb=" CH3 ACE D 0 " pdb=" C ACE D 0 " pdb=" N GLU D 1 " pdb=" CA GLU D 1 " ideal model delta sinusoidal sigma weight residual 180.00 139.62 40.38 1 5.00e+00 4.00e-02 9.15e+01 ... (remaining 7265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1397 0.048 - 0.095: 304 0.095 - 0.143: 102 0.143 - 0.190: 7 0.190 - 0.238: 2 Chirality restraints: 1812 Sorted by residual: chirality pdb=" CA GLU D 3 " pdb=" N GLU D 3 " pdb=" C GLU D 3 " pdb=" CB GLU D 3 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA ILE C 4 " pdb=" N ILE C 4 " pdb=" C ILE C 4 " pdb=" CB ILE C 4 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA VAL D 8 " pdb=" N VAL D 8 " pdb=" C VAL D 8 " pdb=" CB VAL D 8 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.00e-01 ... (remaining 1809 not shown) Planarity restraints: 2096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ACE B 0 " 0.064 2.00e-02 2.50e+03 2.81e-01 9.85e+02 pdb=" O ACE B 0 " -0.139 2.00e-02 2.50e+03 pdb=" CH3 ACE B 0 " -0.105 2.00e-02 2.50e+03 pdb=" N GLU B 1 " 0.504 2.00e-02 2.50e+03 pdb=" CA GLU B 1 " -0.324 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE D 0 " 0.139 2.00e-02 2.50e+03 2.00e-01 4.98e+02 pdb=" O ACE D 0 " 0.019 2.00e-02 2.50e+03 pdb=" CH3 ACE D 0 " -0.197 2.00e-02 2.50e+03 pdb=" N GLU D 1 " 0.284 2.00e-02 2.50e+03 pdb=" CA GLU D 1 " -0.245 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE C 0 " -0.038 2.00e-02 2.50e+03 9.25e-02 1.07e+02 pdb=" O ACE C 0 " -0.024 2.00e-02 2.50e+03 pdb=" CH3 ACE C 0 " 0.088 2.00e-02 2.50e+03 pdb=" N GLU C 1 " -0.141 2.00e-02 2.50e+03 pdb=" CA GLU C 1 " 0.115 2.00e-02 2.50e+03 ... (remaining 2093 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2948 2.79 - 3.32: 9710 3.32 - 3.85: 16516 3.85 - 4.37: 19185 4.37 - 4.90: 35150 Nonbonded interactions: 83509 Sorted by model distance: nonbonded pdb="MG MG B 400 " pdb=" O1B ADP B 401 " model vdw 2.266 2.170 nonbonded pdb="MG MG A 400 " pdb=" O1B ADP A 401 " model vdw 2.293 2.170 nonbonded pdb=" N GLU C 363 " pdb=" OE1 GLU C 363 " model vdw 2.391 3.120 nonbonded pdb=" N GLU D 363 " pdb=" OE1 GLU D 363 " model vdw 2.391 3.120 nonbonded pdb=" N GLU B 363 " pdb=" OE1 GLU B 363 " model vdw 2.392 3.120 ... (remaining 83504 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 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: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.170 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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 : 0.005 0.128 12068 Z= 0.240 Angle : 0.684 9.264 16368 Z= 0.358 Chirality : 0.044 0.238 1812 Planarity : 0.010 0.281 2096 Dihedral : 15.956 179.812 4500 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.79 % Allowed : 19.78 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.20), residues: 1476 helix: -0.63 (0.22), residues: 460 sheet: -0.25 (0.36), residues: 204 loop : -0.45 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 205 TYR 0.011 0.001 TYR D 305 PHE 0.004 0.001 PHE D 254 TRP 0.006 0.001 TRP C 85 HIS 0.002 0.000 HIS D 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.24 (12068) covalent geometry : angle 0.68358 / 0.36 (16368) hydrogen bonds : bond 0.34829 / 23.48 ( 434) hydrogen bonds : angle 8.25861 / 5.98 ( 1122) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 216 time to evaluate : 0.394 Fit side-chains REVERT: B 71 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7162 (pt0) REVERT: C 71 GLU cc_start: 0.7501 (mt-10) cc_final: 0.6690 (pp20) REVERT: C 326 ILE cc_start: 0.8850 (mm) cc_final: 0.8592 (mm) REVERT: C 360 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7485 (mt-10) REVERT: D 67 LYS cc_start: 0.7951 (mtpt) cc_final: 0.7449 (mtpp) REVERT: D 79 ASP cc_start: 0.7607 (m-30) cc_final: 0.7057 (t0) REVERT: D 140 SER cc_start: 0.9266 (t) cc_final: 0.9058 (m) REVERT: D 189 MET cc_start: 0.7928 (mtp) cc_final: 0.7712 (mtp) REVERT: D 201 THR cc_start: 0.7078 (m) cc_final: 0.6785 (t) REVERT: D 282 MET cc_start: 0.8464 (mmt) cc_final: 0.7985 (mpp) outliers start: 10 outliers final: 0 residues processed: 222 average time/residue: 0.0917 time to fit residues: 29.5321 Evaluate side-chains 140 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 ASN A 160 HIS A 353 GLN A 370 HIS B 11 ASN B 160 HIS C 11 ASN C 160 HIS D 86 HIS D 160 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.126925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.104129 restraints weight = 16605.629| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 3.08 r_work: 0.3087 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12068 Z= 0.208 Angle : 0.682 8.621 16368 Z= 0.340 Chirality : 0.047 0.162 1812 Planarity : 0.004 0.030 2096 Dihedral : 7.881 179.407 1684 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.40 % Allowed : 17.41 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.21), residues: 1476 helix: -0.41 (0.23), residues: 528 sheet: -0.08 (0.30), residues: 276 loop : -0.65 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 115 TYR 0.014 0.002 TYR B 132 PHE 0.010 0.001 PHE B 254 TRP 0.011 0.001 TRP A 355 HIS 0.006 0.001 HIS D 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.21 (12068) covalent geometry : angle 0.68160 / 0.34 (16368) hydrogen bonds : bond 0.06101 / 4.17 ( 434) hydrogen bonds : angle 5.67862 / 3.99 ( 1122) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 129 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 112 LYS cc_start: 0.7751 (pttt) cc_final: 0.7409 (ptpt) REVERT: B 13 SER cc_start: 0.7517 (OUTLIER) cc_final: 0.7131 (p) REVERT: B 81 MET cc_start: 0.7529 (tpt) cc_final: 0.7269 (tpt) REVERT: B 112 LYS cc_start: 0.7673 (pttt) cc_final: 0.7362 (pttp) REVERT: B 166 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7094 (tm-30) REVERT: B 204 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6933 (mt-10) REVERT: C 71 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7147 (mt-10) REVERT: C 282 MET cc_start: 0.7931 (mmt) cc_final: 0.7464 (tpp) REVERT: C 352 GLN cc_start: 0.7462 (mm-40) cc_final: 0.7206 (mm-40) REVERT: C 360 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7530 (mt-10) REVERT: D 226 MET cc_start: 0.7270 (mmm) cc_final: 0.7045 (mmm) REVERT: D 282 MET cc_start: 0.7408 (mmt) cc_final: 0.6713 (mpp) outliers start: 43 outliers final: 23 residues processed: 155 average time/residue: 0.0783 time to fit residues: 19.0368 Evaluate side-chains 147 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 194 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 33 optimal weight: 0.0670 chunk 98 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 76 optimal weight: 0.0030 chunk 77 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.2132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 ASN B 11 ASN C 370 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.129377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.106483 restraints weight = 16673.372| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 3.10 r_work: 0.3116 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12068 Z= 0.111 Angle : 0.553 6.231 16368 Z= 0.269 Chirality : 0.043 0.127 1812 Planarity : 0.003 0.029 2096 Dihedral : 7.491 179.988 1684 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.82 % Allowed : 19.46 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.22), residues: 1476 helix: -0.10 (0.23), residues: 544 sheet: 0.16 (0.31), residues: 268 loop : -0.65 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 205 TYR 0.008 0.001 TYR B 239 PHE 0.005 0.001 PHE B 254 TRP 0.006 0.001 TRP A 355 HIS 0.002 0.001 HIS A 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (12068) covalent geometry : angle 0.55290 / 0.27 (16368) hydrogen bonds : bond 0.04642 / 3.13 ( 434) hydrogen bonds : angle 5.10273 / 3.60 ( 1122) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.423 Fit side-chains REVERT: A 112 LYS cc_start: 0.7526 (pttt) cc_final: 0.7322 (ptpt) REVERT: B 112 LYS cc_start: 0.7458 (pttt) cc_final: 0.7248 (pttp) REVERT: B 166 GLU cc_start: 0.7491 (tm-30) cc_final: 0.7250 (tm-30) REVERT: B 204 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6706 (mt-10) REVERT: C 282 MET cc_start: 0.7958 (mmt) cc_final: 0.7566 (tpp) REVERT: C 360 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7597 (mt-10) REVERT: D 282 MET cc_start: 0.7410 (mmt) cc_final: 0.6755 (mpp) REVERT: D 315 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7944 (mm-30) outliers start: 23 outliers final: 13 residues processed: 145 average time/residue: 0.0728 time to fit residues: 16.8798 Evaluate side-chains 131 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASN Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 179 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 111 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 139 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 147 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 144 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 ASN B 11 ASN C 11 ASN D 86 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.125488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.102699 restraints weight = 16728.796| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 3.10 r_work: 0.3071 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12068 Z= 0.160 Angle : 0.585 6.583 16368 Z= 0.287 Chirality : 0.045 0.142 1812 Planarity : 0.004 0.030 2096 Dihedral : 7.464 179.526 1684 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.09 % Allowed : 18.12 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.22), residues: 1476 helix: -0.00 (0.24), residues: 540 sheet: 0.09 (0.31), residues: 276 loop : -0.77 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 195 TYR 0.010 0.001 TYR B 239 PHE 0.008 0.001 PHE B 254 TRP 0.009 0.001 TRP A 355 HIS 0.007 0.001 HIS D 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 (12068) covalent geometry : angle 0.58543 / 0.29 (16368) hydrogen bonds : bond 0.05011 / 3.39 ( 434) hydrogen bonds : angle 5.05217 / 3.56 ( 1122) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 0.422 Fit side-chains REVERT: B 122 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7504 (tpp) REVERT: B 166 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7231 (tm-30) REVERT: B 204 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6695 (mt-10) REVERT: C 282 MET cc_start: 0.7811 (mmt) cc_final: 0.7535 (tpp) REVERT: C 360 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7637 (mt-10) REVERT: D 282 MET cc_start: 0.7473 (mmt) cc_final: 0.7270 (tpp) outliers start: 39 outliers final: 27 residues processed: 141 average time/residue: 0.0681 time to fit residues: 15.4878 Evaluate side-chains 138 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 367 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 23 optimal weight: 9.9990 chunk 76 optimal weight: 0.0170 chunk 92 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 104 optimal weight: 6.9990 chunk 41 optimal weight: 0.0470 overall best weight: 1.1520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 ASN C 11 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.127759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.104885 restraints weight = 16636.740| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.10 r_work: 0.3104 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12068 Z= 0.100 Angle : 0.534 6.252 16368 Z= 0.257 Chirality : 0.043 0.130 1812 Planarity : 0.003 0.032 2096 Dihedral : 7.270 179.877 1684 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.69 % Allowed : 19.46 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.22), residues: 1476 helix: 0.12 (0.24), residues: 544 sheet: 0.41 (0.32), residues: 260 loop : -0.70 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 205 TYR 0.007 0.001 TYR B 239 PHE 0.006 0.001 PHE C 30 TRP 0.006 0.001 TRP A 355 HIS 0.002 0.001 HIS A 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (12068) covalent geometry : angle 0.53353 / 0.26 (16368) hydrogen bonds : bond 0.03893 / 2.62 ( 434) hydrogen bonds : angle 4.79693 / 3.38 ( 1122) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 0.326 Fit side-chains REVERT: A 224 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.6622 (mp10) REVERT: B 13 SER cc_start: 0.7676 (OUTLIER) cc_final: 0.7378 (p) REVERT: B 122 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7549 (tpp) REVERT: B 166 GLU cc_start: 0.7555 (tm-30) cc_final: 0.7202 (tm-30) REVERT: B 204 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6631 (mt-10) REVERT: C 106 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.6835 (tm-30) REVERT: C 282 MET cc_start: 0.7829 (mmt) cc_final: 0.7527 (tpp) REVERT: C 333 GLU cc_start: 0.6902 (pm20) cc_final: 0.6311 (pm20) REVERT: C 360 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7690 (mt-10) REVERT: D 282 MET cc_start: 0.7426 (mmt) cc_final: 0.7219 (tpp) outliers start: 34 outliers final: 21 residues processed: 132 average time/residue: 0.0706 time to fit residues: 14.9840 Evaluate side-chains 132 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASN Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 211 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 46 optimal weight: 0.0980 chunk 83 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 89 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 ASN B 11 ASN C 11 ASN C 91 ASN D 370 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.133231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.112642 restraints weight = 17009.563| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.62 r_work: 0.3198 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12068 Z= 0.098 Angle : 0.522 6.228 16368 Z= 0.250 Chirality : 0.043 0.129 1812 Planarity : 0.003 0.033 2096 Dihedral : 7.164 179.828 1684 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.85 % Allowed : 19.54 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.22), residues: 1476 helix: 0.28 (0.24), residues: 536 sheet: 0.43 (0.32), residues: 272 loop : -0.77 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 61 TYR 0.007 0.001 TYR B 239 PHE 0.006 0.001 PHE C 30 TRP 0.006 0.001 TRP A 355 HIS 0.002 0.001 HIS A 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (12068) covalent geometry : angle 0.52186 / 0.25 (16368) hydrogen bonds : bond 0.03684 / 2.47 ( 434) hydrogen bonds : angle 4.69157 / 3.31 ( 1122) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 0.480 Fit side-chains REVERT: A 224 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7327 (mp10) REVERT: B 13 SER cc_start: 0.8036 (OUTLIER) cc_final: 0.7746 (p) REVERT: B 122 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7685 (tpp) REVERT: B 166 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7185 (tm-30) REVERT: B 204 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7173 (mt-10) REVERT: C 106 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7150 (tm-30) REVERT: C 333 GLU cc_start: 0.7049 (pm20) cc_final: 0.6452 (pm20) REVERT: C 360 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7974 (mt-10) outliers start: 36 outliers final: 28 residues processed: 143 average time/residue: 0.0752 time to fit residues: 17.0518 Evaluate side-chains 139 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 211 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 80 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 chunk 116 optimal weight: 0.7980 chunk 101 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 11 ASN ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 ASN C 91 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.121674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.098832 restraints weight = 16922.396| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.10 r_work: 0.3017 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 12068 Z= 0.226 Angle : 0.663 9.387 16368 Z= 0.327 Chirality : 0.048 0.159 1812 Planarity : 0.004 0.038 2096 Dihedral : 7.419 179.191 1684 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.40 % Allowed : 19.78 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.22), residues: 1476 helix: -0.05 (0.24), residues: 540 sheet: 0.27 (0.32), residues: 268 loop : -1.02 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 255 TYR 0.016 0.002 TYR B 132 PHE 0.012 0.002 PHE D 278 TRP 0.010 0.002 TRP A 355 HIS 0.005 0.001 HIS A 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.23 (12068) covalent geometry : angle 0.66324 / 0.33 (16368) hydrogen bonds : bond 0.05961 / 4.02 ( 434) hydrogen bonds : angle 5.16597 / 3.63 ( 1122) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 115 time to evaluate : 0.419 Fit side-chains REVERT: A 166 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7407 (tm-30) REVERT: B 112 LYS cc_start: 0.7939 (pttt) cc_final: 0.7489 (ptpt) REVERT: B 122 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7468 (tpp) REVERT: B 166 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7251 (tm-30) REVERT: B 204 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6861 (mt-10) REVERT: B 353 GLN cc_start: 0.8506 (tm-30) cc_final: 0.8064 (tm-30) REVERT: C 71 GLU cc_start: 0.7496 (mt-10) cc_final: 0.6966 (pm20) REVERT: C 106 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.6941 (tm-30) REVERT: C 204 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7124 (mt-10) REVERT: C 360 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7631 (mt-10) REVERT: D 282 MET cc_start: 0.7121 (tpp) cc_final: 0.6814 (mpp) outliers start: 43 outliers final: 31 residues processed: 146 average time/residue: 0.0639 time to fit residues: 15.0898 Evaluate side-chains 145 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 110 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 367 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 66 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 11 ASN C 11 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.124850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.101938 restraints weight = 16648.275| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.10 r_work: 0.3053 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12068 Z= 0.136 Angle : 0.565 8.189 16368 Z= 0.274 Chirality : 0.044 0.135 1812 Planarity : 0.003 0.045 2096 Dihedral : 7.282 179.649 1684 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.16 % Allowed : 19.94 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.22), residues: 1476 helix: 0.06 (0.24), residues: 540 sheet: 0.32 (0.33), residues: 264 loop : -0.95 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 255 TYR 0.008 0.001 TYR B 239 PHE 0.009 0.001 PHE C 278 TRP 0.008 0.001 TRP A 355 HIS 0.003 0.001 HIS A 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (12068) covalent geometry : angle 0.56471 / 0.27 (16368) hydrogen bonds : bond 0.04453 / 3.00 ( 434) hydrogen bonds : angle 4.91575 / 3.47 ( 1122) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 114 time to evaluate : 0.347 Fit side-chains REVERT: A 166 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7431 (tm-30) REVERT: A 224 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.6712 (mp10) REVERT: B 112 LYS cc_start: 0.7858 (pttt) cc_final: 0.7402 (ptpt) REVERT: B 122 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7513 (tpp) REVERT: B 166 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7235 (tm-30) REVERT: B 204 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6729 (mt-10) REVERT: B 353 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8056 (tm-30) REVERT: C 71 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7175 (pm20) REVERT: C 106 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.6921 (tm-30) REVERT: C 210 ASP cc_start: 0.8448 (t0) cc_final: 0.8028 (t0) REVERT: C 333 GLU cc_start: 0.6983 (pm20) cc_final: 0.6439 (pm20) REVERT: C 360 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7613 (mt-10) REVERT: D 282 MET cc_start: 0.7162 (tpp) cc_final: 0.6757 (tpp) outliers start: 40 outliers final: 32 residues processed: 144 average time/residue: 0.0679 time to fit residues: 15.7479 Evaluate side-chains 148 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 287 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 115 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 49 optimal weight: 0.0020 chunk 50 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 overall best weight: 1.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 11 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.130951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.110469 restraints weight = 17099.709| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.63 r_work: 0.3170 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12068 Z= 0.122 Angle : 0.545 8.001 16368 Z= 0.261 Chirality : 0.044 0.129 1812 Planarity : 0.003 0.042 2096 Dihedral : 7.111 179.658 1684 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.09 % Allowed : 19.94 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.22), residues: 1476 helix: 0.18 (0.24), residues: 536 sheet: 0.65 (0.32), residues: 292 loop : -1.03 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 255 TYR 0.008 0.001 TYR B 239 PHE 0.007 0.001 PHE B 30 TRP 0.007 0.001 TRP B 355 HIS 0.003 0.001 HIS D 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (12068) covalent geometry : angle 0.54522 / 0.26 (16368) hydrogen bonds : bond 0.03989 / 2.68 ( 434) hydrogen bonds : angle 4.76415 / 3.36 ( 1122) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 115 time to evaluate : 0.355 Fit side-chains REVERT: A 166 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7643 (tm-30) REVERT: A 224 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7307 (mp10) REVERT: B 112 LYS cc_start: 0.8151 (pttt) cc_final: 0.7833 (ptpt) REVERT: B 122 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7902 (tpp) REVERT: B 166 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7429 (tm-30) REVERT: B 204 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7469 (mt-10) REVERT: B 353 GLN cc_start: 0.8479 (tm-30) cc_final: 0.8138 (tm-30) REVERT: C 71 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7840 (pm20) REVERT: C 106 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7341 (tm-30) REVERT: C 210 ASP cc_start: 0.9080 (t0) cc_final: 0.8602 (t0) REVERT: C 251 ASN cc_start: 0.9052 (p0) cc_final: 0.8821 (p0) REVERT: C 333 GLU cc_start: 0.7363 (pm20) cc_final: 0.6810 (pm20) REVERT: C 360 GLU cc_start: 0.8278 (mm-30) cc_final: 0.8002 (mt-10) REVERT: D 279 ASN cc_start: 0.8699 (m-40) cc_final: 0.8480 (m-40) REVERT: D 282 MET cc_start: 0.7914 (tpp) cc_final: 0.7620 (mpp) outliers start: 39 outliers final: 33 residues processed: 146 average time/residue: 0.0706 time to fit residues: 16.5897 Evaluate side-chains 148 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 111 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 367 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 82 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 137 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 125 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 11 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.129772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.109359 restraints weight = 17267.246| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.63 r_work: 0.3165 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12068 Z= 0.138 Angle : 0.561 7.903 16368 Z= 0.270 Chirality : 0.044 0.152 1812 Planarity : 0.003 0.047 2096 Dihedral : 7.114 179.734 1684 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.24 % Allowed : 19.94 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.22), residues: 1476 helix: 0.19 (0.24), residues: 532 sheet: 0.53 (0.31), residues: 300 loop : -1.06 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 255 TYR 0.009 0.001 TYR B 239 PHE 0.010 0.001 PHE A 278 TRP 0.008 0.001 TRP C 355 HIS 0.003 0.001 HIS A 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (12068) covalent geometry : angle 0.56136 / 0.27 (16368) hydrogen bonds : bond 0.04359 / 2.93 ( 434) hydrogen bonds : angle 4.80836 / 3.39 ( 1122) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 117 time to evaluate : 0.371 Fit side-chains REVERT: A 166 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7636 (tm-30) REVERT: A 224 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7356 (mp10) REVERT: A 282 MET cc_start: 0.8101 (tpp) cc_final: 0.7784 (mpp) REVERT: B 112 LYS cc_start: 0.8160 (pttt) cc_final: 0.7829 (ptpt) REVERT: B 122 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7888 (tpp) REVERT: B 166 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7447 (tm-30) REVERT: B 204 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7525 (mt-10) REVERT: B 353 GLN cc_start: 0.8496 (tm-30) cc_final: 0.8167 (tm-30) REVERT: C 71 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7903 (pm20) REVERT: C 106 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7375 (tm-30) REVERT: C 210 ASP cc_start: 0.9116 (t0) cc_final: 0.8635 (t0) REVERT: C 333 GLU cc_start: 0.7447 (pm20) cc_final: 0.6879 (pm20) REVERT: C 360 GLU cc_start: 0.8284 (mm-30) cc_final: 0.8011 (mt-10) REVERT: D 282 MET cc_start: 0.7982 (tpp) cc_final: 0.7681 (mpp) REVERT: D 359 GLN cc_start: 0.8389 (mm110) cc_final: 0.7731 (tp40) outliers start: 41 outliers final: 34 residues processed: 148 average time/residue: 0.0731 time to fit residues: 17.0969 Evaluate side-chains 149 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 111 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 367 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 86 optimal weight: 0.0980 chunk 50 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 116 optimal weight: 0.7980 chunk 137 optimal weight: 0.8980 chunk 134 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 ASN C 11 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.130375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.109961 restraints weight = 17162.481| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.61 r_work: 0.3167 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12068 Z= 0.126 Angle : 0.552 7.866 16368 Z= 0.265 Chirality : 0.044 0.136 1812 Planarity : 0.003 0.043 2096 Dihedral : 7.073 179.801 1684 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.40 % Allowed : 20.02 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.22), residues: 1476 helix: 0.19 (0.24), residues: 536 sheet: 0.73 (0.32), residues: 292 loop : -1.07 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 255 TYR 0.008 0.001 TYR B 239 PHE 0.015 0.001 PHE A 278 TRP 0.008 0.001 TRP C 355 HIS 0.003 0.001 HIS A 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (12068) covalent geometry : angle 0.55210 / 0.26 (16368) hydrogen bonds : bond 0.04099 / 2.74 ( 434) hydrogen bonds : angle 4.75739 / 3.35 ( 1122) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2022.57 seconds wall clock time: 35 minutes 30.07 seconds (2130.07 seconds total)