Starting phenix.real_space_refine on Sat Aug 23 12:19:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dnf_27565/08_2025/8dnf_27565.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dnf_27565/08_2025/8dnf_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 { model { file = "/net/cci-nas-00/data/ceres_data/8dnf_27565/08_2025/8dnf_27565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dnf_27565/08_2025/8dnf_27565.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dnf_27565/08_2025/8dnf_27565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dnf_27565/08_2025/8dnf_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-2.0-5787/lib/python3.9/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: 3.08, per 1000 atoms: 0.26 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: 0.86 Conformation dependent library (CDL) restraints added in 541.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.33 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: 1.40 Time building geometry restraints manager: 1.16 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 - 1.99: 15997 1.99 - 3.99: 295 3.99 - 5.98: 55 5.98 - 7.98: 13 7.98 - 9.97: 8 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.880 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 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 : 0.004 0.128 12068 Z= 0.238 Angle : 0.686 9.969 16368 Z= 0.359 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 aren 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 covalent geometry : bond 0.00449 (12068) covalent geometry : angle 0.68571 (16368) hydrogen bonds : bond 0.34829 ( 434) hydrogen bonds : angle 8.25861 ( 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 : 0.340 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: 0.1003 time to fit residues: 32.1558 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 : 0.473 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3500 r_free = 0.3500 target = 0.126924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.104156 restraints weight = 16601.650| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.06 r_work: 0.3089 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2310 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= 0.209 Angle : 0.684 8.590 16368 Z= 0.342 Chirality : 0.047 0.162 1812 Planarity : 0.004 0.030 2096 Dihedral : 7.889 179.379 1684 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.24 % Allowed : 17.56 % 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 aren not related in a simple way. whole: -0.74 (0.21), residues: 1476 helix: -0.36 (0.23), residues: 528 sheet: -0.07 (0.30), residues: 276 loop : -0.64 (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 0.010 0.001 TRP A 355 HIS 0.007 0.001 HIS D 86 Details of bonding type rmsd covalent geometry : bond 0.00498 (12068) covalent geometry : angle 0.68407 (16368) hydrogen bonds : bond 0.06257 ( 434) hydrogen bonds : angle 5.70921 ( 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 173 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 132 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: B 13 SER cc_start: 0.7490 (OUTLIER) cc_final: 0.7104 (p) REVERT: B 81 MET cc_start: 0.7564 (tpt) cc_final: 0.7325 (tpt) REVERT: B 112 LYS cc_start: 0.7664 (pttt) cc_final: 0.7364 (pttp) REVERT: B 166 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7098 (tm-30) REVERT: B 204 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6940 (mt-10) REVERT: C 71 GLU cc_start: 0.7327 (mt-10) cc_final: 0.7119 (mt-10) REVERT: C 282 MET cc_start: 0.7947 (mmt) cc_final: 0.7498 (tpp) REVERT: C 352 GLN cc_start: 0.7419 (mm-40) cc_final: 0.7156 (mm-40) REVERT: C 360 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7547 (mt-10) REVERT: D 226 MET cc_start: 0.7291 (mmm) cc_final: 0.7070 (mmm) REVERT: D 282 MET cc_start: 0.7420 (mmt) cc_final: 0.6740 (mpp) outliers start: 41 outliers final: 23 residues processed: 155 average time/residue: 0.0845 time to fit residues: 20.6385 Evaluate side-chains 148 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 98 optimal weight: 5.9990 chunk 146 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 chunk 76 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3519 r_free = 0.3519 target = 0.128588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.105702 restraints weight = 16707.715| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 3.11 r_work: 0.3111 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12068 Z= 0.118 Angle : 0.566 6.275 16368 Z= 0.277 Chirality : 0.043 0.128 1812 Planarity : 0.004 0.029 2096 Dihedral : 7.575 179.886 1684 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.98 % Allowed : 19.22 % 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 aren not related in a simple way. whole: -0.59 (0.21), residues: 1476 helix: -0.08 (0.23), residues: 540 sheet: -0.06 (0.31), residues: 272 loop : -0.66 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 205 TYR 0.008 0.001 TYR B 239 PHE 0.006 0.001 PHE B 254 TRP 0.006 0.001 TRP A 355 HIS 0.003 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00266 (12068) covalent geometry : angle 0.56648 (16368) hydrogen bonds : bond 0.04858 ( 434) hydrogen bonds : angle 5.17828 ( 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 158 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.373 Fit side-chains REVERT: B 166 GLU cc_start: 0.7532 (tm-30) cc_final: 0.7289 (tm-30) REVERT: B 204 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6748 (mt-10) REVERT: C 268 MET cc_start: 0.7996 (mtp) cc_final: 0.7748 (ptp) REVERT: C 282 MET cc_start: 0.7966 (mmt) cc_final: 0.7578 (tpp) REVERT: C 360 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7607 (mt-10) REVERT: D 282 MET cc_start: 0.7444 (mmt) cc_final: 0.6752 (mpp) outliers start: 25 outliers final: 12 residues processed: 147 average time/residue: 0.0839 time to fit residues: 19.5030 Evaluate side-chains 128 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 200 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 111 optimal weight: 9.9990 chunk 114 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 139 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 147 optimal weight: 0.0980 chunk 72 optimal weight: 7.9990 chunk 144 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN B 11 ASN C 11 ASN D 370 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.124477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.101712 restraints weight = 16779.370| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 3.07 r_work: 0.3057 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12068 Z= 0.166 Angle : 0.603 6.715 16368 Z= 0.297 Chirality : 0.045 0.148 1812 Planarity : 0.004 0.029 2096 Dihedral : 7.491 179.512 1684 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.32 % Allowed : 17.72 % Favored : 78.96 % 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 aren not related in a simple way. whole: -0.63 (0.22), residues: 1476 helix: -0.06 (0.24), residues: 540 sheet: 0.11 (0.31), residues: 276 loop : -0.84 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 255 TYR 0.011 0.001 TYR B 165 PHE 0.009 0.001 PHE B 254 TRP 0.009 0.001 TRP A 355 HIS 0.004 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00397 (12068) covalent geometry : angle 0.60251 (16368) hydrogen bonds : bond 0.05159 ( 434) hydrogen bonds : angle 5.06366 ( 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 164 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 122 time to evaluate : 0.334 Fit side-chains REVERT: A 224 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.6618 (mp10) REVERT: B 112 LYS cc_start: 0.7563 (pttp) cc_final: 0.7071 (ptpt) REVERT: B 166 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7263 (tm-30) REVERT: B 204 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6804 (mt-10) REVERT: C 191 ILE cc_start: 0.7439 (tt) cc_final: 0.7233 (tt) REVERT: C 282 MET cc_start: 0.7816 (mmt) cc_final: 0.7536 (tpp) REVERT: C 360 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7627 (mt-10) REVERT: D 282 MET cc_start: 0.7432 (mmt) cc_final: 0.7231 (tpp) outliers start: 42 outliers final: 30 residues processed: 150 average time/residue: 0.0824 time to fit residues: 19.5832 Evaluate side-chains 146 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 105 THR 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 33 ILE Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 105 THR 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 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 200 THR Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 322 SER 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 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: 6.9990 chunk 92 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 113 optimal weight: 0.3980 chunk 101 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.123259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.100495 restraints weight = 16836.405| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 3.08 r_work: 0.3039 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12068 Z= 0.200 Angle : 0.619 6.815 16368 Z= 0.306 Chirality : 0.046 0.143 1812 Planarity : 0.004 0.031 2096 Dihedral : 7.501 179.524 1684 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.64 % Allowed : 18.20 % Favored : 78.16 % 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 aren not related in a simple way. whole: -0.75 (0.21), residues: 1476 helix: -0.12 (0.23), residues: 540 sheet: 0.16 (0.32), residues: 268 loop : -1.01 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 255 TYR 0.012 0.001 TYR B 132 PHE 0.009 0.001 PHE B 254 TRP 0.010 0.001 TRP A 355 HIS 0.005 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00490 (12068) covalent geometry : angle 0.61939 (16368) hydrogen bonds : bond 0.05395 ( 434) hydrogen bonds : angle 5.12196 ( 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 161 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 115 time to evaluate : 0.491 Fit side-chains REVERT: A 224 GLN cc_start: 0.7341 (OUTLIER) cc_final: 0.6700 (mp10) REVERT: B 13 SER cc_start: 0.7765 (OUTLIER) cc_final: 0.7449 (p) REVERT: B 112 LYS cc_start: 0.7699 (pttp) cc_final: 0.7240 (ptpt) REVERT: B 166 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7269 (tm-30) REVERT: B 204 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6912 (mt-10) REVERT: C 106 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.6977 (tm-30) REVERT: C 191 ILE cc_start: 0.7580 (tt) cc_final: 0.7361 (tt) REVERT: C 204 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.7102 (mt-10) REVERT: C 282 MET cc_start: 0.7781 (mmt) cc_final: 0.7493 (tpp) REVERT: C 360 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7627 (mt-10) REVERT: D 282 MET cc_start: 0.7428 (mmt) cc_final: 0.7101 (tpp) outliers start: 46 outliers final: 36 residues processed: 149 average time/residue: 0.0777 time to fit residues: 18.5439 Evaluate side-chains 153 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 112 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 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 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 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 151 VAL Chi-restraints excluded: chain B residue 161 THR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 46 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 98 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 89 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN B 11 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.124442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.101525 restraints weight = 16691.059| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.11 r_work: 0.3049 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12068 Z= 0.155 Angle : 0.580 6.772 16368 Z= 0.283 Chirality : 0.045 0.135 1812 Planarity : 0.003 0.034 2096 Dihedral : 7.423 179.665 1684 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.09 % Allowed : 19.15 % Favored : 77.77 % 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 aren not related in a simple way. whole: -0.71 (0.22), residues: 1476 helix: 0.02 (0.24), residues: 532 sheet: 0.23 (0.31), residues: 300 loop : -1.16 (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 0.007 0.001 PHE B 30 TRP 0.008 0.001 TRP A 355 HIS 0.004 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00375 (12068) covalent geometry : angle 0.58009 (16368) hydrogen bonds : bond 0.04767 ( 434) hydrogen bonds : angle 4.97648 ( 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 156 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 0.472 Fit side-chains REVERT: A 224 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.6646 (mp10) REVERT: B 13 SER cc_start: 0.7843 (OUTLIER) cc_final: 0.7497 (p) REVERT: B 112 LYS cc_start: 0.7632 (pttp) cc_final: 0.7136 (ptpt) REVERT: B 122 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7500 (tpp) REVERT: B 166 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7210 (tm-30) REVERT: B 204 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6810 (mt-10) REVERT: C 106 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.6953 (tm-30) REVERT: C 191 ILE cc_start: 0.7519 (tt) cc_final: 0.7290 (tt) REVERT: C 210 ASP cc_start: 0.8450 (t0) cc_final: 0.8029 (t0) REVERT: C 282 MET cc_start: 0.7787 (mmt) cc_final: 0.7492 (tpp) REVERT: C 360 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7631 (mt-10) REVERT: D 282 MET cc_start: 0.7398 (mmt) cc_final: 0.7117 (tpp) outliers start: 39 outliers final: 31 residues processed: 145 average time/residue: 0.0812 time to fit residues: 18.8235 Evaluate side-chains 149 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 113 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 200 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 302 THR 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 131 MET Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 161 THR 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 80 optimal weight: 0.0020 chunk 140 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 147 optimal weight: 0.2980 chunk 24 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 overall best weight: 1.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.131341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.110891 restraints weight = 17071.811| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.61 r_work: 0.3180 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3474 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= 0.111 Angle : 0.537 6.305 16368 Z= 0.258 Chirality : 0.043 0.131 1812 Planarity : 0.003 0.033 2096 Dihedral : 7.191 179.878 1684 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.61 % Allowed : 19.62 % Favored : 77.77 % 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 aren not related in a simple way. whole: -0.52 (0.22), residues: 1476 helix: 0.16 (0.24), residues: 536 sheet: 0.38 (0.32), residues: 272 loop : -1.01 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 61 TYR 0.008 0.001 TYR D 305 PHE 0.007 0.001 PHE B 351 TRP 0.007 0.001 TRP C 355 HIS 0.003 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00262 (12068) covalent geometry : angle 0.53690 (16368) hydrogen bonds : bond 0.03862 ( 434) hydrogen bonds : angle 4.75227 ( 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 150 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 0.311 Fit side-chains REVERT: A 224 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7268 (mp10) REVERT: B 112 LYS cc_start: 0.7980 (pttp) cc_final: 0.7601 (ptpt) REVERT: B 122 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7914 (tpp) REVERT: B 166 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7416 (tm-30) REVERT: B 204 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7485 (mt-10) REVERT: B 353 GLN cc_start: 0.8502 (tm-30) cc_final: 0.8273 (tm-30) REVERT: C 106 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7392 (tm-30) REVERT: C 191 ILE cc_start: 0.8465 (tt) cc_final: 0.8219 (tt) REVERT: C 204 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7801 (mt-10) REVERT: C 210 ASP cc_start: 0.9072 (t0) cc_final: 0.8616 (t0) REVERT: C 251 ASN cc_start: 0.9033 (p0) cc_final: 0.8809 (p0) REVERT: C 282 MET cc_start: 0.8363 (mmt) cc_final: 0.8151 (tpp) REVERT: C 333 GLU cc_start: 0.7402 (pm20) cc_final: 0.6851 (pm20) REVERT: C 360 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7948 (mt-10) REVERT: D 282 MET cc_start: 0.7979 (mmt) cc_final: 0.7759 (tpp) outliers start: 33 outliers final: 25 residues processed: 142 average time/residue: 0.0820 time to fit residues: 18.2422 Evaluate side-chains 143 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASN 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 302 THR 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 131 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 B residue 337 SER 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 162 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 66 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 130 optimal weight: 0.0020 chunk 86 optimal weight: 0.6980 chunk 140 optimal weight: 6.9990 overall best weight: 1.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.130698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.110314 restraints weight = 17040.361| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.61 r_work: 0.3183 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3523 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= 0.123 Angle : 0.551 9.716 16368 Z= 0.264 Chirality : 0.044 0.132 1812 Planarity : 0.003 0.035 2096 Dihedral : 7.155 179.828 1684 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.01 % Allowed : 19.46 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.22), residues: 1476 helix: 0.21 (0.24), residues: 536 sheet: 0.42 (0.32), residues: 272 loop : -1.01 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 371 TYR 0.008 0.001 TYR B 239 PHE 0.006 0.001 PHE A 30 TRP 0.007 0.001 TRP C 355 HIS 0.003 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00293 (12068) covalent geometry : angle 0.55139 (16368) hydrogen bonds : bond 0.04089 ( 434) hydrogen bonds : angle 4.72644 ( 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 155 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 117 time to evaluate : 0.450 Fit side-chains REVERT: A 224 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7435 (mp10) REVERT: B 112 LYS cc_start: 0.7967 (pttp) cc_final: 0.7648 (ptpt) REVERT: B 122 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7686 (tpp) REVERT: B 166 GLU cc_start: 0.7525 (tm-30) cc_final: 0.7193 (tm-30) REVERT: B 204 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7401 (mt-10) REVERT: C 71 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7748 (pm20) REVERT: C 106 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7238 (tm-30) REVERT: C 191 ILE cc_start: 0.8570 (tt) cc_final: 0.8340 (tt) REVERT: C 204 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7752 (mt-10) REVERT: C 210 ASP cc_start: 0.9023 (t0) cc_final: 0.8560 (t0) REVERT: C 333 GLU cc_start: 0.7137 (pm20) cc_final: 0.6587 (pm20) outliers start: 38 outliers final: 32 residues processed: 146 average time/residue: 0.0694 time to fit residues: 16.2986 Evaluate side-chains 151 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 114 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 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 302 THR 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 131 MET Chi-restraints excluded: chain B residue 150 ILE 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 161 THR Chi-restraints excluded: chain C residue 162 VAL 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 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 Chi-restraints excluded: chain D residue 287 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.0396 > 50: distance: 43 - 61: 32.288 distance: 47 - 68: 19.170 distance: 51 - 77: 20.562 distance: 57 - 61: 29.380 distance: 58 - 85: 26.031 distance: 61 - 62: 35.014 distance: 62 - 63: 45.333 distance: 62 - 65: 8.425 distance: 63 - 64: 5.414 distance: 63 - 68: 40.842 distance: 64 - 93: 33.222 distance: 65 - 66: 24.493 distance: 65 - 67: 7.989 distance: 68 - 69: 13.958 distance: 69 - 70: 18.088 distance: 69 - 72: 31.932 distance: 70 - 71: 44.889 distance: 70 - 77: 15.733 distance: 71 - 104: 31.963 distance: 72 - 73: 35.873 distance: 73 - 74: 31.427 distance: 74 - 75: 39.424 distance: 74 - 76: 22.165 distance: 77 - 78: 17.009 distance: 78 - 79: 16.542 distance: 78 - 81: 27.570 distance: 79 - 80: 47.224 distance: 79 - 85: 41.812 distance: 80 - 113: 34.207 distance: 81 - 82: 44.587 distance: 81 - 83: 30.510 distance: 82 - 84: 17.267 distance: 85 - 86: 27.242 distance: 86 - 87: 9.544 distance: 86 - 89: 30.105 distance: 87 - 88: 25.573 distance: 87 - 93: 18.994 distance: 89 - 90: 48.362 distance: 90 - 91: 45.828 distance: 91 - 92: 24.362 distance: 93 - 94: 28.420 distance: 94 - 95: 29.944 distance: 94 - 97: 35.698 distance: 95 - 96: 26.374 distance: 95 - 104: 12.023 distance: 97 - 98: 26.536 distance: 98 - 99: 17.316 distance: 98 - 100: 12.267 distance: 99 - 101: 5.301 distance: 100 - 102: 12.046 distance: 101 - 103: 4.859 distance: 102 - 103: 8.464 distance: 104 - 105: 20.830 distance: 105 - 106: 18.183 distance: 105 - 108: 4.233 distance: 106 - 107: 23.374 distance: 106 - 113: 31.402 distance: 108 - 109: 27.922 distance: 109 - 110: 32.614 distance: 110 - 111: 7.394 distance: 110 - 112: 19.485 distance: 113 - 114: 4.120 distance: 114 - 115: 25.631 distance: 114 - 117: 3.756 distance: 115 - 116: 30.097 distance: 115 - 120: 26.980 distance: 117 - 118: 15.265 distance: 117 - 119: 40.652 distance: 120 - 121: 22.932 distance: 121 - 122: 30.006 distance: 121 - 124: 15.024 distance: 122 - 123: 7.946 distance: 122 - 131: 41.450 distance: 124 - 125: 31.490 distance: 125 - 126: 43.478 distance: 125 - 127: 28.478 distance: 126 - 128: 35.873 distance: 127 - 129: 27.362 distance: 128 - 130: 28.666 distance: 129 - 130: 17.301 distance: 131 - 132: 43.004 distance: 132 - 133: 57.883 distance: 132 - 135: 10.725 distance: 133 - 134: 5.496 distance: 133 - 139: 22.098 distance: 135 - 136: 24.876 distance: 136 - 137: 21.114 distance: 136 - 138: 38.138 distance: 139 - 140: 38.869 distance: 140 - 141: 28.471 distance: 140 - 143: 35.091 distance: 141 - 142: 45.414 distance: 141 - 146: 14.158 distance: 143 - 144: 45.861 distance: 143 - 145: 44.299