Starting phenix.real_space_refine on Wed May 14 16:31:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dnf_27565/05_2025/8dnf_27565.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dnf_27565/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dnf_27565/05_2025/8dnf_27565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dnf_27565/05_2025/8dnf_27565.map" model { file = "/net/cci-nas-00/data/ceres_data/8dnf_27565/05_2025/8dnf_27565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dnf_27565/05_2025/8dnf_27565.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.55, per 1000 atoms: 0.64 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: 2.81 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.71 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: 3.79 Time building geometry restraints manager: 3.33 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: 0.03 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.530 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.180 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (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 TRP 0.006 0.001 TRP C 85 HIS 0.002 0.000 HIS D 100 PHE 0.004 0.001 PHE D 254 TYR 0.011 0.001 TYR D 305 ARG 0.006 0.001 ARG C 205 Details of bonding type rmsd hydrogen bonds : bond 0.34829 ( 434) hydrogen bonds : angle 8.25861 ( 1122) covalent geometry : bond 0.00449 (12068) covalent geometry : angle 0.68571 (16368) *********************** 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 : 1.317 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: 0.2336 time to fit residues: 73.8928 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 : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 86 optimal weight: 0.4980 chunk 134 optimal weight: 5.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- 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 160 HIS ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 HIS ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.126052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.103270 restraints weight = 16654.934| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.09 r_work: 0.3077 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12068 Z= 0.222 Angle : 0.697 8.779 16368 Z= 0.349 Chirality : 0.048 0.168 1812 Planarity : 0.004 0.031 2096 Dihedral : 7.907 179.329 1684 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 4.14 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.21), residues: 1476 helix: -0.35 (0.23), residues: 528 sheet: -0.06 (0.30), residues: 276 loop : -0.68 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 355 HIS 0.007 0.001 HIS D 86 PHE 0.010 0.001 PHE B 254 TYR 0.015 0.002 TYR B 132 ARG 0.004 0.001 ARG D 115 Details of bonding type rmsd hydrogen bonds : bond 0.06763 ( 434) hydrogen bonds : angle 5.77758 ( 1122) covalent geometry : bond 0.00533 (12068) covalent geometry : angle 0.69717 (16368) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 1.353 Fit side-chains revert: symmetry clash REVERT: B 13 SER cc_start: 0.7491 (OUTLIER) cc_final: 0.7101 (p) REVERT: B 112 LYS cc_start: 0.7696 (pttt) cc_final: 0.7387 (pttp) REVERT: B 166 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7070 (tm-30) REVERT: B 204 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6935 (mt-10) REVERT: C 71 GLU cc_start: 0.7361 (mt-10) cc_final: 0.7157 (mt-10) REVERT: C 282 MET cc_start: 0.7922 (mmt) cc_final: 0.7477 (tpp) REVERT: C 352 GLN cc_start: 0.7421 (mm-40) cc_final: 0.7152 (mm-40) REVERT: C 360 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7536 (mt-10) REVERT: D 226 MET cc_start: 0.7265 (mmm) cc_final: 0.7047 (mmm) REVERT: D 282 MET cc_start: 0.7409 (mmt) cc_final: 0.6508 (mpp) outliers start: 41 outliers final: 24 residues processed: 154 average time/residue: 0.1915 time to fit residues: 45.5408 Evaluate side-chains 151 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 1.372 ------------------------------------------------------------------------------- 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 75 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 194 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 82 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 124 optimal weight: 0.0060 chunk 110 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 overall best weight: 4.0004 ------------------------------------------------------------------------------- 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 C 370 HIS ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.121418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.098809 restraints weight = 17070.504| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 3.10 r_work: 0.3014 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 12068 Z= 0.256 Angle : 0.696 7.075 16368 Z= 0.350 Chirality : 0.049 0.171 1812 Planarity : 0.004 0.032 2096 Dihedral : 7.963 179.258 1684 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.88 % Allowed : 18.12 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.21), residues: 1476 helix: -0.30 (0.23), residues: 528 sheet: -0.09 (0.30), residues: 276 loop : -1.05 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 355 HIS 0.005 0.001 HIS B 100 PHE 0.011 0.002 PHE B 254 TYR 0.015 0.002 TYR B 132 ARG 0.005 0.001 ARG D 115 Details of bonding type rmsd hydrogen bonds : bond 0.06942 ( 434) hydrogen bonds : angle 5.56647 ( 1122) covalent geometry : bond 0.00631 (12068) covalent geometry : angle 0.69617 (16368) *********************** 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 174 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 125 time to evaluate : 1.216 Fit side-chains REVERT: B 13 SER cc_start: 0.7585 (OUTLIER) cc_final: 0.7252 (p) REVERT: B 112 LYS cc_start: 0.8196 (pttt) cc_final: 0.7915 (ptmt) REVERT: B 166 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7380 (tm-30) REVERT: B 204 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.7056 (mt-10) REVERT: C 282 MET cc_start: 0.7881 (mmt) cc_final: 0.7555 (tpp) REVERT: C 360 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7599 (mt-10) outliers start: 49 outliers final: 32 residues processed: 159 average time/residue: 0.1803 time to fit residues: 44.4423 Evaluate side-chains 152 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 118 time to evaluate : 1.276 ------------------------------------------------------------------------------- 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 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 105 THR Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 151 VAL 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 75 VAL Chi-restraints excluded: chain C residue 200 THR 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 193 THR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 367 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 16 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 60 optimal weight: 0.0000 chunk 59 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.124593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.101786 restraints weight = 16599.997| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 3.09 r_work: 0.3056 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12068 Z= 0.142 Angle : 0.582 6.688 16368 Z= 0.286 Chirality : 0.044 0.133 1812 Planarity : 0.003 0.031 2096 Dihedral : 7.627 179.648 1684 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.14 % Allowed : 19.94 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.21), residues: 1476 helix: -0.18 (0.23), residues: 540 sheet: 0.02 (0.31), residues: 276 loop : -1.01 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 355 HIS 0.003 0.001 HIS B 100 PHE 0.008 0.001 PHE D 278 TYR 0.010 0.001 TYR B 239 ARG 0.003 0.000 ARG A 205 Details of bonding type rmsd hydrogen bonds : bond 0.04807 ( 434) hydrogen bonds : angle 5.14329 ( 1122) covalent geometry : bond 0.00334 (12068) covalent geometry : angle 0.58228 (16368) *********************** 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 147 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 1.355 Fit side-chains REVERT: A 224 GLN cc_start: 0.7293 (OUTLIER) cc_final: 0.6632 (mp10) REVERT: B 166 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7224 (tm-30) REVERT: B 204 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6838 (mt-10) REVERT: C 282 MET cc_start: 0.7777 (mmt) cc_final: 0.7370 (tpp) REVERT: C 360 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7613 (mt-10) REVERT: D 282 MET cc_start: 0.7177 (tpp) cc_final: 0.6776 (mpp) outliers start: 27 outliers final: 18 residues processed: 138 average time/residue: 0.1878 time to fit residues: 40.9264 Evaluate side-chains 130 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 1.326 ------------------------------------------------------------------------------- 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 224 GLN Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 58 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 133 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 chunk 76 optimal weight: 0.0270 chunk 23 optimal weight: 8.9990 chunk 134 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 overall best weight: 1.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.130101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.109912 restraints weight = 16945.115| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.55 r_work: 0.3170 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12068 Z= 0.130 Angle : 0.558 6.444 16368 Z= 0.270 Chirality : 0.044 0.130 1812 Planarity : 0.003 0.030 2096 Dihedral : 7.337 179.712 1684 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.24 % Allowed : 19.07 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.22), residues: 1476 helix: 0.05 (0.24), residues: 532 sheet: 0.24 (0.30), residues: 300 loop : -1.07 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 355 HIS 0.003 0.001 HIS B 100 PHE 0.007 0.001 PHE C 30 TYR 0.009 0.001 TYR B 239 ARG 0.003 0.000 ARG C 255 Details of bonding type rmsd hydrogen bonds : bond 0.04338 ( 434) hydrogen bonds : angle 4.87361 ( 1122) covalent geometry : bond 0.00309 (12068) covalent geometry : angle 0.55847 (16368) *********************** 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 157 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 116 time to evaluate : 1.270 Fit side-chains REVERT: A 166 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7714 (tm-30) REVERT: A 224 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7347 (mp10) REVERT: B 152 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7752 (tpp) REVERT: B 166 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7453 (tm-30) REVERT: B 204 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7548 (mt-10) REVERT: C 106 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7437 (tm-30) REVERT: C 204 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7839 (mt-10) REVERT: C 210 ASP cc_start: 0.9104 (t0) cc_final: 0.8633 (t0) REVERT: C 282 MET cc_start: 0.8440 (mmt) cc_final: 0.8207 (tpp) REVERT: C 360 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7968 (mt-10) REVERT: D 282 MET cc_start: 0.8044 (tpp) cc_final: 0.7580 (mpp) outliers start: 41 outliers final: 29 residues processed: 145 average time/residue: 0.1781 time to fit residues: 40.8820 Evaluate side-chains 142 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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 350 THR Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 152 MET 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 75 VAL Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 177 LEU 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 287 ASP 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 118 optimal weight: 6.9990 chunk 87 optimal weight: 0.0980 chunk 48 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 82 optimal weight: 0.6980 chunk 89 optimal weight: 8.9990 chunk 122 optimal weight: 0.8980 chunk 117 optimal weight: 6.9990 chunk 142 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 ASN ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.129490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.108984 restraints weight = 17328.540| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.62 r_work: 0.3156 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12068 Z= 0.136 Angle : 0.561 6.568 16368 Z= 0.271 Chirality : 0.044 0.134 1812 Planarity : 0.003 0.033 2096 Dihedral : 7.256 179.794 1684 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.64 % Allowed : 18.75 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.22), residues: 1476 helix: 0.13 (0.24), residues: 532 sheet: 0.24 (0.31), residues: 296 loop : -1.09 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 355 HIS 0.003 0.001 HIS B 100 PHE 0.007 0.001 PHE C 30 TYR 0.009 0.001 TYR B 165 ARG 0.002 0.000 ARG C 27 Details of bonding type rmsd hydrogen bonds : bond 0.04408 ( 434) hydrogen bonds : angle 4.83924 ( 1122) covalent geometry : bond 0.00325 (12068) covalent geometry : angle 0.56062 (16368) *********************** 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 162 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 116 time to evaluate : 1.412 Fit side-chains REVERT: A 224 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7228 (mp10) REVERT: B 112 LYS cc_start: 0.8307 (pttt) cc_final: 0.8001 (ptpt) REVERT: B 152 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7805 (tpp) REVERT: B 166 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7452 (tm-30) REVERT: B 204 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7521 (mt-10) REVERT: C 106 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7412 (tm-30) REVERT: C 204 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7821 (mt-10) REVERT: C 210 ASP cc_start: 0.9110 (t0) cc_final: 0.8648 (t0) REVERT: C 251 ASN cc_start: 0.9060 (p0) cc_final: 0.8841 (p0) REVERT: C 282 MET cc_start: 0.8399 (mmt) cc_final: 0.8144 (tpp) REVERT: C 360 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7923 (mt-10) REVERT: D 24 ASP cc_start: 0.7427 (t0) cc_final: 0.7192 (t0) REVERT: D 282 MET cc_start: 0.8125 (tpp) cc_final: 0.7579 (mpp) outliers start: 46 outliers final: 37 residues processed: 152 average time/residue: 0.1931 time to fit residues: 45.7141 Evaluate side-chains 152 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 110 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 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 131 MET Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 152 MET 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 75 VAL Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 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 1 GLU 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 302 THR 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 95 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 143 optimal weight: 8.9990 chunk 115 optimal weight: 0.0020 chunk 78 optimal weight: 9.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.131358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.110812 restraints weight = 17181.866| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.61 r_work: 0.3173 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12068 Z= 0.106 Angle : 0.529 6.331 16368 Z= 0.253 Chirality : 0.043 0.129 1812 Planarity : 0.003 0.033 2096 Dihedral : 7.089 179.921 1684 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.16 % Allowed : 19.38 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.22), residues: 1476 helix: 0.21 (0.24), residues: 536 sheet: 0.57 (0.31), residues: 292 loop : -1.01 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 355 HIS 0.003 0.001 HIS B 100 PHE 0.007 0.001 PHE B 351 TYR 0.007 0.001 TYR B 239 ARG 0.002 0.000 ARG A 61 Details of bonding type rmsd hydrogen bonds : bond 0.03731 ( 434) hydrogen bonds : angle 4.67416 ( 1122) covalent geometry : bond 0.00247 (12068) covalent geometry : angle 0.52912 (16368) *********************** 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 161 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 1.256 Fit side-chains REVERT: A 224 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7335 (mp10) REVERT: A 282 MET cc_start: 0.8433 (tpp) cc_final: 0.8146 (tpp) REVERT: B 112 LYS cc_start: 0.8209 (pttt) cc_final: 0.7909 (ptpt) REVERT: B 152 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7714 (tpp) REVERT: B 166 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7445 (tm-30) REVERT: B 204 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7451 (mt-10) REVERT: B 353 GLN cc_start: 0.8461 (tm-30) cc_final: 0.8170 (tm-30) REVERT: C 106 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7398 (tm-30) REVERT: C 204 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7764 (mt-10) REVERT: C 210 ASP cc_start: 0.9092 (t0) cc_final: 0.8634 (t0) REVERT: C 282 MET cc_start: 0.8452 (mmt) cc_final: 0.8190 (tpp) REVERT: C 333 GLU cc_start: 0.7347 (pm20) cc_final: 0.6766 (pm20) REVERT: C 360 GLU cc_start: 0.8247 (mm-30) cc_final: 0.8005 (mt-10) REVERT: D 24 ASP cc_start: 0.7572 (t0) cc_final: 0.7334 (t0) REVERT: D 282 MET cc_start: 0.8182 (tpp) cc_final: 0.7534 (mpp) outliers start: 40 outliers final: 28 residues processed: 153 average time/residue: 0.1907 time to fit residues: 45.4224 Evaluate side-chains 143 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 1.219 ------------------------------------------------------------------------------- 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 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 B residue 33 ILE Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 204 GLU 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 C residue 13 SER Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain D residue 1 GLU Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 179 LEU 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 83 optimal weight: 0.0030 chunk 115 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 76 optimal weight: 0.5980 chunk 127 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 160 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.134475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.113900 restraints weight = 17077.733| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.61 r_work: 0.3230 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 12068 Z= 0.080 Angle : 0.500 6.437 16368 Z= 0.236 Chirality : 0.042 0.125 1812 Planarity : 0.003 0.036 2096 Dihedral : 6.838 179.999 1684 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.37 % Allowed : 20.41 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.23), residues: 1476 helix: 0.41 (0.25), residues: 536 sheet: 0.72 (0.32), residues: 292 loop : -0.84 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 355 HIS 0.002 0.000 HIS B 100 PHE 0.006 0.001 PHE B 351 TYR 0.006 0.001 TYR D 305 ARG 0.002 0.000 ARG A 61 Details of bonding type rmsd hydrogen bonds : bond 0.02816 ( 434) hydrogen bonds : angle 4.42740 ( 1122) covalent geometry : bond 0.00173 (12068) covalent geometry : angle 0.49979 (16368) *********************** 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 150 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 1.329 Fit side-chains REVERT: A 112 LYS cc_start: 0.8345 (ptmt) cc_final: 0.8013 (mtpt) REVERT: A 224 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7402 (mp10) REVERT: A 282 MET cc_start: 0.8381 (tpp) cc_final: 0.8016 (tpp) REVERT: B 112 LYS cc_start: 0.7898 (pttt) cc_final: 0.7647 (ptpt) REVERT: B 166 GLU cc_start: 0.7433 (tm-30) cc_final: 0.7118 (tm-30) REVERT: B 353 GLN cc_start: 0.8141 (tm-30) cc_final: 0.7925 (tm-30) REVERT: C 106 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7188 (tm-30) REVERT: C 122 MET cc_start: 0.8522 (mmt) cc_final: 0.8181 (mmt) REVERT: C 210 ASP cc_start: 0.9006 (t0) cc_final: 0.8582 (t0) REVERT: D 24 ASP cc_start: 0.7510 (t0) cc_final: 0.7268 (t0) REVERT: D 282 MET cc_start: 0.8204 (tpp) cc_final: 0.7655 (mpp) outliers start: 30 outliers final: 19 residues processed: 141 average time/residue: 0.1978 time to fit residues: 42.7077 Evaluate side-chains 138 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 224 GLN 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 150 ILE Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain C residue 75 VAL 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 269 GLU Chi-restraints excluded: chain D residue 1 GLU Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 287 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 14 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 122 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.126659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.106487 restraints weight = 17473.887| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.59 r_work: 0.3119 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 12068 Z= 0.239 Angle : 0.653 7.022 16368 Z= 0.322 Chirality : 0.048 0.160 1812 Planarity : 0.004 0.046 2096 Dihedral : 7.225 179.813 1684 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.56 % Allowed : 19.15 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.22), residues: 1476 helix: 0.08 (0.24), residues: 532 sheet: 0.42 (0.31), residues: 300 loop : -1.17 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 339 HIS 0.006 0.001 HIS A 100 PHE 0.015 0.002 PHE C 278 TYR 0.015 0.002 TYR B 132 ARG 0.003 0.000 ARG B 253 Details of bonding type rmsd hydrogen bonds : bond 0.05798 ( 434) hydrogen bonds : angle 5.00676 ( 1122) covalent geometry : bond 0.00588 (12068) covalent geometry : angle 0.65311 (16368) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 120 time to evaluate : 1.322 Fit side-chains REVERT: A 112 LYS cc_start: 0.8710 (ptmt) cc_final: 0.8482 (mtpt) REVERT: A 166 GLU cc_start: 0.8331 (tm-30) cc_final: 0.8039 (tm-30) REVERT: A 224 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7383 (mp10) REVERT: B 152 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7810 (tpp) REVERT: B 166 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7516 (tm-30) REVERT: B 204 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7651 (mt-10) REVERT: C 106 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7507 (tm-30) REVERT: C 204 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7972 (mt-10) REVERT: C 333 GLU cc_start: 0.7463 (pm20) cc_final: 0.6878 (pm20) REVERT: D 24 ASP cc_start: 0.7627 (t0) cc_final: 0.7352 (t0) REVERT: D 282 MET cc_start: 0.8258 (tpp) cc_final: 0.7641 (mpp) REVERT: D 359 GLN cc_start: 0.8448 (mm110) cc_final: 0.8000 (tp40) outliers start: 45 outliers final: 33 residues processed: 156 average time/residue: 0.1820 time to fit residues: 44.0303 Evaluate side-chains 151 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 113 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 224 GLN 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 105 THR Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 302 THR 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 75 VAL Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain D residue 1 GLU Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 367 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 28 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.130278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.109939 restraints weight = 17150.936| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.58 r_work: 0.3167 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12068 Z= 0.119 Angle : 0.554 6.444 16368 Z= 0.268 Chirality : 0.044 0.138 1812 Planarity : 0.003 0.047 2096 Dihedral : 7.097 179.954 1684 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.45 % Allowed : 20.49 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.22), residues: 1476 helix: 0.25 (0.24), residues: 532 sheet: 0.44 (0.31), residues: 296 loop : -1.08 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 355 HIS 0.003 0.001 HIS B 100 PHE 0.015 0.001 PHE A 278 TYR 0.008 0.001 TYR B 239 ARG 0.002 0.000 ARG D 115 Details of bonding type rmsd hydrogen bonds : bond 0.04137 ( 434) hydrogen bonds : angle 4.73598 ( 1122) covalent geometry : bond 0.00280 (12068) covalent geometry : angle 0.55416 (16368) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 1.237 Fit side-chains REVERT: A 112 LYS cc_start: 0.8557 (ptmt) cc_final: 0.8352 (mtpt) REVERT: A 166 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7709 (tm-30) REVERT: A 224 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7458 (mp10) REVERT: A 282 MET cc_start: 0.8066 (tpp) cc_final: 0.7539 (mpp) REVERT: B 166 GLU cc_start: 0.7546 (tm-30) cc_final: 0.7221 (tm-30) REVERT: B 204 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7414 (mt-10) REVERT: C 106 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7273 (tm-30) REVERT: C 210 ASP cc_start: 0.8997 (t0) cc_final: 0.8539 (t0) REVERT: C 333 GLU cc_start: 0.7099 (pm20) cc_final: 0.6518 (pm20) REVERT: D 24 ASP cc_start: 0.7479 (t0) cc_final: 0.7223 (t0) REVERT: D 282 MET cc_start: 0.8216 (tpp) cc_final: 0.7687 (mpp) REVERT: D 359 GLN cc_start: 0.8356 (mm110) cc_final: 0.7785 (tp40) outliers start: 31 outliers final: 25 residues processed: 140 average time/residue: 0.1873 time to fit residues: 40.7768 Evaluate side-chains 139 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 224 GLN 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 150 ILE Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain D residue 1 GLU Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 287 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 101 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 144 optimal weight: 0.0470 chunk 73 optimal weight: 0.0670 chunk 96 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 overall best weight: 1.8020 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.130028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.109728 restraints weight = 17116.022| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.60 r_work: 0.3158 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12068 Z= 0.131 Angle : 0.558 6.354 16368 Z= 0.270 Chirality : 0.044 0.134 1812 Planarity : 0.004 0.047 2096 Dihedral : 7.054 179.974 1684 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.93 % Allowed : 20.17 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.22), residues: 1476 helix: 0.26 (0.24), residues: 532 sheet: 0.43 (0.31), residues: 308 loop : -1.01 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 355 HIS 0.003 0.001 HIS B 100 PHE 0.012 0.001 PHE A 278 TYR 0.009 0.001 TYR B 239 ARG 0.002 0.000 ARG D 115 Details of bonding type rmsd hydrogen bonds : bond 0.04197 ( 434) hydrogen bonds : angle 4.72233 ( 1122) covalent geometry : bond 0.00312 (12068) covalent geometry : angle 0.55820 (16368) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4957.64 seconds wall clock time: 86 minutes 38.43 seconds (5198.43 seconds total)