Starting phenix.real_space_refine on Mon Dec 30 02:37:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dnf_27565/12_2024/8dnf_27565.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dnf_27565/12_2024/8dnf_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_27565/12_2024/8dnf_27565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dnf_27565/12_2024/8dnf_27565.map" model { file = "/net/cci-nas-00/data/ceres_data/8dnf_27565/12_2024/8dnf_27565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dnf_27565/12_2024/8dnf_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-5532/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: 7.15, per 1000 atoms: 0.61 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: 3.16 Conformation dependent library (CDL) restraints added in 1.6 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: 1.76 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: 3.37 Time building geometry restraints manager: 3.57 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: 0.00 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.690 Find NCS groups from input model: 0.450 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.660 ------------------------------------------------------------------------------- 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= 0.316 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 *********************** 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 : 1.569 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: 0.2440 time to fit residues: 77.3394 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 : 1.652 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 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= 0.349 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 *********************** 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 : 1.349 Fit side-chains revert: symmetry clash REVERT: B 13 SER cc_start: 0.7536 (OUTLIER) cc_final: 0.7130 (p) REVERT: B 112 LYS cc_start: 0.7700 (pttt) cc_final: 0.7320 (pttp) REVERT: B 166 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7301 (tm-30) REVERT: B 204 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6682 (mt-10) REVERT: C 71 GLU cc_start: 0.7375 (mt-10) cc_final: 0.7154 (mt-10) REVERT: C 282 MET cc_start: 0.8210 (mmt) cc_final: 0.7795 (tpp) REVERT: C 352 GLN cc_start: 0.7493 (mm-40) cc_final: 0.7261 (mm-40) REVERT: C 360 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7598 (mt-10) REVERT: D 86 HIS cc_start: 0.6866 (OUTLIER) cc_final: 0.6642 (t-90) REVERT: D 226 MET cc_start: 0.7291 (mmm) cc_final: 0.7085 (mmm) REVERT: D 282 MET cc_start: 0.8015 (mmt) cc_final: 0.7200 (mpp) outliers start: 41 outliers final: 24 residues processed: 154 average time/residue: 0.1960 time to fit residues: 46.6830 Evaluate side-chains 151 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 1.443 ------------------------------------------------------------------------------- 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 86 HIS 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 74 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 145 optimal weight: 9.9990 chunk 119 optimal weight: 0.9990 chunk 133 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 ASN C 370 HIS D 86 HIS ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 12068 Z= 0.491 Angle : 0.746 7.537 16368 Z= 0.377 Chirality : 0.050 0.175 1812 Planarity : 0.004 0.035 2096 Dihedral : 8.078 179.041 1684 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.19 % Allowed : 17.72 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.21), residues: 1476 helix: -0.44 (0.23), residues: 528 sheet: -0.14 (0.30), residues: 276 loop : -1.16 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 355 HIS 0.033 0.002 HIS D 86 PHE 0.012 0.002 PHE B 254 TYR 0.018 0.002 TYR B 132 ARG 0.004 0.001 ARG D 115 *********************** 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 177 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 124 time to evaluate : 1.254 Fit side-chains REVERT: A 112 LYS cc_start: 0.8149 (pttt) cc_final: 0.7900 (ptmt) REVERT: A 166 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7947 (tm-30) REVERT: B 13 SER cc_start: 0.7639 (OUTLIER) cc_final: 0.7285 (p) REVERT: B 112 LYS cc_start: 0.8293 (pttt) cc_final: 0.7940 (pttp) REVERT: B 166 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7595 (tm-30) REVERT: B 204 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6676 (mt-10) REVERT: C 71 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7406 (mt-10) REVERT: C 282 MET cc_start: 0.8179 (mmt) cc_final: 0.7898 (tpp) REVERT: C 360 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7648 (mt-10) outliers start: 53 outliers final: 33 residues processed: 163 average time/residue: 0.1948 time to fit residues: 48.9738 Evaluate side-chains 153 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 1.434 ------------------------------------------------------------------------------- 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 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 200 THR Chi-restraints excluded: chain C residue 228 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 7.9990 chunk 101 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 143 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN D 160 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3144 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= 0.173 Angle : 0.563 6.580 16368 Z= 0.275 Chirality : 0.044 0.131 1812 Planarity : 0.003 0.031 2096 Dihedral : 7.609 179.794 1684 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.90 % Allowed : 20.25 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.80 (0.22), residues: 1476 helix: -0.14 (0.24), residues: 540 sheet: -0.01 (0.31), residues: 276 loop : -0.99 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 339 HIS 0.003 0.001 HIS B 100 PHE 0.007 0.001 PHE B 30 TYR 0.009 0.001 TYR B 239 ARG 0.003 0.000 ARG C 205 *********************** 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 146 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 1.356 Fit side-chains REVERT: A 166 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7625 (tm-30) REVERT: A 224 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.6767 (mp10) REVERT: B 166 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7374 (tm-30) REVERT: B 204 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6474 (mt-10) REVERT: C 106 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.6928 (tm-30) REVERT: C 191 ILE cc_start: 0.7412 (tt) cc_final: 0.7207 (tt) REVERT: C 282 MET cc_start: 0.8082 (mmt) cc_final: 0.7681 (tpp) REVERT: C 360 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7689 (mt-10) REVERT: D 282 MET cc_start: 0.7970 (tpp) cc_final: 0.7659 (mpp) outliers start: 24 outliers final: 14 residues processed: 137 average time/residue: 0.1992 time to fit residues: 42.5575 Evaluate side-chains 128 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASN 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 B residue 46 MET Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain 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 177 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 287 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 122 optimal weight: 0.9990 chunk 98 optimal weight: 0.0370 chunk 0 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 128 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 overall best weight: 0.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN C 11 ASN D 86 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12068 Z= 0.124 Angle : 0.527 6.187 16368 Z= 0.253 Chirality : 0.042 0.127 1812 Planarity : 0.003 0.030 2096 Dihedral : 7.291 179.879 1684 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.90 % Allowed : 20.97 % Favored : 77.14 % 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: -0.50 (0.22), residues: 1476 helix: 0.04 (0.24), residues: 544 sheet: 0.40 (0.32), residues: 260 loop : -0.85 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 355 HIS 0.008 0.001 HIS D 86 PHE 0.006 0.001 PHE B 30 TYR 0.007 0.001 TYR B 239 ARG 0.002 0.000 ARG C 205 *********************** 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 141 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 1.501 Fit side-chains REVERT: A 166 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7548 (tm-30) REVERT: A 224 GLN cc_start: 0.7484 (OUTLIER) cc_final: 0.6755 (mp10) REVERT: B 166 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7344 (tm-30) REVERT: B 204 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.6277 (mt-10) REVERT: C 191 ILE cc_start: 0.7374 (tt) cc_final: 0.7157 (tt) REVERT: C 204 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6555 (mt-10) REVERT: C 210 ASP cc_start: 0.8117 (t0) cc_final: 0.7740 (t0) REVERT: C 282 MET cc_start: 0.8084 (mmt) cc_final: 0.7789 (tpp) REVERT: C 360 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7690 (mt-10) REVERT: D 279 ASN cc_start: 0.8629 (m-40) cc_final: 0.8408 (m-40) REVERT: D 282 MET cc_start: 0.7972 (tpp) cc_final: 0.7563 (mpp) outliers start: 24 outliers final: 16 residues processed: 132 average time/residue: 0.1929 time to fit residues: 40.3835 Evaluate side-chains 128 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 268 MET 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 204 GLU Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 75 VAL 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 D residue 179 LEU Chi-restraints excluded: chain D residue 287 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 143 optimal weight: 0.6980 chunk 118 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3370 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= 0.197 Angle : 0.552 6.386 16368 Z= 0.266 Chirality : 0.044 0.133 1812 Planarity : 0.003 0.031 2096 Dihedral : 7.173 179.736 1684 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.85 % Allowed : 19.86 % 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: -0.45 (0.22), residues: 1476 helix: 0.17 (0.24), residues: 536 sheet: 0.48 (0.31), residues: 292 loop : -1.00 (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 A 278 TYR 0.009 0.001 TYR B 165 ARG 0.003 0.000 ARG C 255 *********************** 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 151 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 1.421 Fit side-chains REVERT: B 112 LYS cc_start: 0.7868 (pttt) cc_final: 0.7381 (ptpt) REVERT: B 166 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7374 (tm-30) REVERT: B 204 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6341 (mt-10) REVERT: B 353 GLN cc_start: 0.8297 (tm-30) cc_final: 0.7929 (tm-30) REVERT: C 71 GLU cc_start: 0.7563 (mt-10) cc_final: 0.6962 (pm20) REVERT: C 106 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.6865 (tm-30) REVERT: C 191 ILE cc_start: 0.7511 (tt) cc_final: 0.7301 (tt) REVERT: C 204 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6590 (mt-10) REVERT: C 210 ASP cc_start: 0.8178 (t0) cc_final: 0.7799 (t0) REVERT: C 251 ASN cc_start: 0.8554 (p0) cc_final: 0.8178 (p0) REVERT: C 282 MET cc_start: 0.8106 (mmt) cc_final: 0.7742 (tpp) REVERT: C 333 GLU cc_start: 0.6811 (pm20) cc_final: 0.6240 (pm20) REVERT: C 360 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7639 (mt-10) REVERT: D 282 MET cc_start: 0.8120 (tpp) cc_final: 0.7593 (mpp) outliers start: 36 outliers final: 27 residues processed: 141 average time/residue: 0.1951 time to fit residues: 43.5542 Evaluate side-chains 144 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain B residue 33 ILE 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 162 VAL Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 29 VAL 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 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 211 ILE Chi-restraints excluded: chain D residue 287 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 104 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 142 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN C 11 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12068 Z= 0.227 Angle : 0.565 6.480 16368 Z= 0.274 Chirality : 0.044 0.134 1812 Planarity : 0.003 0.034 2096 Dihedral : 7.178 179.783 1684 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.56 % Allowed : 19.46 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.19 (0.24), residues: 532 sheet: 0.41 (0.31), residues: 300 loop : -1.01 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 355 HIS 0.004 0.001 HIS B 100 PHE 0.007 0.001 PHE B 254 TYR 0.009 0.001 TYR B 239 ARG 0.002 0.000 ARG D 115 *********************** 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 159 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 114 time to evaluate : 1.333 Fit side-chains REVERT: A 224 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.6792 (mp10) REVERT: B 112 LYS cc_start: 0.7812 (pttt) cc_final: 0.7303 (ptpt) REVERT: B 152 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7772 (tpp) REVERT: B 166 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7394 (tm-30) REVERT: B 204 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6457 (mt-10) REVERT: C 71 GLU cc_start: 0.7559 (mt-10) cc_final: 0.6988 (pm20) REVERT: C 106 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.6948 (tm-30) REVERT: C 191 ILE cc_start: 0.7433 (tt) cc_final: 0.7200 (tt) REVERT: C 204 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6684 (mt-10) REVERT: C 251 ASN cc_start: 0.8650 (p0) cc_final: 0.8296 (p0) REVERT: C 282 MET cc_start: 0.8079 (mmt) cc_final: 0.7705 (tpp) REVERT: C 333 GLU cc_start: 0.6767 (pm20) cc_final: 0.6225 (pm20) REVERT: C 360 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7668 (mt-10) REVERT: D 282 MET cc_start: 0.8189 (tpp) cc_final: 0.7592 (mpp) outliers start: 45 outliers final: 31 residues processed: 151 average time/residue: 0.1946 time to fit residues: 45.9729 Evaluate side-chains 147 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 111 time to evaluate : 1.440 ------------------------------------------------------------------------------- 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 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 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 162 VAL Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 70 optimal weight: 0.0050 chunk 13 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 overall best weight: 2.5800 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12068 Z= 0.273 Angle : 0.590 6.791 16368 Z= 0.287 Chirality : 0.045 0.138 1812 Planarity : 0.004 0.039 2096 Dihedral : 7.263 179.924 1684 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.48 % Allowed : 19.54 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.56 (0.22), residues: 1476 helix: 0.11 (0.24), residues: 532 sheet: 0.40 (0.31), residues: 300 loop : -1.10 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 355 HIS 0.004 0.001 HIS B 100 PHE 0.008 0.001 PHE B 199 TYR 0.011 0.001 TYR B 165 ARG 0.003 0.000 ARG C 255 *********************** 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 162 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 118 time to evaluate : 1.451 Fit side-chains REVERT: A 166 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7839 (tm-30) REVERT: A 224 GLN cc_start: 0.7452 (OUTLIER) cc_final: 0.6831 (mp10) REVERT: A 282 MET cc_start: 0.7983 (tpp) cc_final: 0.7524 (tpp) REVERT: B 112 LYS cc_start: 0.7889 (pttt) cc_final: 0.7346 (ptpt) REVERT: B 122 MET cc_start: 0.7880 (ttm) cc_final: 0.7534 (tpp) REVERT: B 152 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7768 (tpp) REVERT: B 166 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7381 (tm-30) REVERT: B 204 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6499 (mt-10) REVERT: C 71 GLU cc_start: 0.7507 (mt-10) cc_final: 0.6970 (pm20) REVERT: C 106 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.6997 (tm-30) REVERT: C 191 ILE cc_start: 0.7457 (tt) cc_final: 0.7213 (tt) REVERT: C 204 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6698 (mt-10) REVERT: C 210 ASP cc_start: 0.8191 (t0) cc_final: 0.7796 (t0) REVERT: C 282 MET cc_start: 0.8060 (mmt) cc_final: 0.7691 (tpp) REVERT: C 360 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7652 (mt-10) REVERT: D 282 MET cc_start: 0.8266 (tpp) cc_final: 0.7619 (mpp) REVERT: D 359 GLN cc_start: 0.8346 (mm110) cc_final: 0.7917 (tp40) outliers start: 44 outliers final: 33 residues processed: 152 average time/residue: 0.1918 time to fit residues: 45.0359 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 : 1.452 ------------------------------------------------------------------------------- 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 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 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 162 VAL Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 chunk 125 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12068 Z= 0.159 Angle : 0.532 6.335 16368 Z= 0.255 Chirality : 0.043 0.129 1812 Planarity : 0.003 0.037 2096 Dihedral : 7.061 179.962 1684 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.93 % Allowed : 20.02 % 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: -0.37 (0.22), residues: 1476 helix: 0.22 (0.24), residues: 536 sheet: 0.67 (0.32), residues: 292 loop : -1.01 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 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 *********************** 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 157 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 120 time to evaluate : 1.335 Fit side-chains REVERT: A 112 LYS cc_start: 0.8168 (ptmt) cc_final: 0.7869 (mtpt) REVERT: A 166 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7746 (tm-30) REVERT: A 224 GLN cc_start: 0.7415 (OUTLIER) cc_final: 0.6773 (mp10) REVERT: B 112 LYS cc_start: 0.7680 (pttt) cc_final: 0.7166 (ptpt) REVERT: B 122 MET cc_start: 0.7809 (ttm) cc_final: 0.7556 (tpp) REVERT: B 152 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7674 (tpp) REVERT: B 166 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7345 (tm-30) REVERT: B 204 GLU cc_start: 0.6746 (OUTLIER) cc_final: 0.6333 (mt-10) REVERT: C 71 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7070 (pm20) REVERT: C 106 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.6927 (tm-30) REVERT: C 191 ILE cc_start: 0.7411 (tt) cc_final: 0.7168 (tt) REVERT: C 204 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6615 (mt-10) REVERT: C 210 ASP cc_start: 0.8153 (t0) cc_final: 0.7771 (t0) REVERT: C 251 ASN cc_start: 0.8607 (p0) cc_final: 0.8273 (p0) REVERT: C 333 GLU cc_start: 0.6822 (pm20) cc_final: 0.6216 (pm20) REVERT: C 360 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7701 (mt-10) REVERT: D 282 MET cc_start: 0.8221 (tpp) cc_final: 0.7631 (mpp) REVERT: D 359 GLN cc_start: 0.8297 (mm110) cc_final: 0.7698 (tp40) outliers start: 37 outliers final: 27 residues processed: 148 average time/residue: 0.1972 time to fit residues: 45.5788 Evaluate side-chains 149 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 1.405 ------------------------------------------------------------------------------- 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 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 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 162 VAL Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 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 350 THR 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 85 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 147 optimal weight: 0.5980 chunk 135 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12068 Z= 0.242 Angle : 0.575 6.479 16368 Z= 0.279 Chirality : 0.045 0.145 1812 Planarity : 0.004 0.040 2096 Dihedral : 7.120 179.928 1684 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.69 % Allowed : 20.41 % 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: -0.45 (0.22), residues: 1476 helix: 0.24 (0.24), residues: 524 sheet: 0.50 (0.31), residues: 300 loop : -1.09 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 355 HIS 0.004 0.001 HIS B 100 PHE 0.012 0.001 PHE A 278 TYR 0.009 0.001 TYR B 239 ARG 0.003 0.000 ARG C 255 ********************** 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 149 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 1.405 Fit side-chains REVERT: A 112 LYS cc_start: 0.8221 (ptmt) cc_final: 0.7972 (mtpt) REVERT: A 166 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7818 (tm-30) REVERT: A 224 GLN cc_start: 0.7433 (OUTLIER) cc_final: 0.6807 (mp10) REVERT: A 282 MET cc_start: 0.7768 (tpp) cc_final: 0.7255 (mpp) REVERT: B 122 MET cc_start: 0.7773 (ttm) cc_final: 0.7478 (tpp) REVERT: B 152 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7770 (tpp) REVERT: B 166 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7319 (tm-30) REVERT: B 204 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.6415 (mt-10) REVERT: C 71 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7086 (pm20) REVERT: C 106 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.6951 (tm-30) REVERT: C 191 ILE cc_start: 0.7478 (tt) cc_final: 0.7240 (tt) REVERT: C 204 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6658 (mt-10) REVERT: C 210 ASP cc_start: 0.8198 (t0) cc_final: 0.7811 (t0) REVERT: C 251 ASN cc_start: 0.8655 (p0) cc_final: 0.8314 (p0) REVERT: C 333 GLU cc_start: 0.6869 (pm20) cc_final: 0.6254 (pm20) REVERT: C 360 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7687 (mt-10) REVERT: D 282 MET cc_start: 0.8264 (tpp) cc_final: 0.7614 (mpp) REVERT: D 359 GLN cc_start: 0.8362 (mm110) cc_final: 0.7937 (tp40) outliers start: 34 outliers final: 27 residues processed: 142 average time/residue: 0.1995 time to fit residues: 44.4022 Evaluate side-chains 146 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 1.433 ------------------------------------------------------------------------------- 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 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 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 162 VAL Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 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 287 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.3493 r_free = 0.3493 target = 0.125161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.105225 restraints weight = 17199.576| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.55 r_work: 0.3102 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 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 : 0.007 0.045 12068 Z= 0.435 Angle : 0.690 8.039 16368 Z= 0.343 Chirality : 0.049 0.165 1812 Planarity : 0.004 0.048 2096 Dihedral : 7.557 179.990 1684 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.69 % Allowed : 20.17 % Favored : 77.14 % 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: -0.92 (0.22), residues: 1476 helix: -0.20 (0.23), residues: 532 sheet: 0.28 (0.31), residues: 300 loop : -1.34 (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 0.011 0.002 PHE A 126 TYR 0.016 0.002 TYR B 132 ARG 0.004 0.000 ARG D 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2175.04 seconds wall clock time: 40 minutes 43.90 seconds (2443.90 seconds total)