Starting phenix.real_space_refine on Sat Sep 12 11:39:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5jlf_8162/09_2026/5jlf_8162.cif Found real_map, /net/cci-nas-00/data/ceres_data/5jlf_8162/09_2026/5jlf_8162.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5jlf_8162/09_2026/5jlf_8162.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5jlf_8162/09_2026/5jlf_8162.map" model { file = "/net/cci-nas-00/data/ceres_data/5jlf_8162/09_2026/5jlf_8162.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5jlf_8162/09_2026/5jlf_8162.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/5jlf_8162/09_2026/5jlf_8162.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5jlf_8162/09_2026/5jlf_8162.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.001 sd= 0.010 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 10 5.49 5 Mg 5 5.21 5 S 100 5.16 5 C 9925 2.51 5 N 2700 2.21 5 O 3060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15800 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 346} 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: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 346} 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: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 346} 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: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 346} 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: "E" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 346} 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: "F" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "G" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 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} Chain: "E" 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: 4.39, per 1000 atoms: 0.28 Number of scatterers: 15800 At special positions: 0 Unit cell: (99, 93.5, 207.9, 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 100 16.00 P 10 15.00 Mg 5 11.99 O 3060 8.00 N 2700 7.00 C 9925 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: 1.17 Conformation dependent library (CDL) restraints added in 693.7 milliseconds 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3930 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 25 sheets defined 68.2% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 93 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.242A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 171 through 175 Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 252 through 260 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 261 through 262 No H-bonds generated for 'chain 'A' and resid 261 through 262' Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 285 removed outlier: 3.520A pdb=" N CYS A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 356 removed outlier: 3.892A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TRP A 356 " --> pdb=" O GLN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 371 removed outlier: 3.832A pdb=" N HIS A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 93 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.227A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 171 through 175 Processing helix chain 'B' and resid 181 through 194 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 251 through 260 removed outlier: 4.374A pdb=" N PHE B 255 " --> pdb=" O GLY B 251 " (cutoff:3.500A) Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 261 through 262 No H-bonds generated for 'chain 'B' and resid 261 through 262' Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 285 removed outlier: 3.518A pdb=" N CYS B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 350 through 356 removed outlier: 3.896A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TRP B 356 " --> pdb=" O GLN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 371 removed outlier: 3.834A pdb=" N HIS B 371 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 93 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.226A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 181 through 194 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 251 through 260 removed outlier: 4.378A pdb=" N PHE C 255 " --> pdb=" O GLY C 251 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 through 262' Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.514A pdb=" N CYS C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 356 removed outlier: 3.892A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TRP C 356 " --> pdb=" O GLN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 371 removed outlier: 3.833A pdb=" N HIS C 371 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 93 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.216A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 171 through 175 Processing helix chain 'D' and resid 181 through 194 Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 230 Processing helix chain 'D' and resid 251 through 260 removed outlier: 4.380A pdb=" N PHE D 255 " --> pdb=" O GLY D 251 " (cutoff:3.500A) Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 261 through 262 No H-bonds generated for 'chain 'D' and resid 261 through 262' Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 285 removed outlier: 3.517A pdb=" N CYS D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 296 Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 350 through 356 removed outlier: 3.896A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TRP D 356 " --> pdb=" O GLN D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 367 through 371 removed outlier: 3.839A pdb=" N HIS D 371 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 93 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 112 through 126 removed outlier: 4.240A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 181 through 194 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 230 Processing helix chain 'E' and resid 251 through 260 removed outlier: 4.377A pdb=" N PHE E 255 " --> pdb=" O GLY E 251 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 261 through 262 No H-bonds generated for 'chain 'E' and resid 261 through 262' Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 285 removed outlier: 3.525A pdb=" N CYS E 285 " --> pdb=" O SER E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 296 Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 349 Processing helix chain 'E' and resid 350 through 356 removed outlier: 3.897A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TRP E 356 " --> pdb=" O GLN E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 367 through 371 removed outlier: 3.834A pdb=" N HIS E 371 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 231 removed outlier: 3.830A pdb=" N UNK F 129 " --> pdb=" O UNK F 125 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N UNK F 143 " --> pdb=" O UNK F 139 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N UNK F 164 " --> pdb=" O UNK F 160 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N UNK F 170 " --> pdb=" O UNK F 166 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N UNK F 177 " --> pdb=" O UNK F 173 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N UNK F 178 " --> pdb=" O UNK F 174 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N UNK F 205 " --> pdb=" O UNK F 201 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N UNK F 209 " --> pdb=" O UNK F 205 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N UNK F 220 " --> pdb=" O UNK F 216 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N UNK F 223 " --> pdb=" O UNK F 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 231 removed outlier: 3.577A pdb=" N UNK G 123 " --> pdb=" O UNK G 119 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N UNK G 129 " --> pdb=" O UNK G 125 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N UNK G 143 " --> pdb=" O UNK G 139 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N UNK G 164 " --> pdb=" O UNK G 160 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N UNK G 165 " --> pdb=" O UNK G 161 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N UNK G 198 " --> pdb=" O UNK G 194 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N UNK G 219 " --> pdb=" O UNK G 215 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N UNK G 226 " --> pdb=" O UNK G 222 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N UNK G 227 " --> pdb=" O UNK G 223 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 6.454A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 removed outlier: 6.344A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.458A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA9, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.352A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB2, first strand: chain 'C' and resid 29 through 31 removed outlier: 6.461A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB4, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB5, first strand: chain 'C' and resid 176 through 178 removed outlier: 6.353A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB7, first strand: chain 'D' and resid 29 through 31 removed outlier: 6.457A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB9, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC1, first strand: chain 'D' and resid 176 through 178 removed outlier: 6.359A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC3, first strand: chain 'E' and resid 29 through 31 removed outlier: 6.453A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC5, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AC6, first strand: chain 'E' and resid 176 through 178 removed outlier: 6.354A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 238 through 241 971 hydrogen bonds defined for protein. 2583 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: 2.64 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2705 1.31 - 1.44: 4170 1.44 - 1.57: 9014 1.57 - 1.70: 44 1.70 - 1.83: 180 Bond restraints: 16113 Sorted by residual: bond pdb=" C ILE D 165 " pdb=" O ILE D 165 " ideal model delta sigma weight residual 1.236 1.301 -0.066 1.00e-02 1.00e+04 4.35e+01 bond pdb=" C ILE A 165 " pdb=" O ILE A 165 " ideal model delta sigma weight residual 1.236 1.299 -0.063 1.04e-02 9.25e+03 3.69e+01 bond pdb=" C ILE B 165 " pdb=" O ILE B 165 " ideal model delta sigma weight residual 1.236 1.297 -0.061 1.04e-02 9.25e+03 3.39e+01 bond pdb=" C ILE C 165 " pdb=" O ILE C 165 " ideal model delta sigma weight residual 1.236 1.294 -0.058 1.04e-02 9.25e+03 3.09e+01 bond pdb=" C ILE E 165 " pdb=" O ILE E 165 " ideal model delta sigma weight residual 1.236 1.292 -0.056 1.04e-02 9.25e+03 2.90e+01 ... (remaining 16108 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 20115 2.71 - 5.41: 1661 5.41 - 8.12: 145 8.12 - 10.83: 8 10.83 - 13.53: 5 Bond angle restraints: 21934 Sorted by residual: angle pdb=" N PHE C 127 " pdb=" CA PHE C 127 " pdb=" C PHE C 127 " ideal model delta sigma weight residual 110.55 97.02 13.53 1.35e+00 5.49e-01 1.00e+02 angle pdb=" N PHE E 127 " pdb=" CA PHE E 127 " pdb=" C PHE E 127 " ideal model delta sigma weight residual 110.48 96.98 13.50 1.48e+00 4.57e-01 8.32e+01 angle pdb=" N PHE A 127 " pdb=" CA PHE A 127 " pdb=" C PHE A 127 " ideal model delta sigma weight residual 110.48 97.12 13.36 1.48e+00 4.57e-01 8.15e+01 angle pdb=" N PHE D 127 " pdb=" CA PHE D 127 " pdb=" C PHE D 127 " ideal model delta sigma weight residual 110.48 97.21 13.27 1.48e+00 4.57e-01 8.04e+01 angle pdb=" N PHE B 127 " pdb=" CA PHE B 127 " pdb=" C PHE B 127 " ideal model delta sigma weight residual 110.48 97.30 13.18 1.48e+00 4.57e-01 7.93e+01 ... (remaining 21929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.56: 9095 18.56 - 37.13: 485 37.13 - 55.69: 91 55.69 - 74.25: 2 74.25 - 92.81: 5 Dihedral angle restraints: 9678 sinusoidal: 3570 harmonic: 6108 Sorted by residual: dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 32.82 -92.81 1 2.00e+01 2.50e-03 2.52e+01 dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 31.39 -91.39 1 2.00e+01 2.50e-03 2.46e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 30.05 -90.05 1 2.00e+01 2.50e-03 2.40e+01 ... (remaining 9675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1565 0.085 - 0.170: 648 0.170 - 0.254: 186 0.254 - 0.339: 78 0.339 - 0.424: 28 Chirality restraints: 2505 Sorted by residual: chirality pdb=" CA VAL B 17 " pdb=" N VAL B 17 " pdb=" C VAL B 17 " pdb=" CB VAL B 17 " both_signs ideal model delta sigma weight residual False 2.44 2.87 -0.42 2.00e-01 2.50e+01 4.49e+00 chirality pdb=" CA VAL E 17 " pdb=" N VAL E 17 " pdb=" C VAL E 17 " pdb=" CB VAL E 17 " both_signs ideal model delta sigma weight residual False 2.44 2.85 -0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" CA VAL A 17 " pdb=" N VAL A 17 " pdb=" C VAL A 17 " pdb=" CB VAL A 17 " both_signs ideal model delta sigma weight residual False 2.44 2.84 -0.40 2.00e-01 2.50e+01 4.05e+00 ... (remaining 2502 not shown) Planarity restraints: 2828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 340 " -0.046 2.00e-02 2.50e+03 2.58e-02 1.67e+01 pdb=" CG TRP A 340 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TRP A 340 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP A 340 " 0.023 2.00e-02 2.50e+03 pdb=" NE1 TRP A 340 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TRP A 340 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 340 " 0.020 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 340 " -0.044 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 340 " 0.021 2.00e-02 2.50e+03 pdb=" CH2 TRP A 340 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 340 " -0.047 2.00e-02 2.50e+03 2.58e-02 1.67e+01 pdb=" CG TRP E 340 " 0.004 2.00e-02 2.50e+03 pdb=" CD1 TRP E 340 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP E 340 " 0.020 2.00e-02 2.50e+03 pdb=" NE1 TRP E 340 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TRP E 340 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP E 340 " 0.019 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 340 " -0.044 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 340 " 0.022 2.00e-02 2.50e+03 pdb=" CH2 TRP E 340 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 340 " -0.044 2.00e-02 2.50e+03 2.50e-02 1.57e+01 pdb=" CG TRP D 340 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TRP D 340 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP D 340 " 0.020 2.00e-02 2.50e+03 pdb=" NE1 TRP D 340 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TRP D 340 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP D 340 " 0.017 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 340 " -0.044 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 340 " 0.023 2.00e-02 2.50e+03 pdb=" CH2 TRP D 340 " -0.012 2.00e-02 2.50e+03 ... (remaining 2825 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 927 2.73 - 3.27: 16847 3.27 - 3.81: 26019 3.81 - 4.36: 33045 4.36 - 4.90: 54065 Nonbonded interactions: 130903 Sorted by model distance: nonbonded pdb=" OD2 ASP D 286 " pdb=" O GLY E 63 " model vdw 2.184 3.040 nonbonded pdb=" O ALA A 295 " pdb=" O LYS A 328 " model vdw 2.322 3.040 nonbonded pdb=" O ALA C 295 " pdb=" O LYS C 328 " model vdw 2.324 3.040 nonbonded pdb=" O ALA D 295 " pdb=" O LYS D 328 " model vdw 2.326 3.040 nonbonded pdb=" O ALA B 295 " pdb=" O LYS B 328 " model vdw 2.332 3.040 ... (remaining 130898 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.090 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 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 : 0.013 0.066 16113 Z= 0.884 Angle : 1.579 13.532 21934 Z= 1.040 Chirality : 0.111 0.424 2505 Planarity : 0.010 0.055 2828 Dihedral : 12.258 92.812 5748 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.55 % Allowed : 2.87 % Favored : 96.57 % Rotamer: Outliers : 1.29 % Allowed : 4.34 % Favored : 94.37 % Cbeta Deviations : 0.87 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.19), residues: 1810 helix: -0.40 (0.18), residues: 710 sheet: -0.88 (0.25), residues: 350 loop : -0.04 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.003 ARG E 39 TYR 0.037 0.006 TYR E 166 PHE 0.060 0.008 PHE C 262 TRP 0.047 0.011 TRP E 340 HIS 0.033 0.007 HIS D 275 Details of bonding type rmsd/Z covalent geometry : bond 0.01273 / 0.88 (16113) covalent geometry : angle 1.57863 / 1.04 (21934) hydrogen bonds : bond 0.19145 / 12.73 ( 971) hydrogen bonds : angle 8.23836 / 5.77 ( 2583) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 487 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 GLN cc_start: 0.9234 (tt0) cc_final: 0.8962 (tm-30) REVERT: B 40 HIS cc_start: 0.7884 (m-70) cc_final: 0.7647 (m-70) REVERT: B 47 MET cc_start: 0.1902 (ptm) cc_final: 0.0927 (ttt) REVERT: B 86 TRP cc_start: 0.9389 (m-10) cc_final: 0.9175 (m-10) REVERT: B 115 ASN cc_start: 0.8510 (m-40) cc_final: 0.8260 (m110) REVERT: B 250 ILE cc_start: 0.9266 (pt) cc_final: 0.9024 (mm) REVERT: C 162 ASN cc_start: 0.8330 (m-40) cc_final: 0.8081 (m-40) REVERT: C 186 THR cc_start: 0.9580 (OUTLIER) cc_final: 0.9360 (t) REVERT: C 191 LYS cc_start: 0.8957 (ptmt) cc_final: 0.8472 (mtpp) REVERT: C 327 ILE cc_start: 0.9163 (mt) cc_final: 0.8927 (mp) REVERT: D 12 ASN cc_start: 0.8865 (m-40) cc_final: 0.8645 (m110) REVERT: D 44 MET cc_start: 0.8291 (mmm) cc_final: 0.7466 (mtt) REVERT: D 78 ASN cc_start: 0.8862 (t0) cc_final: 0.8520 (t0) REVERT: D 80 ASP cc_start: 0.8576 (p0) cc_final: 0.8323 (p0) REVERT: D 81 ASP cc_start: 0.9090 (m-30) cc_final: 0.8688 (m-30) REVERT: D 110 LEU cc_start: 0.9224 (tp) cc_final: 0.9019 (tt) REVERT: D 160 THR cc_start: 0.9438 (m) cc_final: 0.9196 (p) REVERT: D 353 GLN cc_start: 0.8783 (mt0) cc_final: 0.8522 (tm-30) REVERT: D 355 MET cc_start: 0.8740 (mtt) cc_final: 0.8348 (tpt) REVERT: E 12 ASN cc_start: 0.9209 (m-40) cc_final: 0.8786 (p0) REVERT: E 75 ILE cc_start: 0.9298 (mt) cc_final: 0.9073 (pt) REVERT: E 106 THR cc_start: 0.8429 (m) cc_final: 0.8125 (t) REVERT: E 157 ASP cc_start: 0.8577 (t0) cc_final: 0.8252 (t0) REVERT: E 162 ASN cc_start: 0.8471 (m-40) cc_final: 0.8174 (m-40) outliers start: 20 outliers final: 2 residues processed: 502 average time/residue: 0.1269 time to fit residues: 94.1067 Evaluate side-chains 285 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 282 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain E residue 186 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 30.0000 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 30.0000 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 HIS A 92 ASN A 246 GLN A 296 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN B 280 ASN B 296 ASN C 12 ASN ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN C 296 ASN D 12 ASN D 88 HIS D 92 ASN D 162 ASN D 296 ASN ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN E 59 GLN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN E 246 GLN E 280 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.102231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.095387 restraints weight = 53339.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.097216 restraints weight = 28539.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.098450 restraints weight = 17643.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.099231 restraints weight = 12369.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.099741 restraints weight = 9440.997| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16113 Z= 0.180 Angle : 0.771 12.902 21934 Z= 0.390 Chirality : 0.046 0.265 2505 Planarity : 0.006 0.083 2828 Dihedral : 7.241 69.307 2326 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.82 % Favored : 97.90 % Rotamer: Outliers : 3.37 % Allowed : 14.24 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.19), residues: 1810 helix: 0.12 (0.18), residues: 740 sheet: -0.35 (0.26), residues: 320 loop : 0.06 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 95 TYR 0.018 0.002 TYR A 294 PHE 0.023 0.002 PHE B 255 TRP 0.029 0.002 TRP C 340 HIS 0.008 0.002 HIS E 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (16113) covalent geometry : angle 0.77085 / 0.39 (21934) hydrogen bonds : bond 0.05022 / 3.32 ( 971) hydrogen bonds : angle 5.51151 / 3.86 ( 2583) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 328 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 VAL cc_start: 0.8801 (OUTLIER) cc_final: 0.8564 (m) REVERT: A 78 ASN cc_start: 0.8679 (t0) cc_final: 0.8424 (t0) REVERT: A 132 MET cc_start: 0.8515 (ptm) cc_final: 0.8184 (ppp) REVERT: A 325 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.7051 (ptm) REVERT: B 40 HIS cc_start: 0.7565 (m-70) cc_final: 0.7334 (m90) REVERT: B 44 MET cc_start: 0.8322 (mpp) cc_final: 0.7682 (mpp) REVERT: B 47 MET cc_start: 0.1604 (ptm) cc_final: 0.0972 (ttt) REVERT: B 65 LEU cc_start: 0.8953 (mt) cc_final: 0.8705 (mt) REVERT: B 72 GLU cc_start: 0.7973 (mp0) cc_final: 0.7761 (mp0) REVERT: B 107 GLU cc_start: 0.7024 (pm20) cc_final: 0.6777 (tt0) REVERT: B 137 GLN cc_start: 0.8426 (mt0) cc_final: 0.7606 (mp10) REVERT: B 222 ASP cc_start: 0.8720 (t0) cc_final: 0.8380 (t70) REVERT: B 327 ILE cc_start: 0.9274 (mt) cc_final: 0.8985 (mt) REVERT: B 360 GLN cc_start: 0.8872 (pp30) cc_final: 0.8107 (pp30) REVERT: C 65 LEU cc_start: 0.9173 (mt) cc_final: 0.8944 (mt) REVERT: C 137 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8544 (mm-40) REVERT: C 180 LEU cc_start: 0.9007 (mt) cc_final: 0.8717 (mt) REVERT: C 190 MET cc_start: 0.8730 (mmm) cc_final: 0.8491 (mtp) REVERT: C 280 ASN cc_start: 0.9312 (m-40) cc_final: 0.9057 (m110) REVERT: C 340 TRP cc_start: 0.8575 (t60) cc_final: 0.8356 (t60) REVERT: D 44 MET cc_start: 0.7670 (mmm) cc_final: 0.7089 (mtt) REVERT: D 82 MET cc_start: 0.9073 (tpt) cc_final: 0.8738 (tpt) REVERT: D 110 LEU cc_start: 0.9161 (tp) cc_final: 0.8705 (tt) REVERT: D 142 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9021 (mp) REVERT: D 162 ASN cc_start: 0.8900 (OUTLIER) cc_final: 0.8637 (t0) REVERT: D 328 LYS cc_start: 0.8921 (ttpp) cc_final: 0.8515 (ttpp) REVERT: E 162 ASN cc_start: 0.8359 (m-40) cc_final: 0.8150 (m-40) REVERT: E 227 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8349 (tpp) REVERT: E 276 GLU cc_start: 0.7680 (mp0) cc_final: 0.7468 (mp0) REVERT: E 305 MET cc_start: 0.8881 (mmm) cc_final: 0.8637 (mmt) outliers start: 52 outliers final: 22 residues processed: 365 average time/residue: 0.1024 time to fit residues: 57.7988 Evaluate side-chains 274 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 247 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 227 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 56 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 176 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS B 263 GLN ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN E 12 ASN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN E 246 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.100113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.093326 restraints weight = 54509.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.094920 restraints weight = 29227.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.096374 restraints weight = 18666.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.097062 restraints weight = 13214.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.097634 restraints weight = 10092.255| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16113 Z= 0.183 Angle : 0.699 9.350 21934 Z= 0.352 Chirality : 0.045 0.212 2505 Planarity : 0.004 0.057 2828 Dihedral : 6.667 64.564 2324 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.99 % Favored : 97.73 % Rotamer: Outliers : 3.43 % Allowed : 16.63 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.19), residues: 1810 helix: 0.26 (0.19), residues: 745 sheet: -0.31 (0.27), residues: 320 loop : 0.15 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 95 TYR 0.025 0.001 TYR C 166 PHE 0.020 0.002 PHE A 352 TRP 0.018 0.002 TRP C 340 HIS 0.007 0.001 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (16113) covalent geometry : angle 0.69880 / 0.35 (21934) hydrogen bonds : bond 0.04379 / 2.92 ( 971) hydrogen bonds : angle 5.06409 / 3.54 ( 2583) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 269 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8746 (t0) cc_final: 0.8464 (t0) REVERT: A 132 MET cc_start: 0.8466 (ptm) cc_final: 0.8250 (ppp) REVERT: A 325 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6999 (ptm) REVERT: B 40 HIS cc_start: 0.7578 (m-70) cc_final: 0.7313 (m90) REVERT: B 44 MET cc_start: 0.8195 (mpp) cc_final: 0.7515 (mpp) REVERT: B 47 MET cc_start: 0.1330 (ptm) cc_final: 0.0961 (ttm) REVERT: B 65 LEU cc_start: 0.8955 (mt) cc_final: 0.8741 (mt) REVERT: B 137 GLN cc_start: 0.8519 (mt0) cc_final: 0.7691 (mp10) REVERT: B 176 MET cc_start: 0.8598 (mtt) cc_final: 0.8317 (mtt) REVERT: B 246 GLN cc_start: 0.7842 (tm-30) cc_final: 0.7569 (tm-30) REVERT: B 247 VAL cc_start: 0.9266 (t) cc_final: 0.8921 (p) REVERT: B 360 GLN cc_start: 0.8823 (pp30) cc_final: 0.8108 (pp30) REVERT: C 44 MET cc_start: 0.8323 (tpp) cc_final: 0.7952 (tpp) REVERT: C 137 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8435 (mm-40) REVERT: C 192 ILE cc_start: 0.8669 (tp) cc_final: 0.8381 (tp) REVERT: C 270 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6964 (mp0) REVERT: C 271 SER cc_start: 0.9065 (m) cc_final: 0.8654 (p) REVERT: C 280 ASN cc_start: 0.9325 (m-40) cc_final: 0.8983 (m110) REVERT: D 44 MET cc_start: 0.7644 (mmm) cc_final: 0.6930 (mtt) REVERT: D 47 MET cc_start: 0.2661 (tmm) cc_final: 0.1409 (tmm) REVERT: D 110 LEU cc_start: 0.9180 (tp) cc_final: 0.8857 (tt) REVERT: D 142 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.8994 (mp) REVERT: D 162 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8503 (t0) REVERT: E 227 MET cc_start: 0.8708 (mmm) cc_final: 0.8380 (tpp) REVERT: E 276 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: E 280 ASN cc_start: 0.8835 (m-40) cc_final: 0.8626 (m110) REVERT: E 305 MET cc_start: 0.8798 (mmm) cc_final: 0.8571 (mmt) outliers start: 53 outliers final: 26 residues processed: 305 average time/residue: 0.0993 time to fit residues: 49.3753 Evaluate side-chains 258 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 228 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 32 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 chunk 101 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 180 optimal weight: 30.0000 chunk 163 optimal weight: 7.9990 chunk 171 optimal weight: 0.5980 chunk 158 optimal weight: 0.8980 chunk 200 optimal weight: 40.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 12 ASN B 92 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.098351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.092863 restraints weight = 51546.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.093843 restraints weight = 27268.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.094595 restraints weight = 16764.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.095502 restraints weight = 12697.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.095789 restraints weight = 9980.575| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16113 Z= 0.156 Angle : 0.663 9.605 21934 Z= 0.328 Chirality : 0.045 0.249 2505 Planarity : 0.004 0.051 2828 Dihedral : 6.229 59.956 2324 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.60 % Favored : 97.13 % Rotamer: Outliers : 3.50 % Allowed : 17.99 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.20), residues: 1810 helix: 0.50 (0.19), residues: 730 sheet: -0.25 (0.27), residues: 320 loop : 0.22 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 95 TYR 0.021 0.001 TYR C 166 PHE 0.011 0.001 PHE C 262 TRP 0.013 0.001 TRP C 340 HIS 0.007 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (16113) covalent geometry : angle 0.66271 / 0.33 (21934) hydrogen bonds : bond 0.03949 / 2.64 ( 971) hydrogen bonds : angle 4.80566 / 3.35 ( 2583) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 255 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8797 (t0) cc_final: 0.8460 (t0) REVERT: A 225 ASN cc_start: 0.8988 (m-40) cc_final: 0.8697 (t0) REVERT: A 305 MET cc_start: 0.8729 (tpp) cc_final: 0.8390 (mmt) REVERT: B 40 HIS cc_start: 0.7513 (m-70) cc_final: 0.7231 (m90) REVERT: B 44 MET cc_start: 0.8096 (tpp) cc_final: 0.7331 (mpp) REVERT: B 47 MET cc_start: 0.1352 (ptm) cc_final: 0.0676 (ttt) REVERT: B 72 GLU cc_start: 0.7979 (mp0) cc_final: 0.7723 (mp0) REVERT: B 137 GLN cc_start: 0.8425 (mt0) cc_final: 0.7967 (mp10) REVERT: B 167 GLU cc_start: 0.9244 (mm-30) cc_final: 0.8620 (mp0) REVERT: B 176 MET cc_start: 0.8630 (mtt) cc_final: 0.8278 (mtt) REVERT: B 247 VAL cc_start: 0.9234 (t) cc_final: 0.9025 (p) REVERT: B 276 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8089 (mp0) REVERT: B 279 TYR cc_start: 0.9132 (t80) cc_final: 0.8761 (t80) REVERT: B 283 MET cc_start: 0.9078 (mmp) cc_final: 0.8870 (mmm) REVERT: B 360 GLN cc_start: 0.8868 (pp30) cc_final: 0.8246 (pp30) REVERT: C 44 MET cc_start: 0.8378 (tpp) cc_final: 0.8060 (tpp) REVERT: C 137 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8623 (mm-40) REVERT: C 192 ILE cc_start: 0.8543 (tp) cc_final: 0.8200 (tp) REVERT: C 270 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7049 (mp0) REVERT: C 271 SER cc_start: 0.9074 (m) cc_final: 0.8735 (p) REVERT: C 280 ASN cc_start: 0.9354 (m-40) cc_final: 0.9049 (m-40) REVERT: C 299 MET cc_start: 0.8449 (mmt) cc_final: 0.8165 (mmm) REVERT: C 314 GLN cc_start: 0.8969 (tp40) cc_final: 0.8514 (tp40) REVERT: C 353 GLN cc_start: 0.9083 (tp40) cc_final: 0.8425 (tp-100) REVERT: D 44 MET cc_start: 0.7934 (mmm) cc_final: 0.7018 (mtt) REVERT: D 47 MET cc_start: 0.2165 (tmm) cc_final: 0.1305 (tmm) REVERT: D 142 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.8996 (mp) REVERT: D 192 ILE cc_start: 0.9216 (tp) cc_final: 0.8725 (tp) REVERT: D 356 TRP cc_start: 0.8685 (m100) cc_final: 0.8356 (m100) REVERT: E 78 ASN cc_start: 0.8463 (t0) cc_final: 0.7001 (t0) REVERT: E 81 ASP cc_start: 0.7987 (m-30) cc_final: 0.7743 (m-30) REVERT: E 206 ARG cc_start: 0.8671 (mtp-110) cc_final: 0.8274 (ttp-170) REVERT: E 227 MET cc_start: 0.8787 (mmm) cc_final: 0.8432 (tpp) REVERT: E 276 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7258 (mp0) REVERT: E 280 ASN cc_start: 0.8866 (m-40) cc_final: 0.8516 (m110) REVERT: E 305 MET cc_start: 0.8814 (mmm) cc_final: 0.8605 (mmt) outliers start: 54 outliers final: 32 residues processed: 298 average time/residue: 0.1017 time to fit residues: 49.1904 Evaluate side-chains 271 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 236 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 66 optimal weight: 0.8980 chunk 170 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 193 optimal weight: 40.0000 chunk 17 optimal weight: 7.9990 chunk 200 optimal weight: 40.0000 chunk 172 optimal weight: 0.4980 chunk 50 optimal weight: 7.9990 chunk 110 optimal weight: 0.0040 chunk 32 optimal weight: 6.9990 chunk 194 optimal weight: 30.0000 overall best weight: 2.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 12 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN D 115 ASN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.097669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.091231 restraints weight = 55432.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.092806 restraints weight = 29097.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.094053 restraints weight = 17744.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.094716 restraints weight = 12338.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.095276 restraints weight = 9540.437| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16113 Z= 0.220 Angle : 0.693 8.329 21934 Z= 0.344 Chirality : 0.045 0.176 2505 Planarity : 0.004 0.055 2828 Dihedral : 6.138 60.135 2323 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.93 % Favored : 96.80 % Rotamer: Outliers : 4.85 % Allowed : 17.80 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.20), residues: 1810 helix: 0.54 (0.19), residues: 725 sheet: -0.35 (0.27), residues: 320 loop : 0.31 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 290 TYR 0.023 0.001 TYR C 166 PHE 0.026 0.002 PHE C 352 TRP 0.039 0.002 TRP C 340 HIS 0.006 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.22 (16113) covalent geometry : angle 0.69344 / 0.34 (21934) hydrogen bonds : bond 0.03862 / 2.58 ( 971) hydrogen bonds : angle 4.73769 / 3.30 ( 2583) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 244 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8739 (t0) cc_final: 0.8427 (t0) REVERT: A 107 GLU cc_start: 0.7976 (tp30) cc_final: 0.7580 (tm-30) REVERT: A 211 ASP cc_start: 0.8675 (t0) cc_final: 0.8409 (t0) REVERT: A 225 ASN cc_start: 0.8958 (m-40) cc_final: 0.8740 (t0) REVERT: B 40 HIS cc_start: 0.7566 (m-70) cc_final: 0.7306 (m90) REVERT: B 44 MET cc_start: 0.8308 (tpp) cc_final: 0.7529 (mpp) REVERT: B 47 MET cc_start: 0.1384 (ptm) cc_final: 0.0512 (ttt) REVERT: B 88 HIS cc_start: 0.8575 (OUTLIER) cc_final: 0.7848 (t-90) REVERT: B 110 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8790 (tt) REVERT: B 137 GLN cc_start: 0.8553 (mt0) cc_final: 0.8023 (mp10) REVERT: B 167 GLU cc_start: 0.9233 (mm-30) cc_final: 0.8613 (mp0) REVERT: B 246 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7857 (tm-30) REVERT: B 276 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8063 (mp0) REVERT: B 279 TYR cc_start: 0.9256 (t80) cc_final: 0.8873 (t80) REVERT: B 283 MET cc_start: 0.9095 (mmp) cc_final: 0.8883 (mmm) REVERT: B 360 GLN cc_start: 0.8782 (pp30) cc_final: 0.8105 (pp30) REVERT: C 44 MET cc_start: 0.8386 (tpp) cc_final: 0.8079 (tpp) REVERT: C 137 GLN cc_start: 0.8840 (mt0) cc_final: 0.8623 (mm-40) REVERT: C 191 LYS cc_start: 0.8787 (ttmm) cc_final: 0.8544 (mmtp) REVERT: C 192 ILE cc_start: 0.8667 (tp) cc_final: 0.8305 (tp) REVERT: C 270 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7004 (mp0) REVERT: C 271 SER cc_start: 0.9117 (m) cc_final: 0.8817 (p) REVERT: C 276 GLU cc_start: 0.8309 (mp0) cc_final: 0.8057 (mp0) REVERT: C 280 ASN cc_start: 0.9384 (m-40) cc_final: 0.9089 (m-40) REVERT: C 314 GLN cc_start: 0.9039 (tp40) cc_final: 0.8501 (tp40) REVERT: C 353 GLN cc_start: 0.8977 (tp40) cc_final: 0.8592 (tp-100) REVERT: D 44 MET cc_start: 0.7998 (mmm) cc_final: 0.7039 (mtt) REVERT: D 47 MET cc_start: 0.2201 (tmm) cc_final: 0.1473 (tmm) REVERT: D 142 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9041 (mp) REVERT: D 192 ILE cc_start: 0.9275 (tp) cc_final: 0.8824 (tp) REVERT: E 78 ASN cc_start: 0.8594 (t0) cc_final: 0.7750 (t0) REVERT: E 81 ASP cc_start: 0.8087 (m-30) cc_final: 0.7748 (m-30) REVERT: E 119 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7895 (ttm) REVERT: E 180 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9088 (tt) REVERT: E 206 ARG cc_start: 0.8658 (mtp-110) cc_final: 0.8398 (ttm-80) REVERT: E 227 MET cc_start: 0.8754 (mmm) cc_final: 0.8452 (tpp) REVERT: E 276 GLU cc_start: 0.7411 (mp0) cc_final: 0.7186 (mp0) REVERT: E 299 MET cc_start: 0.8940 (mmt) cc_final: 0.8606 (mmt) REVERT: E 305 MET cc_start: 0.8696 (mmm) cc_final: 0.8427 (mmt) outliers start: 75 outliers final: 45 residues processed: 303 average time/residue: 0.0991 time to fit residues: 49.1120 Evaluate side-chains 276 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 225 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 60 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 22 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN B 12 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.097917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.091009 restraints weight = 54494.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.092751 restraints weight = 28845.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.094179 restraints weight = 18126.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.095045 restraints weight = 12285.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.095366 restraints weight = 9019.652| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16113 Z= 0.154 Angle : 0.660 12.113 21934 Z= 0.320 Chirality : 0.044 0.252 2505 Planarity : 0.004 0.058 2828 Dihedral : 5.922 56.764 2323 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.93 % Favored : 96.80 % Rotamer: Outliers : 4.08 % Allowed : 19.35 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.20), residues: 1810 helix: 0.69 (0.19), residues: 725 sheet: -0.39 (0.27), residues: 320 loop : 0.33 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 290 TYR 0.024 0.001 TYR C 166 PHE 0.024 0.001 PHE C 352 TRP 0.038 0.002 TRP C 340 HIS 0.005 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (16113) covalent geometry : angle 0.65997 / 0.32 (21934) hydrogen bonds : bond 0.03644 / 2.43 ( 971) hydrogen bonds : angle 4.61921 / 3.21 ( 2583) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 263 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8770 (t0) cc_final: 0.7573 (t0) REVERT: A 81 ASP cc_start: 0.9060 (m-30) cc_final: 0.8413 (m-30) REVERT: A 121 GLN cc_start: 0.9283 (tt0) cc_final: 0.8914 (tm-30) REVERT: A 225 ASN cc_start: 0.9023 (m-40) cc_final: 0.8769 (t0) REVERT: A 360 GLN cc_start: 0.8849 (pp30) cc_final: 0.8563 (pp30) REVERT: B 40 HIS cc_start: 0.7466 (m-70) cc_final: 0.7160 (m90) REVERT: B 44 MET cc_start: 0.8318 (tpp) cc_final: 0.7874 (tpp) REVERT: B 47 MET cc_start: 0.1486 (ptm) cc_final: 0.0744 (ttt) REVERT: B 88 HIS cc_start: 0.8593 (OUTLIER) cc_final: 0.7962 (t-90) REVERT: B 110 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8746 (tt) REVERT: B 125 GLU cc_start: 0.9182 (mp0) cc_final: 0.8974 (mp0) REVERT: B 137 GLN cc_start: 0.8551 (mt0) cc_final: 0.8012 (mp10) REVERT: B 167 GLU cc_start: 0.9222 (mm-30) cc_final: 0.8578 (mp0) REVERT: B 276 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8319 (mp0) REVERT: B 279 TYR cc_start: 0.9182 (t80) cc_final: 0.8782 (t80) REVERT: B 360 GLN cc_start: 0.8894 (pp30) cc_final: 0.8163 (pp30) REVERT: C 44 MET cc_start: 0.8371 (tpp) cc_final: 0.8071 (tpp) REVERT: C 59 GLN cc_start: 0.8414 (mm-40) cc_final: 0.7709 (tp40) REVERT: C 137 GLN cc_start: 0.8844 (mt0) cc_final: 0.8635 (mm-40) REVERT: C 191 LYS cc_start: 0.8739 (ttmm) cc_final: 0.8505 (mmtp) REVERT: C 192 ILE cc_start: 0.8594 (tp) cc_final: 0.8344 (pt) REVERT: C 270 GLU cc_start: 0.7670 (mt-10) cc_final: 0.6960 (mp0) REVERT: C 271 SER cc_start: 0.9143 (m) cc_final: 0.8843 (p) REVERT: C 276 GLU cc_start: 0.8380 (mp0) cc_final: 0.8143 (mp0) REVERT: C 314 GLN cc_start: 0.9056 (tp40) cc_final: 0.8524 (tp40) REVERT: D 44 MET cc_start: 0.8129 (mmm) cc_final: 0.7071 (mtt) REVERT: D 47 MET cc_start: 0.2102 (tmm) cc_final: 0.1567 (tmm) REVERT: D 72 GLU cc_start: 0.8074 (pp20) cc_final: 0.7803 (pp20) REVERT: D 142 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9028 (mp) REVERT: D 192 ILE cc_start: 0.9192 (tp) cc_final: 0.8712 (tp) REVERT: D 269 MET cc_start: 0.7997 (mtm) cc_final: 0.7763 (ptm) REVERT: D 276 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8380 (mm-30) REVERT: D 280 ASN cc_start: 0.9016 (m-40) cc_final: 0.8717 (m-40) REVERT: D 356 TRP cc_start: 0.8790 (m100) cc_final: 0.8440 (m100) REVERT: E 78 ASN cc_start: 0.8548 (t0) cc_final: 0.7436 (t0) REVERT: E 81 ASP cc_start: 0.8133 (m-30) cc_final: 0.7684 (m-30) REVERT: E 206 ARG cc_start: 0.8632 (mtp-110) cc_final: 0.8377 (ttm-80) REVERT: E 227 MET cc_start: 0.8761 (mmm) cc_final: 0.8438 (tpp) REVERT: E 276 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7219 (mp0) outliers start: 63 outliers final: 39 residues processed: 307 average time/residue: 0.0995 time to fit residues: 49.4206 Evaluate side-chains 284 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 240 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 99 optimal weight: 2.9990 chunk 182 optimal weight: 50.0000 chunk 79 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 167 optimal weight: 7.9990 chunk 200 optimal weight: 40.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.096218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.089427 restraints weight = 54800.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.091265 restraints weight = 29174.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.092399 restraints weight = 17894.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.093177 restraints weight = 12903.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.093521 restraints weight = 9971.128| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16113 Z= 0.227 Angle : 0.714 10.925 21934 Z= 0.349 Chirality : 0.045 0.185 2505 Planarity : 0.004 0.057 2828 Dihedral : 5.939 57.294 2323 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.09 % Favored : 96.63 % Rotamer: Outliers : 4.40 % Allowed : 19.87 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.20), residues: 1810 helix: 0.69 (0.19), residues: 725 sheet: -0.61 (0.27), residues: 325 loop : 0.37 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 290 TYR 0.026 0.001 TYR C 166 PHE 0.019 0.002 PHE C 352 TRP 0.029 0.002 TRP C 340 HIS 0.007 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.23 (16113) covalent geometry : angle 0.71351 / 0.35 (21934) hydrogen bonds : bond 0.03655 / 2.45 ( 971) hydrogen bonds : angle 4.63287 / 3.22 ( 2583) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 247 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8745 (t0) cc_final: 0.7564 (t0) REVERT: A 81 ASP cc_start: 0.9016 (m-30) cc_final: 0.8284 (m-30) REVERT: A 107 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7796 (tm-30) REVERT: A 121 GLN cc_start: 0.9218 (tt0) cc_final: 0.8913 (tm-30) REVERT: A 211 ASP cc_start: 0.8722 (t0) cc_final: 0.8471 (t0) REVERT: B 40 HIS cc_start: 0.7413 (m-70) cc_final: 0.7073 (m90) REVERT: B 44 MET cc_start: 0.8361 (tpp) cc_final: 0.7942 (tpp) REVERT: B 47 MET cc_start: 0.1787 (ptm) cc_final: 0.1035 (ttt) REVERT: B 88 HIS cc_start: 0.8604 (OUTLIER) cc_final: 0.7920 (t-90) REVERT: B 137 GLN cc_start: 0.8603 (mt0) cc_final: 0.8327 (mp10) REVERT: B 276 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8076 (mp0) REVERT: B 360 GLN cc_start: 0.8910 (pp30) cc_final: 0.8634 (pp30) REVERT: C 44 MET cc_start: 0.8398 (tpp) cc_final: 0.8042 (tpp) REVERT: C 137 GLN cc_start: 0.8860 (mt0) cc_final: 0.8496 (mm-40) REVERT: C 191 LYS cc_start: 0.8749 (ttmm) cc_final: 0.8520 (mmtp) REVERT: C 192 ILE cc_start: 0.8682 (tp) cc_final: 0.8377 (pt) REVERT: C 270 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6523 (mp0) REVERT: C 271 SER cc_start: 0.9090 (m) cc_final: 0.8798 (p) REVERT: C 276 GLU cc_start: 0.8318 (mp0) cc_final: 0.8084 (mp0) REVERT: C 314 GLN cc_start: 0.9080 (tp40) cc_final: 0.8518 (tp-100) REVERT: D 44 MET cc_start: 0.8074 (mmm) cc_final: 0.6971 (mtt) REVERT: D 47 MET cc_start: 0.2241 (tmm) cc_final: 0.1592 (tmm) REVERT: D 72 GLU cc_start: 0.8106 (pp20) cc_final: 0.7834 (pp20) REVERT: D 142 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9047 (mp) REVERT: D 192 ILE cc_start: 0.9244 (tp) cc_final: 0.8808 (tp) REVERT: D 227 MET cc_start: 0.8704 (mmm) cc_final: 0.8483 (mmm) REVERT: E 162 ASN cc_start: 0.8868 (t0) cc_final: 0.8506 (t0) REVERT: E 206 ARG cc_start: 0.8710 (mtp-110) cc_final: 0.8498 (ttm-80) REVERT: E 227 MET cc_start: 0.8809 (mmm) cc_final: 0.8451 (tpp) REVERT: E 314 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8569 (tm-30) outliers start: 68 outliers final: 44 residues processed: 296 average time/residue: 0.0959 time to fit residues: 46.7281 Evaluate side-chains 280 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 232 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 178 optimal weight: 0.9980 chunk 104 optimal weight: 0.2980 chunk 96 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 186 optimal weight: 30.0000 chunk 26 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 118 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 167 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN A 280 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN D 162 ASN E 78 ASN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.095267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.089060 restraints weight = 52015.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.090661 restraints weight = 28906.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.091563 restraints weight = 19252.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.092169 restraints weight = 14735.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.092780 restraints weight = 12265.635| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16113 Z= 0.151 Angle : 0.688 11.049 21934 Z= 0.336 Chirality : 0.044 0.184 2505 Planarity : 0.004 0.058 2828 Dihedral : 5.771 52.799 2323 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.98 % Favored : 96.74 % Rotamer: Outliers : 4.08 % Allowed : 20.65 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.20), residues: 1810 helix: 0.76 (0.20), residues: 725 sheet: -0.45 (0.27), residues: 320 loop : 0.35 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 290 TYR 0.032 0.001 TYR B 279 PHE 0.011 0.001 PHE C 352 TRP 0.065 0.002 TRP C 340 HIS 0.006 0.001 HIS E 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (16113) covalent geometry : angle 0.68752 / 0.34 (21934) hydrogen bonds : bond 0.03552 / 2.37 ( 971) hydrogen bonds : angle 4.58078 / 3.18 ( 2583) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 255 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8716 (t0) cc_final: 0.7630 (t0) REVERT: A 81 ASP cc_start: 0.8982 (m-30) cc_final: 0.8252 (m-30) REVERT: A 107 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7669 (tm-30) REVERT: A 121 GLN cc_start: 0.9222 (tt0) cc_final: 0.8933 (tm-30) REVERT: B 40 HIS cc_start: 0.7378 (m-70) cc_final: 0.6990 (m90) REVERT: B 47 MET cc_start: 0.1683 (ptm) cc_final: 0.0927 (ttt) REVERT: B 88 HIS cc_start: 0.8633 (OUTLIER) cc_final: 0.8078 (t-90) REVERT: B 110 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8859 (tt) REVERT: B 137 GLN cc_start: 0.8502 (mt0) cc_final: 0.8069 (mp10) REVERT: B 167 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8799 (mp0) REVERT: B 176 MET cc_start: 0.8380 (mtt) cc_final: 0.8152 (mtt) REVERT: B 276 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8013 (mp0) REVERT: B 360 GLN cc_start: 0.8858 (pp30) cc_final: 0.8215 (pp30) REVERT: C 44 MET cc_start: 0.8389 (tpp) cc_final: 0.8045 (tpp) REVERT: C 137 GLN cc_start: 0.8823 (mt0) cc_final: 0.8529 (mm-40) REVERT: C 192 ILE cc_start: 0.8685 (tp) cc_final: 0.8435 (pt) REVERT: C 263 GLN cc_start: 0.9076 (mm110) cc_final: 0.8866 (mm-40) REVERT: C 270 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6522 (mp0) REVERT: C 271 SER cc_start: 0.9041 (m) cc_final: 0.8763 (p) REVERT: C 276 GLU cc_start: 0.8418 (mp0) cc_final: 0.8173 (mp0) REVERT: C 290 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.7660 (mtp85) REVERT: C 314 GLN cc_start: 0.9035 (tp40) cc_final: 0.8475 (tp-100) REVERT: D 44 MET cc_start: 0.8229 (mmm) cc_final: 0.7091 (mtt) REVERT: D 47 MET cc_start: 0.2048 (tmm) cc_final: 0.1566 (tmm) REVERT: D 72 GLU cc_start: 0.8084 (pp20) cc_final: 0.7843 (pp20) REVERT: D 82 MET cc_start: 0.8882 (tpp) cc_final: 0.8453 (tmm) REVERT: D 142 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9036 (mp) REVERT: D 192 ILE cc_start: 0.9255 (tp) cc_final: 0.8807 (tp) REVERT: D 280 ASN cc_start: 0.9005 (m-40) cc_final: 0.8765 (m-40) REVERT: E 162 ASN cc_start: 0.8783 (t0) cc_final: 0.8428 (t0) REVERT: E 206 ARG cc_start: 0.8634 (mtp-110) cc_final: 0.8387 (ttm-80) REVERT: E 227 MET cc_start: 0.8816 (mmm) cc_final: 0.8475 (tpp) REVERT: E 314 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8477 (tm-30) outliers start: 63 outliers final: 42 residues processed: 305 average time/residue: 0.0962 time to fit residues: 47.1606 Evaluate side-chains 285 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 237 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 143 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 195 optimal weight: 30.0000 chunk 164 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 172 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 181 optimal weight: 50.0000 chunk 7 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN A 280 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.094985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.088821 restraints weight = 52101.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.090458 restraints weight = 29035.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.091503 restraints weight = 18614.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.092001 restraints weight = 14037.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.092645 restraints weight = 11805.391| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.5058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16113 Z= 0.157 Angle : 0.703 11.156 21934 Z= 0.342 Chirality : 0.044 0.188 2505 Planarity : 0.004 0.059 2828 Dihedral : 5.733 51.188 2323 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.82 % Favored : 96.91 % Rotamer: Outliers : 3.56 % Allowed : 21.49 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.20), residues: 1810 helix: 0.75 (0.19), residues: 725 sheet: -0.41 (0.28), residues: 320 loop : 0.33 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 290 TYR 0.025 0.001 TYR C 166 PHE 0.017 0.001 PHE D 124 TRP 0.067 0.002 TRP C 340 HIS 0.005 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (16113) covalent geometry : angle 0.70279 / 0.34 (21934) hydrogen bonds : bond 0.03500 / 2.34 ( 971) hydrogen bonds : angle 4.54205 / 3.14 ( 2583) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 246 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8754 (t0) cc_final: 0.8464 (t0) REVERT: A 82 MET cc_start: 0.8932 (tpp) cc_final: 0.8674 (mmm) REVERT: A 121 GLN cc_start: 0.9198 (tt0) cc_final: 0.8866 (tm-30) REVERT: B 40 HIS cc_start: 0.7442 (m-70) cc_final: 0.7037 (m90) REVERT: B 47 MET cc_start: 0.1511 (ptm) cc_final: 0.0812 (ttt) REVERT: B 88 HIS cc_start: 0.8652 (OUTLIER) cc_final: 0.8127 (t-90) REVERT: B 110 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8864 (tt) REVERT: B 137 GLN cc_start: 0.8537 (mt0) cc_final: 0.8040 (mp10) REVERT: B 167 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8811 (mp0) REVERT: B 176 MET cc_start: 0.8335 (mtt) cc_final: 0.8055 (mtt) REVERT: B 222 ASP cc_start: 0.8781 (OUTLIER) cc_final: 0.8379 (p0) REVERT: B 227 MET cc_start: 0.9298 (mmm) cc_final: 0.9072 (mmm) REVERT: B 276 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8012 (mp0) REVERT: B 279 TYR cc_start: 0.9007 (t80) cc_final: 0.8644 (t80) REVERT: B 360 GLN cc_start: 0.8842 (pp30) cc_final: 0.8188 (pp30) REVERT: C 44 MET cc_start: 0.8376 (tpp) cc_final: 0.8077 (tpp) REVERT: C 137 GLN cc_start: 0.8849 (mt0) cc_final: 0.8596 (mm-40) REVERT: C 192 ILE cc_start: 0.8679 (tp) cc_final: 0.8435 (pt) REVERT: C 263 GLN cc_start: 0.9069 (mm110) cc_final: 0.8852 (mm-40) REVERT: C 270 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6509 (mp0) REVERT: C 271 SER cc_start: 0.9042 (m) cc_final: 0.8785 (p) REVERT: C 276 GLU cc_start: 0.8399 (mp0) cc_final: 0.8175 (mp0) REVERT: C 290 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.7709 (mtp85) REVERT: C 313 MET cc_start: 0.9122 (mmm) cc_final: 0.8901 (mmm) REVERT: C 314 GLN cc_start: 0.9043 (tp40) cc_final: 0.8496 (tp-100) REVERT: C 340 TRP cc_start: 0.8523 (t60) cc_final: 0.7830 (t60) REVERT: D 44 MET cc_start: 0.8079 (mmm) cc_final: 0.7149 (mtt) REVERT: D 47 MET cc_start: 0.1919 (tmm) cc_final: 0.1551 (tmm) REVERT: D 72 GLU cc_start: 0.8067 (pp20) cc_final: 0.7837 (pp20) REVERT: D 82 MET cc_start: 0.8906 (tpp) cc_final: 0.8457 (tmm) REVERT: D 142 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9036 (mp) REVERT: D 192 ILE cc_start: 0.9245 (tp) cc_final: 0.8793 (tp) REVERT: D 280 ASN cc_start: 0.8989 (m-40) cc_final: 0.8754 (m-40) REVERT: E 162 ASN cc_start: 0.8853 (t0) cc_final: 0.8483 (t0) REVERT: E 206 ARG cc_start: 0.8634 (mtp-110) cc_final: 0.8378 (ttm-80) REVERT: E 227 MET cc_start: 0.8863 (mmm) cc_final: 0.8524 (tpp) REVERT: E 314 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8515 (tm-30) outliers start: 55 outliers final: 43 residues processed: 287 average time/residue: 0.0919 time to fit residues: 43.2493 Evaluate side-chains 286 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 236 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 86 TRP Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 36 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 59 optimal weight: 0.0070 chunk 113 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 201 optimal weight: 50.0000 chunk 204 optimal weight: 30.0000 chunk 151 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 200 optimal weight: 30.0000 chunk 144 optimal weight: 10.0000 overall best weight: 2.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN B 353 GLN ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN E 78 ASN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.094378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.088136 restraints weight = 52214.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.089662 restraints weight = 29001.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.090901 restraints weight = 18764.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.091702 restraints weight = 13721.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.091941 restraints weight = 10822.596| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16113 Z= 0.182 Angle : 0.721 12.492 21934 Z= 0.352 Chirality : 0.045 0.203 2505 Planarity : 0.004 0.058 2828 Dihedral : 5.701 51.093 2323 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.31 % Favored : 96.41 % Rotamer: Outliers : 3.56 % Allowed : 22.01 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.20), residues: 1810 helix: 0.72 (0.19), residues: 725 sheet: -0.55 (0.28), residues: 325 loop : 0.33 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 290 TYR 0.025 0.001 TYR C 166 PHE 0.012 0.001 PHE C 352 TRP 0.061 0.002 TRP C 340 HIS 0.011 0.001 HIS D 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (16113) covalent geometry : angle 0.72125 / 0.35 (21934) hydrogen bonds : bond 0.03451 / 2.32 ( 971) hydrogen bonds : angle 4.55355 / 3.15 ( 2583) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 234 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8739 (t0) cc_final: 0.8459 (t0) REVERT: A 82 MET cc_start: 0.8996 (tpp) cc_final: 0.8686 (mmm) REVERT: A 107 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7745 (tm-30) REVERT: A 121 GLN cc_start: 0.9201 (tt0) cc_final: 0.8866 (tm-30) REVERT: B 40 HIS cc_start: 0.7489 (m-70) cc_final: 0.7078 (m90) REVERT: B 47 MET cc_start: 0.1564 (ptm) cc_final: 0.0894 (ttt) REVERT: B 137 GLN cc_start: 0.8564 (mt0) cc_final: 0.8013 (mp10) REVERT: B 167 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8787 (mp0) REVERT: B 176 MET cc_start: 0.8357 (mtt) cc_final: 0.8060 (mtt) REVERT: B 222 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.8276 (p0) REVERT: B 276 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7996 (mp0) REVERT: B 279 TYR cc_start: 0.9161 (t80) cc_final: 0.8629 (t80) REVERT: C 44 MET cc_start: 0.8413 (tpp) cc_final: 0.8089 (tpp) REVERT: C 137 GLN cc_start: 0.8866 (mt0) cc_final: 0.8605 (mm-40) REVERT: C 192 ILE cc_start: 0.8707 (tp) cc_final: 0.8449 (pt) REVERT: C 263 GLN cc_start: 0.9073 (mm110) cc_final: 0.8855 (mm-40) REVERT: C 270 GLU cc_start: 0.7246 (mt-10) cc_final: 0.6510 (mp0) REVERT: C 271 SER cc_start: 0.9049 (m) cc_final: 0.8788 (p) REVERT: C 276 GLU cc_start: 0.8403 (mp0) cc_final: 0.8177 (mp0) REVERT: C 290 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.7710 (mtp85) REVERT: C 314 GLN cc_start: 0.9024 (tp40) cc_final: 0.8461 (tp-100) REVERT: C 340 TRP cc_start: 0.8556 (t60) cc_final: 0.7911 (t60) REVERT: D 44 MET cc_start: 0.8076 (mmm) cc_final: 0.7101 (mtt) REVERT: D 47 MET cc_start: 0.1979 (tmm) cc_final: 0.1559 (tmm) REVERT: D 72 GLU cc_start: 0.8082 (pp20) cc_final: 0.7839 (pp20) REVERT: D 82 MET cc_start: 0.8903 (tpp) cc_final: 0.8479 (tmm) REVERT: D 142 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9045 (mp) REVERT: D 192 ILE cc_start: 0.9260 (tp) cc_final: 0.8827 (tp) REVERT: D 280 ASN cc_start: 0.9022 (m-40) cc_final: 0.8774 (m-40) REVERT: E 162 ASN cc_start: 0.8894 (t0) cc_final: 0.8528 (t0) REVERT: E 206 ARG cc_start: 0.8643 (mtp-110) cc_final: 0.8379 (ttm-80) REVERT: E 227 MET cc_start: 0.8878 (mmm) cc_final: 0.8529 (tpp) REVERT: E 314 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8509 (tm-30) outliers start: 55 outliers final: 45 residues processed: 274 average time/residue: 0.0967 time to fit residues: 43.2746 Evaluate side-chains 278 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 228 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain E residue 86 TRP Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 124 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 133 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 197 optimal weight: 40.0000 chunk 201 optimal weight: 50.0000 chunk 106 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN A 280 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN E 78 ASN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.094960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.088642 restraints weight = 51840.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.090410 restraints weight = 28085.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.091589 restraints weight = 17728.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.092366 restraints weight = 12730.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.092611 restraints weight = 10107.966| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16113 Z= 0.145 Angle : 0.727 16.667 21934 Z= 0.350 Chirality : 0.044 0.187 2505 Planarity : 0.004 0.059 2828 Dihedral : 5.630 48.658 2323 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.20 % Favored : 96.52 % Rotamer: Outliers : 3.69 % Allowed : 21.68 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.20), residues: 1810 helix: 0.77 (0.20), residues: 725 sheet: -0.39 (0.28), residues: 320 loop : 0.35 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 290 TYR 0.025 0.001 TYR C 166 PHE 0.014 0.001 PHE C 352 TRP 0.057 0.002 TRP C 340 HIS 0.014 0.001 HIS D 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (16113) covalent geometry : angle 0.72706 / 0.35 (21934) hydrogen bonds : bond 0.03387 / 2.27 ( 971) hydrogen bonds : angle 4.53536 / 3.14 ( 2583) =============================================================================== Job complete usr+sys time: 2227.71 seconds wall clock time: 39 minutes 33.76 seconds (2373.76 seconds total)