Starting phenix.real_space_refine on Sat Sep 12 11:40:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5jlf_8163/09_2026/5jlf_8163.cif Found real_map, /net/cci-nas-00/data/ceres_data/5jlf_8163/09_2026/5jlf_8163.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 { restraint_files = "/net/cci-nas-00/data/ceres_data/5jlf_8163/09_2026/5jlf_8163.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5jlf_8163/09_2026/5jlf_8163.cif" model { file = "/net/cci-nas-00/data/ceres_data/5jlf_8163/09_2026/5jlf_8163.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5jlf_8163/09_2026/5jlf_8163.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5jlf_8163/09_2026/5jlf_8163.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5jlf_8163/09_2026/5jlf_8163.map" } 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= -0.000 sd= 0.011 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: 3.88, per 1000 atoms: 0.25 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: 1.46 Conformation dependent library (CDL) restraints added in 835.3 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: 0.53 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: 2.57 Time building geometry restraints manager: 1.93 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: 0.05 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: 0.000 Normalize map: mean=0, sd=1: 1.460 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: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 15.770 Find NCS groups from input model: 0.300 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 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 537 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 517 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.9202 (m-40) cc_final: 0.8679 (m-40) REVERT: A 78 ASN cc_start: 0.8865 (t0) cc_final: 0.8179 (t0) REVERT: A 81 ASP cc_start: 0.8846 (m-30) cc_final: 0.8426 (m-30) REVERT: A 121 GLN cc_start: 0.9204 (tt0) cc_final: 0.8797 (tm-30) REVERT: A 225 ASN cc_start: 0.8899 (m-40) cc_final: 0.8699 (m-40) REVERT: A 313 MET cc_start: 0.8545 (mmm) cc_final: 0.8152 (mmm) REVERT: A 351 THR cc_start: 0.8723 (p) cc_final: 0.8510 (p) REVERT: B 40 HIS cc_start: 0.7813 (m-70) cc_final: 0.7605 (m-70) REVERT: B 47 MET cc_start: 0.1557 (ptm) cc_final: 0.0880 (ttt) REVERT: B 69 TYR cc_start: 0.9114 (m-10) cc_final: 0.8896 (m-10) REVERT: B 115 ASN cc_start: 0.8348 (m-40) cc_final: 0.8089 (m110) REVERT: B 160 THR cc_start: 0.8978 (m) cc_final: 0.8759 (m) REVERT: B 242 LEU cc_start: 0.9076 (mp) cc_final: 0.8868 (mt) REVERT: B 247 VAL cc_start: 0.9393 (t) cc_final: 0.8873 (p) REVERT: B 279 TYR cc_start: 0.9151 (t80) cc_final: 0.8939 (t80) REVERT: C 123 MET cc_start: 0.8732 (mmt) cc_final: 0.8515 (tpp) REVERT: C 162 ASN cc_start: 0.8216 (m-40) cc_final: 0.7944 (m-40) REVERT: C 186 THR cc_start: 0.9443 (OUTLIER) cc_final: 0.9229 (t) REVERT: C 187 ASP cc_start: 0.8681 (m-30) cc_final: 0.8435 (t0) REVERT: C 191 LYS cc_start: 0.8824 (ptmt) cc_final: 0.8248 (mtpp) REVERT: D 10 CYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8859 (t) REVERT: D 12 ASN cc_start: 0.8786 (m-40) cc_final: 0.8573 (m110) REVERT: D 44 MET cc_start: 0.8117 (mmm) cc_final: 0.7083 (mtt) REVERT: D 78 ASN cc_start: 0.8796 (t0) cc_final: 0.8394 (t0) REVERT: D 81 ASP cc_start: 0.8984 (m-30) cc_final: 0.8667 (m-30) REVERT: D 110 LEU cc_start: 0.9215 (tp) cc_final: 0.8975 (tt) REVERT: D 160 THR cc_start: 0.9399 (m) cc_final: 0.9071 (p) REVERT: D 192 ILE cc_start: 0.9089 (tp) cc_final: 0.8636 (tp) REVERT: D 237 GLU cc_start: 0.8599 (pt0) cc_final: 0.8357 (pm20) REVERT: D 353 GLN cc_start: 0.8727 (mt0) cc_final: 0.8511 (tm-30) REVERT: D 355 MET cc_start: 0.8730 (mtt) cc_final: 0.8302 (tpt) REVERT: E 12 ASN cc_start: 0.9247 (m-40) cc_final: 0.8670 (p0) REVERT: E 78 ASN cc_start: 0.8864 (t0) cc_final: 0.8617 (t0) REVERT: E 157 ASP cc_start: 0.8753 (t0) cc_final: 0.8498 (t0) REVERT: E 162 ASN cc_start: 0.8491 (m-40) cc_final: 0.8134 (m-40) REVERT: E 283 MET cc_start: 0.9321 (mmp) cc_final: 0.9007 (mmt) REVERT: E 327 ILE cc_start: 0.8874 (mt) cc_final: 0.8653 (mp) outliers start: 20 outliers final: 2 residues processed: 532 average time/residue: 0.1348 time to fit residues: 105.1074 Evaluate side-chains 275 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 271 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain D residue 10 CYS 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: 0.9980 chunk 194 optimal weight: 40.0000 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 30.0000 chunk 77 optimal weight: 0.0470 chunk 122 optimal weight: 0.8980 overall best weight: 0.7880 ------------------------------------------------------------------------------- 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 162 ASN A 246 GLN A 280 ASN A 296 ASN B 12 ASN B 59 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN B 280 ASN B 296 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN E 59 GLN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN E 246 GLN E 297 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.096954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.076864 restraints weight = 39917.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.079384 restraints weight = 18875.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.081077 restraints weight = 10845.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.082181 restraints weight = 7067.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.082846 restraints weight = 5064.129| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16113 Z= 0.171 Angle : 0.745 10.634 21934 Z= 0.379 Chirality : 0.047 0.239 2505 Planarity : 0.005 0.086 2828 Dihedral : 7.180 67.484 2327 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.99 % Favored : 97.73 % Rotamer: Outliers : 3.75 % Allowed : 14.43 % Favored : 81.81 % 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: -0.01 (0.19), residues: 1810 helix: 0.19 (0.19), residues: 725 sheet: -0.40 (0.27), residues: 290 loop : 0.18 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 183 TYR 0.017 0.002 TYR A 294 PHE 0.023 0.002 PHE B 255 TRP 0.039 0.002 TRP C 340 HIS 0.008 0.001 HIS E 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (16113) covalent geometry : angle 0.74517 / 0.38 (21934) hydrogen bonds : bond 0.05028 / 3.35 ( 971) hydrogen bonds : angle 5.47720 / 3.83 ( 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 381 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 323 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ILE cc_start: 0.8750 (mt) cc_final: 0.8547 (pt) REVERT: A 78 ASN cc_start: 0.8579 (t0) cc_final: 0.7362 (t0) REVERT: A 81 ASP cc_start: 0.8627 (m-30) cc_final: 0.8253 (m-30) REVERT: A 132 MET cc_start: 0.8375 (ptm) cc_final: 0.8130 (ppp) REVERT: A 325 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.6955 (ptm) REVERT: B 44 MET cc_start: 0.7693 (mpp) cc_final: 0.7132 (mpp) REVERT: B 47 MET cc_start: 0.0448 (ptm) cc_final: 0.0236 (ttt) REVERT: B 65 LEU cc_start: 0.8751 (mt) cc_final: 0.8529 (mt) REVERT: B 80 ASP cc_start: 0.7914 (p0) cc_final: 0.7528 (p0) REVERT: B 313 MET cc_start: 0.8304 (mmm) cc_final: 0.8024 (mmm) REVERT: B 325 MET cc_start: 0.6939 (ptm) cc_final: 0.6632 (ttp) REVERT: C 105 LEU cc_start: 0.8832 (mt) cc_final: 0.8481 (mt) REVERT: C 137 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8398 (mm-40) REVERT: C 162 ASN cc_start: 0.8238 (m-40) cc_final: 0.8028 (m-40) REVERT: C 190 MET cc_start: 0.8445 (mmm) cc_final: 0.8116 (mtp) REVERT: C 263 GLN cc_start: 0.8748 (mm110) cc_final: 0.8364 (mt0) REVERT: C 280 ASN cc_start: 0.9161 (m-40) cc_final: 0.8931 (m-40) REVERT: D 110 LEU cc_start: 0.9156 (tp) cc_final: 0.8763 (tt) REVERT: D 142 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8874 (mp) REVERT: D 192 ILE cc_start: 0.9175 (tp) cc_final: 0.8686 (tp) REVERT: D 292 ASP cc_start: 0.8063 (m-30) cc_final: 0.7861 (m-30) REVERT: E 162 ASN cc_start: 0.8308 (m-40) cc_final: 0.8076 (m-40) REVERT: E 191 LYS cc_start: 0.8814 (ptmt) cc_final: 0.8492 (ptpt) outliers start: 58 outliers final: 27 residues processed: 362 average time/residue: 0.1137 time to fit residues: 63.9400 Evaluate side-chains 263 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 234 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 194 THR 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 B residue 12 ASN Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 145 SER 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 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 238 LYS Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 297 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 56 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 148 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 chunk 123 optimal weight: 0.2980 chunk 80 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 176 optimal weight: 0.0670 chunk 122 optimal weight: 0.7980 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN ** E 297 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 = 0.3584 r_free = 0.3584 target = 0.099639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.079317 restraints weight = 40057.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.081856 restraints weight = 18697.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.083548 restraints weight = 10752.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.084650 restraints weight = 7031.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.085371 restraints weight = 5080.350| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16113 Z= 0.147 Angle : 0.681 7.986 21934 Z= 0.342 Chirality : 0.045 0.206 2505 Planarity : 0.004 0.047 2828 Dihedral : 6.560 60.612 2324 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.04 % Favored : 97.68 % Rotamer: Outliers : 3.56 % Allowed : 16.96 % Favored : 79.48 % 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: 0.02 (0.19), residues: 1810 helix: 0.22 (0.19), residues: 755 sheet: -0.18 (0.27), residues: 320 loop : 0.14 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 95 TYR 0.025 0.001 TYR C 166 PHE 0.015 0.001 PHE A 352 TRP 0.019 0.001 TRP C 340 HIS 0.006 0.001 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (16113) covalent geometry : angle 0.68069 / 0.34 (21934) hydrogen bonds : bond 0.04450 / 2.96 ( 971) hydrogen bonds : angle 5.05017 / 3.53 ( 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 338 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 283 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8474 (t0) cc_final: 0.7322 (t0) REVERT: B 44 MET cc_start: 0.7396 (mpp) cc_final: 0.6841 (mpp) REVERT: B 47 MET cc_start: 0.0263 (ptm) cc_final: 0.0009 (ttt) REVERT: B 80 ASP cc_start: 0.7873 (p0) cc_final: 0.7589 (p0) REVERT: B 313 MET cc_start: 0.8215 (mmm) cc_final: 0.7952 (mmm) REVERT: C 137 GLN cc_start: 0.8682 (mm-40) cc_final: 0.8367 (mm-40) REVERT: C 271 SER cc_start: 0.8942 (m) cc_final: 0.8738 (p) REVERT: D 142 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8710 (mp) REVERT: D 192 ILE cc_start: 0.9161 (tp) cc_final: 0.8621 (tp) REVERT: D 276 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7952 (mm-30) outliers start: 55 outliers final: 31 residues processed: 319 average time/residue: 0.1057 time to fit residues: 54.1296 Evaluate side-chains 268 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 236 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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 57 GLU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 118 LYS 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 64 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 194 THR Chi-restraints excluded: chain B residue 247 VAL 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 261 LEU Chi-restraints excluded: chain D residue 54 VAL 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 238 LYS Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 330 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 32 optimal weight: 6.9990 chunk 78 optimal weight: 0.0570 chunk 21 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 180 optimal weight: 50.0000 chunk 163 optimal weight: 7.9990 chunk 171 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 200 optimal weight: 40.0000 overall best weight: 4.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN B 92 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN B 263 GLN D 59 GLN D 78 ASN D 115 ASN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN ** E 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.092461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.072734 restraints weight = 41075.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.075075 restraints weight = 19549.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.076655 restraints weight = 11368.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.077693 restraints weight = 7496.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.078423 restraints weight = 5468.601| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 16113 Z= 0.342 Angle : 0.832 10.062 21934 Z= 0.419 Chirality : 0.050 0.209 2505 Planarity : 0.005 0.047 2828 Dihedral : 6.774 65.217 2323 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.26 % Favored : 96.46 % Rotamer: Outliers : 5.31 % Allowed : 17.28 % Favored : 77.41 % 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: -0.22 (0.19), residues: 1810 helix: 0.09 (0.19), residues: 725 sheet: -0.68 (0.27), residues: 325 loop : 0.12 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 312 TYR 0.025 0.002 TYR C 166 PHE 0.025 0.003 PHE A 352 TRP 0.016 0.003 TRP C 340 HIS 0.009 0.002 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00759 / 0.34 (16113) covalent geometry : angle 0.83182 / 0.42 (21934) hydrogen bonds : bond 0.04662 / 3.12 ( 971) hydrogen bonds : angle 5.08874 / 3.55 ( 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 308 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 226 time to evaluate : 0.608 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 87 HIS cc_start: 0.8330 (OUTLIER) cc_final: 0.7984 (t-90) REVERT: A 107 GLU cc_start: 0.7619 (tt0) cc_final: 0.6818 (tt0) REVERT: A 227 MET cc_start: 0.8730 (mmm) cc_final: 0.8351 (mmt) REVERT: A 305 MET cc_start: 0.8722 (tpp) cc_final: 0.8308 (mmt) REVERT: B 44 MET cc_start: 0.7811 (tpp) cc_final: 0.7246 (mpp) REVERT: B 47 MET cc_start: 0.0897 (ptm) cc_final: 0.0464 (ttt) REVERT: B 80 ASP cc_start: 0.7966 (p0) cc_final: 0.7740 (p0) REVERT: B 88 HIS cc_start: 0.8292 (OUTLIER) cc_final: 0.7327 (t-90) REVERT: C 65 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8840 (mt) REVERT: D 142 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9055 (mp) REVERT: D 192 ILE cc_start: 0.9269 (tp) cc_final: 0.8843 (tp) outliers start: 82 outliers final: 46 residues processed: 290 average time/residue: 0.1030 time to fit residues: 48.6595 Evaluate side-chains 255 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 205 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 288 ASP 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 64 ILE Chi-restraints excluded: chain B residue 88 HIS 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 247 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 52 SER 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 244 ASP Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 297 ASN 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: 4.9990 chunk 170 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 193 optimal weight: 50.0000 chunk 17 optimal weight: 0.9990 chunk 200 optimal weight: 40.0000 chunk 172 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 110 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 chunk 194 optimal weight: 40.0000 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN D 78 ASN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 ASN E 360 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.096523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.076385 restraints weight = 40423.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.078854 restraints weight = 18911.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.080471 restraints weight = 10849.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.081539 restraints weight = 7147.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.082209 restraints weight = 5179.887| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16113 Z= 0.143 Angle : 0.673 11.799 21934 Z= 0.331 Chirality : 0.044 0.193 2505 Planarity : 0.004 0.059 2828 Dihedral : 6.167 56.947 2323 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.98 % Favored : 96.74 % Rotamer: Outliers : 4.08 % Allowed : 19.68 % Favored : 76.25 % 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: 0.14 (0.20), residues: 1810 helix: 0.49 (0.19), residues: 725 sheet: -0.47 (0.28), residues: 320 loop : 0.18 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 210 TYR 0.025 0.001 TYR C 166 PHE 0.013 0.001 PHE A 352 TRP 0.014 0.002 TRP C 340 HIS 0.004 0.001 HIS D 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (16113) covalent geometry : angle 0.67312 / 0.33 (21934) hydrogen bonds : bond 0.03822 / 2.56 ( 971) hydrogen bonds : angle 4.76179 / 3.31 ( 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 311 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 248 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7552 (tt0) cc_final: 0.6685 (tt0) REVERT: A 227 MET cc_start: 0.8730 (mmm) cc_final: 0.8309 (mmt) REVERT: A 305 MET cc_start: 0.8475 (tpp) cc_final: 0.8216 (mmt) REVERT: B 44 MET cc_start: 0.7683 (tpp) cc_final: 0.7357 (tpp) REVERT: B 47 MET cc_start: 0.0706 (ptm) cc_final: 0.0155 (ttt) REVERT: B 80 ASP cc_start: 0.7928 (p0) cc_final: 0.7677 (p0) REVERT: B 88 HIS cc_start: 0.8251 (OUTLIER) cc_final: 0.7494 (t-90) REVERT: C 137 GLN cc_start: 0.8836 (mm-40) cc_final: 0.8511 (mm-40) REVERT: C 192 ILE cc_start: 0.8823 (tp) cc_final: 0.8608 (pt) REVERT: D 142 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8846 (mp) REVERT: D 192 ILE cc_start: 0.9181 (tp) cc_final: 0.8709 (tp) REVERT: D 349 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7990 (mp) REVERT: E 128 ASN cc_start: 0.8645 (m-40) cc_final: 0.8317 (m-40) REVERT: E 180 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8962 (tt) outliers start: 63 outliers final: 34 residues processed: 297 average time/residue: 0.1070 time to fit residues: 50.7753 Evaluate side-chains 258 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 220 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 118 LYS 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 107 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 194 THR 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 140 LEU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 54 VAL 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 244 ASP Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 107 GLU 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 297 ASN Chi-restraints excluded: chain E residue 334 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 60 optimal weight: 0.2980 chunk 77 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 71 optimal weight: 0.2980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 12 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN ** E 297 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 = 0.3514 r_free = 0.3514 target = 0.095893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.075813 restraints weight = 40624.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.078277 restraints weight = 19172.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.079828 restraints weight = 10984.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.080956 restraints weight = 7277.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.081604 restraints weight = 5223.619| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16113 Z= 0.168 Angle : 0.681 11.902 21934 Z= 0.334 Chirality : 0.044 0.237 2505 Planarity : 0.004 0.059 2828 Dihedral : 6.009 55.598 2323 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.76 % Favored : 96.96 % Rotamer: Outliers : 4.27 % Allowed : 20.71 % Favored : 75.02 % 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: 0.59 (0.19), residues: 730 sheet: -0.47 (0.28), residues: 320 loop : 0.24 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 95 TYR 0.023 0.001 TYR C 166 PHE 0.037 0.002 PHE A 352 TRP 0.045 0.002 TRP C 340 HIS 0.005 0.001 HIS C 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (16113) covalent geometry : angle 0.68113 / 0.33 (21934) hydrogen bonds : bond 0.03797 / 2.57 ( 971) hydrogen bonds : angle 4.69747 / 3.26 ( 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 289 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 223 time to evaluate : 0.599 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 82 MET cc_start: 0.9173 (tpp) cc_final: 0.8954 (tpt) REVERT: A 107 GLU cc_start: 0.7599 (tt0) cc_final: 0.6697 (tt0) REVERT: A 121 GLN cc_start: 0.9037 (tt0) cc_final: 0.8815 (tm-30) REVERT: A 227 MET cc_start: 0.8768 (mmm) cc_final: 0.8342 (mmt) REVERT: A 241 GLU cc_start: 0.7468 (pm20) cc_final: 0.7156 (pm20) REVERT: A 305 MET cc_start: 0.8555 (tpp) cc_final: 0.8264 (mmt) REVERT: B 44 MET cc_start: 0.7600 (tpp) cc_final: 0.7278 (tpp) REVERT: B 47 MET cc_start: 0.0793 (ptm) cc_final: 0.0191 (ttt) REVERT: B 65 LEU cc_start: 0.8344 (mt) cc_final: 0.8144 (mt) REVERT: B 80 ASP cc_start: 0.7896 (p0) cc_final: 0.7345 (p0) REVERT: B 83 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8358 (pp20) REVERT: B 88 HIS cc_start: 0.8228 (OUTLIER) cc_final: 0.7555 (t-90) REVERT: C 44 MET cc_start: 0.8135 (tpp) cc_final: 0.7696 (tpp) REVERT: C 116 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7781 (mmm-85) REVERT: C 192 ILE cc_start: 0.8852 (tp) cc_final: 0.8632 (pt) REVERT: D 142 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8849 (mp) REVERT: D 192 ILE cc_start: 0.9186 (tp) cc_final: 0.8705 (tp) REVERT: D 349 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8056 (mp) REVERT: E 128 ASN cc_start: 0.8632 (m-40) cc_final: 0.8323 (m-40) REVERT: E 180 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9014 (tt) outliers start: 66 outliers final: 49 residues processed: 275 average time/residue: 0.1082 time to fit residues: 47.7721 Evaluate side-chains 274 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 220 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 142 LEU 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 330 ILE 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 30 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 107 GLU 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 160 THR Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 116 ARG Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 140 LEU 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 261 LEU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 148 THR 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 284 LYS Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 107 GLU 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 334 GLU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 358 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 99 optimal weight: 6.9990 chunk 182 optimal weight: 50.0000 chunk 79 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 87 optimal weight: 8.9990 chunk 106 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 167 optimal weight: 0.9980 chunk 200 optimal weight: 40.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 HIS A 246 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN E 297 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.091771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.071829 restraints weight = 40946.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.074172 restraints weight = 19611.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.075732 restraints weight = 11409.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.076708 restraints weight = 7563.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.077464 restraints weight = 5564.687| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 16113 Z= 0.342 Angle : 0.818 12.271 21934 Z= 0.406 Chirality : 0.049 0.261 2505 Planarity : 0.005 0.056 2828 Dihedral : 6.329 62.022 2323 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.81 % Favored : 95.91 % Rotamer: Outliers : 5.05 % Allowed : 20.65 % Favored : 74.30 % 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: -0.11 (0.20), residues: 1810 helix: 0.33 (0.19), residues: 730 sheet: -0.83 (0.27), residues: 325 loop : 0.12 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 312 TYR 0.029 0.002 TYR C 166 PHE 0.026 0.002 PHE A 352 TRP 0.043 0.003 TRP C 340 HIS 0.007 0.002 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00765 / 0.34 (16113) covalent geometry : angle 0.81798 / 0.41 (21934) hydrogen bonds : bond 0.04212 / 2.85 ( 971) hydrogen bonds : angle 4.91986 / 3.40 ( 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 290 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 212 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8889 (pt) REVERT: A 107 GLU cc_start: 0.7848 (tt0) cc_final: 0.6850 (tt0) REVERT: A 121 GLN cc_start: 0.9061 (tt0) cc_final: 0.8846 (tm-30) REVERT: A 205 GLU cc_start: 0.8221 (mp0) cc_final: 0.7990 (mp0) REVERT: B 40 HIS cc_start: 0.7826 (OUTLIER) cc_final: 0.7401 (m90) REVERT: B 44 MET cc_start: 0.7909 (tpp) cc_final: 0.7549 (tpp) REVERT: B 47 MET cc_start: 0.1211 (ptm) cc_final: 0.0805 (ttt) REVERT: B 88 HIS cc_start: 0.8327 (OUTLIER) cc_final: 0.7590 (t-90) REVERT: C 116 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.8032 (tpp80) REVERT: C 290 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.7486 (mtt-85) REVERT: D 75 ILE cc_start: 0.9342 (OUTLIER) cc_final: 0.9040 (pt) REVERT: D 142 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9084 (mp) REVERT: D 192 ILE cc_start: 0.9248 (tp) cc_final: 0.8829 (tp) REVERT: D 254 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8067 (ttp-170) REVERT: D 313 MET cc_start: 0.8306 (mmm) cc_final: 0.8007 (mtp) REVERT: D 349 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8138 (mp) REVERT: E 180 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9051 (tt) outliers start: 78 outliers final: 54 residues processed: 273 average time/residue: 0.1041 time to fit residues: 45.3472 Evaluate side-chains 264 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 200 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 142 LEU 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 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 30 VAL Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 107 GLU 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 212 ILE 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 34 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 116 ARG 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 274 ILE Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 148 THR 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 254 ARG Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 107 GLU 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 180 LEU Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 358 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 178 optimal weight: 7.9990 chunk 104 optimal weight: 0.0980 chunk 96 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 186 optimal weight: 30.0000 chunk 26 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 167 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 HIS ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.095156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.075231 restraints weight = 40846.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.077619 restraints weight = 19383.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.079223 restraints weight = 11248.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.080285 restraints weight = 7387.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.080919 restraints weight = 5353.997| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16113 Z= 0.158 Angle : 0.694 12.107 21934 Z= 0.341 Chirality : 0.044 0.202 2505 Planarity : 0.004 0.060 2828 Dihedral : 5.996 57.163 2323 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.31 % Favored : 96.41 % Rotamer: Outliers : 3.82 % Allowed : 22.14 % Favored : 74.05 % 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: 0.20 (0.20), residues: 1810 helix: 0.62 (0.20), residues: 730 sheet: -0.62 (0.28), residues: 320 loop : 0.21 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 206 TYR 0.023 0.001 TYR C 166 PHE 0.034 0.002 PHE C 352 TRP 0.036 0.002 TRP C 340 HIS 0.004 0.001 HIS D 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (16113) covalent geometry : angle 0.69389 / 0.34 (21934) hydrogen bonds : bond 0.03713 / 2.50 ( 971) hydrogen bonds : angle 4.70247 / 3.25 ( 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 290 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 231 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7784 (tt0) cc_final: 0.6831 (tt0) REVERT: A 205 GLU cc_start: 0.8084 (mp0) cc_final: 0.7844 (mp0) REVERT: B 47 MET cc_start: 0.0951 (ptm) cc_final: 0.0539 (ttt) REVERT: B 83 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8386 (pp20) REVERT: B 88 HIS cc_start: 0.8299 (OUTLIER) cc_final: 0.7668 (t-90) REVERT: C 44 MET cc_start: 0.8207 (tpp) cc_final: 0.7766 (tpp) REVERT: C 104 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8607 (tp) REVERT: C 116 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7947 (tpp80) REVERT: C 137 GLN cc_start: 0.8917 (mm-40) cc_final: 0.8688 (mm110) REVERT: C 290 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7548 (mtt-85) REVERT: C 313 MET cc_start: 0.8925 (tpp) cc_final: 0.8669 (mmm) REVERT: D 47 MET cc_start: 0.4088 (tmm) cc_final: -0.0023 (ttt) REVERT: D 75 ILE cc_start: 0.9310 (OUTLIER) cc_final: 0.9023 (pt) REVERT: D 82 MET cc_start: 0.8864 (tpp) cc_final: 0.8395 (tmm) REVERT: D 142 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8905 (mp) REVERT: D 192 ILE cc_start: 0.9210 (tp) cc_final: 0.8767 (tp) REVERT: D 313 MET cc_start: 0.8224 (mmm) cc_final: 0.7882 (mtp) REVERT: D 349 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8084 (mp) REVERT: E 78 ASN cc_start: 0.8405 (t0) cc_final: 0.7509 (p0) REVERT: E 80 ASP cc_start: 0.8050 (p0) cc_final: 0.7835 (p0) REVERT: E 128 ASN cc_start: 0.8676 (m-40) cc_final: 0.8389 (m-40) REVERT: E 180 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9051 (tt) outliers start: 59 outliers final: 44 residues processed: 275 average time/residue: 0.1051 time to fit residues: 47.0420 Evaluate side-chains 263 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 211 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 288 ASP 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 30 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 107 GLU 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 160 THR Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 116 ARG 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 274 ILE Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 160 THR 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 349 LEU 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 180 LEU Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 358 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 143 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 195 optimal weight: 50.0000 chunk 164 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 172 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 181 optimal weight: 50.0000 chunk 7 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN D 78 ASN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN E 297 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.095790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.075880 restraints weight = 40757.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.078325 restraints weight = 19122.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.079940 restraints weight = 11004.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.081001 restraints weight = 7209.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.081671 restraints weight = 5204.323| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16113 Z= 0.147 Angle : 0.688 12.410 21934 Z= 0.340 Chirality : 0.044 0.203 2505 Planarity : 0.004 0.060 2828 Dihedral : 5.837 53.775 2323 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.31 % Favored : 96.41 % Rotamer: Outliers : 3.88 % Allowed : 22.07 % Favored : 74.05 % 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: 0.32 (0.20), residues: 1810 helix: 0.71 (0.20), residues: 730 sheet: -0.49 (0.28), residues: 320 loop : 0.24 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 206 TYR 0.026 0.001 TYR C 166 PHE 0.038 0.001 PHE C 352 TRP 0.076 0.002 TRP C 340 HIS 0.005 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (16113) covalent geometry : angle 0.68817 / 0.34 (21934) hydrogen bonds : bond 0.03667 / 2.48 ( 971) hydrogen bonds : angle 4.62509 / 3.20 ( 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 290 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 230 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7722 (tt0) cc_final: 0.6756 (tt0) REVERT: A 205 GLU cc_start: 0.8083 (mp0) cc_final: 0.7827 (mp0) REVERT: A 313 MET cc_start: 0.8200 (mmm) cc_final: 0.7835 (mtp) REVERT: B 47 MET cc_start: 0.0942 (ptm) cc_final: 0.0573 (ttt) REVERT: B 83 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8441 (pp20) REVERT: B 88 HIS cc_start: 0.8281 (OUTLIER) cc_final: 0.7681 (t-90) REVERT: B 125 GLU cc_start: 0.9035 (mp0) cc_final: 0.8810 (mp0) REVERT: B 269 MET cc_start: 0.7457 (mtm) cc_final: 0.6917 (ptp) REVERT: C 44 MET cc_start: 0.8181 (tpp) cc_final: 0.7764 (tpp) REVERT: C 104 LEU cc_start: 0.9014 (tt) cc_final: 0.8695 (tp) REVERT: C 116 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7899 (tpp80) REVERT: C 340 TRP cc_start: 0.8191 (t60) cc_final: 0.7616 (t60) REVERT: D 47 MET cc_start: 0.3994 (tmm) cc_final: 0.0036 (ttt) REVERT: D 75 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.9023 (pt) REVERT: D 82 MET cc_start: 0.8891 (tpp) cc_final: 0.8430 (tmm) REVERT: D 142 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8851 (mp) REVERT: D 192 ILE cc_start: 0.9179 (tp) cc_final: 0.8707 (tp) REVERT: D 349 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8048 (mp) REVERT: E 128 ASN cc_start: 0.8627 (m-40) cc_final: 0.8351 (m-40) outliers start: 60 outliers final: 43 residues processed: 276 average time/residue: 0.1059 time to fit residues: 47.3986 Evaluate side-chains 266 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 218 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 303 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 107 GLU 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 160 THR Chi-restraints excluded: chain B residue 161 HIS 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 64 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 116 ARG Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 145 SER 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 274 ILE Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 358 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: 0.8980 chunk 59 optimal weight: 0.5980 chunk 113 optimal weight: 5.9990 chunk 76 optimal weight: 0.0770 chunk 201 optimal weight: 30.0000 chunk 204 optimal weight: 40.0000 chunk 151 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 200 optimal weight: 30.0000 chunk 144 optimal weight: 10.0000 overall best weight: 2.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN ** E 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.094629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.074725 restraints weight = 40723.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.077152 restraints weight = 19342.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.078762 restraints weight = 11165.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.079780 restraints weight = 7353.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.080522 restraints weight = 5371.561| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16113 Z= 0.195 Angle : 0.717 12.957 21934 Z= 0.353 Chirality : 0.045 0.314 2505 Planarity : 0.004 0.059 2828 Dihedral : 5.818 53.324 2323 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.59 % Favored : 96.13 % Rotamer: Outliers : 3.30 % Allowed : 22.85 % Favored : 73.85 % 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: 0.19 (0.20), residues: 1810 helix: 0.61 (0.20), residues: 730 sheet: -0.51 (0.28), residues: 320 loop : 0.15 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 206 TYR 0.026 0.001 TYR C 166 PHE 0.036 0.002 PHE C 352 TRP 0.077 0.002 TRP C 340 HIS 0.005 0.001 HIS D 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.20 (16113) covalent geometry : angle 0.71657 / 0.35 (21934) hydrogen bonds : bond 0.03671 / 2.48 ( 971) hydrogen bonds : angle 4.64590 / 3.21 ( 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 270 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 219 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7741 (tt0) cc_final: 0.6867 (tt0) REVERT: A 205 GLU cc_start: 0.8167 (mp0) cc_final: 0.7905 (mp0) REVERT: B 47 MET cc_start: 0.1042 (ptm) cc_final: 0.0732 (ttt) REVERT: B 83 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8456 (pp20) REVERT: B 88 HIS cc_start: 0.8316 (OUTLIER) cc_final: 0.7709 (t-90) REVERT: B 269 MET cc_start: 0.7500 (mtm) cc_final: 0.6908 (ptp) REVERT: C 44 MET cc_start: 0.8210 (tpp) cc_final: 0.7799 (tpp) REVERT: C 116 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7915 (tpp80) REVERT: C 207 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7926 (mm-30) REVERT: D 47 MET cc_start: 0.3713 (tmm) cc_final: -0.0110 (ttt) REVERT: D 75 ILE cc_start: 0.9291 (OUTLIER) cc_final: 0.9005 (pt) REVERT: D 82 MET cc_start: 0.8775 (tpp) cc_final: 0.8441 (tmm) REVERT: D 142 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8896 (mp) REVERT: D 192 ILE cc_start: 0.9207 (tp) cc_final: 0.8756 (tp) REVERT: D 254 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8134 (ttp-170) REVERT: D 349 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8100 (mp) REVERT: E 128 ASN cc_start: 0.8612 (m-40) cc_final: 0.8339 (m-40) outliers start: 51 outliers final: 43 residues processed: 257 average time/residue: 0.1068 time to fit residues: 44.0631 Evaluate side-chains 261 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 212 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 303 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 107 GLU 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 324 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 116 ARG Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 145 SER 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 274 ILE Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 254 ARG Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 349 LEU 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 297 ASN Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 358 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 124 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 197 optimal weight: 40.0000 chunk 201 optimal weight: 30.0000 chunk 106 optimal weight: 0.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 353 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN E 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.094685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.075022 restraints weight = 40832.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.077437 restraints weight = 19215.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.079060 restraints weight = 11059.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.080056 restraints weight = 7207.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.080790 restraints weight = 5245.045| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.5374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16113 Z= 0.183 Angle : 0.707 12.840 21934 Z= 0.349 Chirality : 0.045 0.277 2505 Planarity : 0.004 0.060 2828 Dihedral : 5.727 52.110 2323 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.43 % Favored : 96.30 % Rotamer: Outliers : 3.75 % Allowed : 22.78 % Favored : 73.46 % 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: 0.17 (0.20), residues: 1810 helix: 0.61 (0.19), residues: 730 sheet: -0.49 (0.28), residues: 320 loop : 0.09 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 206 TYR 0.026 0.001 TYR C 166 PHE 0.035 0.002 PHE C 352 TRP 0.070 0.002 TRP C 340 HIS 0.013 0.001 HIS D 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (16113) covalent geometry : angle 0.70687 / 0.35 (21934) hydrogen bonds : bond 0.03574 / 2.42 ( 971) hydrogen bonds : angle 4.63706 / 3.21 ( 2583) =============================================================================== Job complete usr+sys time: 2570.52 seconds wall clock time: 45 minutes 25.57 seconds (2725.57 seconds total)