Starting phenix.real_space_refine on Thu Sep 18 09:10:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5jlf_8162/09_2025/5jlf_8162.cif Found real_map, /net/cci-nas-00/data/ceres_data/5jlf_8162/09_2025/5jlf_8162.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5jlf_8162/09_2025/5jlf_8162.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5jlf_8162/09_2025/5jlf_8162.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5jlf_8162/09_2025/5jlf_8162.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5jlf_8162/09_2025/5jlf_8162.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= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 100 5.16 5 C 9925 2.51 5 N 2700 2.21 5 O 3060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: 3.91, 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: 1.48 Conformation dependent library (CDL) restraints added in 548.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.79 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: 2.98 Time building geometry restraints manager: 1.91 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.820 Find NCS groups from input model: 0.340 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 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 aren 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 covalent geometry : bond 0.01273 (16113) covalent geometry : angle 1.57863 (21934) hydrogen bonds : bond 0.19145 ( 971) hydrogen bonds : angle 8.23836 ( 2583) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 487 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 GLN cc_start: 0.9234 (tt0) cc_final: 0.8962 (tm-30) REVERT: B 40 HIS cc_start: 0.7884 (m-70) cc_final: 0.7647 (m-70) REVERT: B 47 MET cc_start: 0.1902 (ptm) cc_final: 0.0927 (ttt) REVERT: B 86 TRP cc_start: 0.9389 (m-10) cc_final: 0.9175 (m-10) REVERT: B 115 ASN cc_start: 0.8510 (m-40) cc_final: 0.8260 (m110) REVERT: B 250 ILE cc_start: 0.9266 (pt) cc_final: 0.9024 (mm) REVERT: C 162 ASN cc_start: 0.8330 (m-40) cc_final: 0.8081 (m-40) REVERT: C 186 THR cc_start: 0.9580 (OUTLIER) cc_final: 0.9360 (t) REVERT: C 191 LYS cc_start: 0.8957 (ptmt) cc_final: 0.8472 (mtpp) REVERT: C 327 ILE cc_start: 0.9163 (mt) cc_final: 0.8927 (mp) REVERT: D 12 ASN cc_start: 0.8865 (m-40) cc_final: 0.8645 (m110) REVERT: D 44 MET cc_start: 0.8291 (mmm) cc_final: 0.7466 (mtt) REVERT: D 78 ASN cc_start: 0.8862 (t0) cc_final: 0.8520 (t0) REVERT: D 80 ASP cc_start: 0.8576 (p0) cc_final: 0.8323 (p0) REVERT: D 81 ASP cc_start: 0.9090 (m-30) cc_final: 0.8688 (m-30) REVERT: D 110 LEU cc_start: 0.9224 (tp) cc_final: 0.9019 (tt) REVERT: D 160 THR cc_start: 0.9438 (m) cc_final: 0.9196 (p) REVERT: D 353 GLN cc_start: 0.8783 (mt0) cc_final: 0.8522 (tm-30) REVERT: D 355 MET cc_start: 0.8740 (mtt) cc_final: 0.8348 (tpt) REVERT: E 12 ASN cc_start: 0.9209 (m-40) cc_final: 0.8786 (p0) REVERT: E 75 ILE cc_start: 0.9298 (mt) cc_final: 0.9073 (pt) REVERT: E 106 THR cc_start: 0.8429 (m) cc_final: 0.8125 (t) REVERT: E 157 ASP cc_start: 0.8577 (t0) cc_final: 0.8252 (t0) REVERT: E 162 ASN cc_start: 0.8471 (m-40) cc_final: 0.8174 (m-40) outliers start: 20 outliers final: 2 residues processed: 502 average time/residue: 0.1376 time to fit residues: 100.9467 Evaluate side-chains 285 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 282 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain E residue 186 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 30.0000 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 30.0000 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 HIS A 92 ASN A 246 GLN A 296 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN B 280 ASN B 296 ASN C 12 ASN ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN C 296 ASN D 12 ASN D 88 HIS D 92 ASN D 162 ASN D 296 ASN ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN E 59 GLN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN E 246 GLN E 280 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.102231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.095387 restraints weight = 53339.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.097216 restraints weight = 28539.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.098450 restraints weight = 17643.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.099231 restraints weight = 12369.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.099741 restraints weight = 9440.997| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16113 Z= 0.180 Angle : 0.771 12.902 21934 Z= 0.390 Chirality : 0.046 0.265 2505 Planarity : 0.006 0.083 2828 Dihedral : 7.241 69.307 2326 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.82 % Favored : 97.90 % Rotamer: Outliers : 3.37 % Allowed : 14.24 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.19), residues: 1810 helix: 0.12 (0.18), residues: 740 sheet: -0.35 (0.26), residues: 320 loop : 0.06 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 95 TYR 0.018 0.002 TYR A 294 PHE 0.023 0.002 PHE B 255 TRP 0.029 0.002 TRP C 340 HIS 0.008 0.002 HIS E 101 Details of bonding type rmsd covalent geometry : bond 0.00400 (16113) covalent geometry : angle 0.77085 (21934) hydrogen bonds : bond 0.05022 ( 971) hydrogen bonds : angle 5.51151 ( 2583) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 328 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 VAL cc_start: 0.8801 (OUTLIER) cc_final: 0.8564 (m) REVERT: A 78 ASN cc_start: 0.8679 (t0) cc_final: 0.8424 (t0) REVERT: A 132 MET cc_start: 0.8516 (ptm) cc_final: 0.8184 (ppp) REVERT: A 325 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.7051 (ptm) REVERT: B 40 HIS cc_start: 0.7565 (m-70) cc_final: 0.7334 (m90) REVERT: B 44 MET cc_start: 0.8322 (mpp) cc_final: 0.7682 (mpp) REVERT: B 47 MET cc_start: 0.1604 (ptm) cc_final: 0.0972 (ttt) REVERT: B 65 LEU cc_start: 0.8953 (mt) cc_final: 0.8705 (mt) REVERT: B 72 GLU cc_start: 0.7973 (mp0) cc_final: 0.7761 (mp0) REVERT: B 107 GLU cc_start: 0.7024 (pm20) cc_final: 0.6777 (tt0) REVERT: B 137 GLN cc_start: 0.8426 (mt0) cc_final: 0.7606 (mp10) REVERT: B 222 ASP cc_start: 0.8720 (t0) cc_final: 0.8380 (t70) REVERT: B 327 ILE cc_start: 0.9273 (mt) cc_final: 0.8985 (mt) REVERT: B 360 GLN cc_start: 0.8872 (pp30) cc_final: 0.8107 (pp30) REVERT: C 65 LEU cc_start: 0.9173 (mt) cc_final: 0.8944 (mt) REVERT: C 137 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8544 (mm-40) REVERT: C 180 LEU cc_start: 0.9007 (mt) cc_final: 0.8717 (mt) REVERT: C 190 MET cc_start: 0.8730 (mmm) cc_final: 0.8491 (mtp) REVERT: C 280 ASN cc_start: 0.9312 (m-40) cc_final: 0.9057 (m110) REVERT: C 340 TRP cc_start: 0.8575 (t60) cc_final: 0.8356 (t60) REVERT: D 44 MET cc_start: 0.7670 (mmm) cc_final: 0.7089 (mtt) REVERT: D 82 MET cc_start: 0.9073 (tpt) cc_final: 0.8738 (tpt) REVERT: D 110 LEU cc_start: 0.9161 (tp) cc_final: 0.8705 (tt) REVERT: D 142 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9021 (mp) REVERT: D 162 ASN cc_start: 0.8900 (OUTLIER) cc_final: 0.8637 (t0) REVERT: D 328 LYS cc_start: 0.8921 (ttpp) cc_final: 0.8515 (ttpp) REVERT: E 162 ASN cc_start: 0.8359 (m-40) cc_final: 0.8150 (m-40) REVERT: E 227 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8349 (tpp) REVERT: E 276 GLU cc_start: 0.7680 (mp0) cc_final: 0.7468 (mp0) REVERT: E 305 MET cc_start: 0.8881 (mmm) cc_final: 0.8637 (mmt) outliers start: 52 outliers final: 22 residues processed: 365 average time/residue: 0.1192 time to fit residues: 66.9663 Evaluate side-chains 274 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 247 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 227 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 56 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 176 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS B 263 GLN ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN E 12 ASN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN E 246 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.100113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.093326 restraints weight = 54509.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.094920 restraints weight = 29227.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.096374 restraints weight = 18666.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.097062 restraints weight = 13214.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.097634 restraints weight = 10092.255| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16113 Z= 0.183 Angle : 0.699 9.350 21934 Z= 0.352 Chirality : 0.045 0.212 2505 Planarity : 0.004 0.057 2828 Dihedral : 6.667 64.564 2324 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.99 % Favored : 97.73 % Rotamer: Outliers : 3.43 % Allowed : 16.63 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.19), residues: 1810 helix: 0.26 (0.19), residues: 745 sheet: -0.31 (0.27), residues: 320 loop : 0.15 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 95 TYR 0.025 0.001 TYR C 166 PHE 0.020 0.002 PHE A 352 TRP 0.018 0.002 TRP C 340 HIS 0.007 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00406 (16113) covalent geometry : angle 0.69880 (21934) hydrogen bonds : bond 0.04379 ( 971) hydrogen bonds : angle 5.06409 ( 2583) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 269 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8746 (t0) cc_final: 0.8464 (t0) REVERT: A 132 MET cc_start: 0.8466 (ptm) cc_final: 0.8250 (ppp) REVERT: A 325 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6999 (ptm) REVERT: B 40 HIS cc_start: 0.7578 (m-70) cc_final: 0.7313 (m90) REVERT: B 44 MET cc_start: 0.8195 (mpp) cc_final: 0.7515 (mpp) REVERT: B 47 MET cc_start: 0.1330 (ptm) cc_final: 0.0961 (ttm) REVERT: B 65 LEU cc_start: 0.8955 (mt) cc_final: 0.8741 (mt) REVERT: B 137 GLN cc_start: 0.8519 (mt0) cc_final: 0.7691 (mp10) REVERT: B 176 MET cc_start: 0.8598 (mtt) cc_final: 0.8317 (mtt) REVERT: B 246 GLN cc_start: 0.7842 (tm-30) cc_final: 0.7569 (tm-30) REVERT: B 247 VAL cc_start: 0.9266 (t) cc_final: 0.8921 (p) REVERT: B 360 GLN cc_start: 0.8823 (pp30) cc_final: 0.8108 (pp30) REVERT: C 44 MET cc_start: 0.8323 (tpp) cc_final: 0.7952 (tpp) REVERT: C 137 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8435 (mm-40) REVERT: C 192 ILE cc_start: 0.8669 (tp) cc_final: 0.8381 (tp) REVERT: C 270 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6964 (mp0) REVERT: C 271 SER cc_start: 0.9065 (m) cc_final: 0.8654 (p) REVERT: C 280 ASN cc_start: 0.9325 (m-40) cc_final: 0.8983 (m110) REVERT: D 44 MET cc_start: 0.7644 (mmm) cc_final: 0.6930 (mtt) REVERT: D 47 MET cc_start: 0.2661 (tmm) cc_final: 0.1409 (tmm) REVERT: D 110 LEU cc_start: 0.9180 (tp) cc_final: 0.8857 (tt) REVERT: D 142 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.8994 (mp) REVERT: D 162 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8503 (t0) REVERT: E 227 MET cc_start: 0.8708 (mmm) cc_final: 0.8380 (tpp) REVERT: E 276 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: E 280 ASN cc_start: 0.8835 (m-40) cc_final: 0.8626 (m110) REVERT: E 305 MET cc_start: 0.8798 (mmm) cc_final: 0.8571 (mmt) outliers start: 53 outliers final: 26 residues processed: 305 average time/residue: 0.1031 time to fit residues: 51.0881 Evaluate side-chains 258 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 228 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 32 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 chunk 101 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 180 optimal weight: 30.0000 chunk 163 optimal weight: 7.9990 chunk 171 optimal weight: 0.5980 chunk 158 optimal weight: 0.8980 chunk 200 optimal weight: 40.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN B 92 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.098327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.092329 restraints weight = 51647.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.093930 restraints weight = 27636.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.095000 restraints weight = 17327.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.095658 restraints weight = 12535.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.095750 restraints weight = 9766.441| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16113 Z= 0.157 Angle : 0.665 9.392 21934 Z= 0.329 Chirality : 0.045 0.252 2505 Planarity : 0.004 0.051 2828 Dihedral : 6.219 59.827 2324 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.49 % Favored : 97.24 % Rotamer: Outliers : 3.56 % Allowed : 17.93 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.20), residues: 1810 helix: 0.50 (0.19), residues: 730 sheet: -0.24 (0.27), residues: 320 loop : 0.23 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 95 TYR 0.021 0.001 TYR C 166 PHE 0.011 0.001 PHE C 262 TRP 0.013 0.001 TRP C 340 HIS 0.007 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00347 (16113) covalent geometry : angle 0.66477 (21934) hydrogen bonds : bond 0.03941 ( 971) hydrogen bonds : angle 4.79827 ( 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 310 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 255 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8799 (t0) cc_final: 0.8468 (t0) REVERT: A 225 ASN cc_start: 0.8987 (m-40) cc_final: 0.8696 (t0) REVERT: A 305 MET cc_start: 0.8756 (tpp) cc_final: 0.8412 (mmt) REVERT: B 40 HIS cc_start: 0.7496 (m-70) cc_final: 0.7202 (m90) REVERT: B 44 MET cc_start: 0.8120 (tpp) cc_final: 0.7355 (mpp) REVERT: B 47 MET cc_start: 0.1382 (ptm) cc_final: 0.0699 (ttt) REVERT: B 72 GLU cc_start: 0.7989 (mp0) cc_final: 0.7734 (mp0) REVERT: B 137 GLN cc_start: 0.8426 (mt0) cc_final: 0.7967 (mp10) REVERT: B 167 GLU cc_start: 0.9249 (mm-30) cc_final: 0.8620 (mp0) REVERT: B 176 MET cc_start: 0.8638 (mtt) cc_final: 0.8270 (mtt) REVERT: B 247 VAL cc_start: 0.9239 (t) cc_final: 0.9031 (p) REVERT: B 276 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8323 (mp0) REVERT: B 279 TYR cc_start: 0.9153 (t80) cc_final: 0.8821 (t80) REVERT: B 360 GLN cc_start: 0.8866 (pp30) cc_final: 0.8243 (pp30) REVERT: C 44 MET cc_start: 0.8376 (tpp) cc_final: 0.8063 (tpp) REVERT: C 192 ILE cc_start: 0.8538 (tp) cc_final: 0.8194 (tp) REVERT: C 270 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7058 (mp0) REVERT: C 271 SER cc_start: 0.9073 (m) cc_final: 0.8732 (p) REVERT: C 280 ASN cc_start: 0.9359 (m-40) cc_final: 0.9054 (m-40) REVERT: C 299 MET cc_start: 0.8449 (mmt) cc_final: 0.8168 (mmm) REVERT: C 314 GLN cc_start: 0.8974 (tp40) cc_final: 0.8525 (tp40) REVERT: C 353 GLN cc_start: 0.9075 (tp40) cc_final: 0.8420 (tp-100) REVERT: D 44 MET cc_start: 0.7957 (mmm) cc_final: 0.7029 (mtt) REVERT: D 47 MET cc_start: 0.2168 (tmm) cc_final: 0.1309 (tmm) REVERT: D 142 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.8997 (mp) REVERT: D 192 ILE cc_start: 0.9223 (tp) cc_final: 0.8731 (tp) REVERT: E 78 ASN cc_start: 0.8533 (t0) cc_final: 0.7128 (t0) REVERT: E 81 ASP cc_start: 0.7994 (m-30) cc_final: 0.7745 (m-30) REVERT: E 206 ARG cc_start: 0.8682 (mtp-110) cc_final: 0.8234 (ttm-80) REVERT: E 227 MET cc_start: 0.8786 (mmm) cc_final: 0.8433 (tpp) REVERT: E 276 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: E 280 ASN cc_start: 0.8865 (m-40) cc_final: 0.8515 (m110) REVERT: E 305 MET cc_start: 0.8812 (mmm) cc_final: 0.8603 (mmt) outliers start: 55 outliers final: 32 residues processed: 299 average time/residue: 0.1058 time to fit residues: 51.1989 Evaluate side-chains 270 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 235 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 66 optimal weight: 0.7980 chunk 170 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 193 optimal weight: 40.0000 chunk 17 optimal weight: 7.9990 chunk 200 optimal weight: 40.0000 chunk 172 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 110 optimal weight: 0.0040 chunk 32 optimal weight: 9.9990 chunk 194 optimal weight: 30.0000 overall best weight: 3.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN D 115 ASN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.096112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.089725 restraints weight = 52605.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.091412 restraints weight = 29014.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.092237 restraints weight = 19093.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.093154 restraints weight = 14451.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.093765 restraints weight = 11495.459| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16113 Z= 0.246 Angle : 0.711 8.545 21934 Z= 0.353 Chirality : 0.046 0.221 2505 Planarity : 0.004 0.055 2828 Dihedral : 6.194 60.960 2323 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.09 % Favored : 96.63 % Rotamer: Outliers : 4.92 % Allowed : 17.86 % Favored : 77.22 % 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 aren not related in a simple way. whole: 0.25 (0.20), residues: 1810 helix: 0.51 (0.19), residues: 725 sheet: -0.38 (0.27), residues: 320 loop : 0.31 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 290 TYR 0.023 0.002 TYR C 166 PHE 0.026 0.002 PHE C 352 TRP 0.042 0.002 TRP C 340 HIS 0.006 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00545 (16113) covalent geometry : angle 0.71134 (21934) hydrogen bonds : bond 0.03906 ( 971) hydrogen bonds : angle 4.77607 ( 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 313 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 237 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8762 (t0) cc_final: 0.8411 (t0) REVERT: A 107 GLU cc_start: 0.7972 (tp30) cc_final: 0.7542 (tm-30) REVERT: A 211 ASP cc_start: 0.8769 (t0) cc_final: 0.8479 (t0) REVERT: A 225 ASN cc_start: 0.9034 (m-40) cc_final: 0.8752 (t0) REVERT: B 40 HIS cc_start: 0.7452 (m-70) cc_final: 0.7128 (m90) REVERT: B 44 MET cc_start: 0.8478 (tpp) cc_final: 0.7708 (mpp) REVERT: B 47 MET cc_start: 0.1602 (ptm) cc_final: 0.0719 (ttt) REVERT: B 88 HIS cc_start: 0.8662 (OUTLIER) cc_final: 0.7928 (t-90) REVERT: B 110 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8781 (tt) REVERT: B 137 GLN cc_start: 0.8634 (mt0) cc_final: 0.8072 (mp10) REVERT: B 176 MET cc_start: 0.8692 (mtt) cc_final: 0.8290 (mtt) REVERT: B 246 GLN cc_start: 0.8160 (tm-30) cc_final: 0.7914 (tm-30) REVERT: B 276 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8024 (mp0) REVERT: B 360 GLN cc_start: 0.8825 (pp30) cc_final: 0.8155 (pp30) REVERT: C 44 MET cc_start: 0.8405 (tpp) cc_final: 0.8072 (tpp) REVERT: C 137 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8522 (mm-40) REVERT: C 191 LYS cc_start: 0.8803 (ttmm) cc_final: 0.8546 (mmtp) REVERT: C 192 ILE cc_start: 0.8549 (tp) cc_final: 0.8224 (tp) REVERT: C 270 GLU cc_start: 0.7680 (mt-10) cc_final: 0.6972 (mp0) REVERT: C 271 SER cc_start: 0.9062 (m) cc_final: 0.8713 (p) REVERT: C 276 GLU cc_start: 0.8408 (mp0) cc_final: 0.8171 (mp0) REVERT: C 280 ASN cc_start: 0.9425 (m-40) cc_final: 0.9118 (m-40) REVERT: C 314 GLN cc_start: 0.9055 (tp40) cc_final: 0.8535 (tp40) REVERT: C 353 GLN cc_start: 0.9112 (tp40) cc_final: 0.8514 (tp-100) REVERT: D 44 MET cc_start: 0.8140 (mmm) cc_final: 0.7120 (mtt) REVERT: D 47 MET cc_start: 0.2412 (tmm) cc_final: 0.1569 (tmm) REVERT: D 142 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9047 (mp) REVERT: D 192 ILE cc_start: 0.9236 (tp) cc_final: 0.8794 (tp) REVERT: E 78 ASN cc_start: 0.8670 (t0) cc_final: 0.7770 (t0) REVERT: E 81 ASP cc_start: 0.8249 (m-30) cc_final: 0.7882 (m-30) REVERT: E 119 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8025 (ttm) REVERT: E 180 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9094 (tt) REVERT: E 206 ARG cc_start: 0.8668 (mtp-110) cc_final: 0.8399 (ttm-80) REVERT: E 227 MET cc_start: 0.8793 (mmm) cc_final: 0.8419 (tpp) REVERT: E 276 GLU cc_start: 0.7482 (mp0) cc_final: 0.7240 (mp0) REVERT: E 299 MET cc_start: 0.8999 (mmt) cc_final: 0.8614 (mmt) REVERT: E 305 MET cc_start: 0.8768 (mmm) cc_final: 0.8523 (mmt) outliers start: 76 outliers final: 47 residues processed: 296 average time/residue: 0.0996 time to fit residues: 48.2521 Evaluate side-chains 273 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 220 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 60 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.098148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.091237 restraints weight = 54088.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.092969 restraints weight = 28768.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.094109 restraints weight = 18197.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.095131 restraints weight = 13612.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.095552 restraints weight = 10128.710| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16113 Z= 0.137 Angle : 0.662 12.356 21934 Z= 0.321 Chirality : 0.044 0.212 2505 Planarity : 0.004 0.059 2828 Dihedral : 5.898 56.060 2323 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.76 % Favored : 96.96 % Rotamer: Outliers : 3.69 % Allowed : 19.55 % Favored : 76.76 % 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 aren not related in a simple way. whole: 0.39 (0.20), residues: 1810 helix: 0.69 (0.19), residues: 725 sheet: -0.40 (0.27), residues: 320 loop : 0.35 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 290 TYR 0.024 0.001 TYR C 166 PHE 0.031 0.001 PHE C 352 TRP 0.037 0.002 TRP C 340 HIS 0.005 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00306 (16113) covalent geometry : angle 0.66157 (21934) hydrogen bonds : bond 0.03634 ( 971) hydrogen bonds : angle 4.63081 ( 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 324 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 267 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8749 (t0) cc_final: 0.8449 (t0) REVERT: A 121 GLN cc_start: 0.9256 (tt0) cc_final: 0.8945 (tm-30) REVERT: A 225 ASN cc_start: 0.8977 (m-40) cc_final: 0.8741 (t0) REVERT: A 360 GLN cc_start: 0.8784 (pp30) cc_final: 0.8580 (pp30) REVERT: B 40 HIS cc_start: 0.7454 (m-70) cc_final: 0.7143 (m90) REVERT: B 44 MET cc_start: 0.8247 (tpp) cc_final: 0.7808 (tpp) REVERT: B 47 MET cc_start: 0.1422 (ptm) cc_final: 0.0698 (ttt) REVERT: B 65 LEU cc_start: 0.8591 (mt) cc_final: 0.8281 (mt) REVERT: B 86 TRP cc_start: 0.9035 (OUTLIER) cc_final: 0.8786 (m-10) REVERT: B 88 HIS cc_start: 0.8578 (OUTLIER) cc_final: 0.7964 (t-90) REVERT: B 110 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8743 (tt) REVERT: B 137 GLN cc_start: 0.8518 (mt0) cc_final: 0.8041 (mp10) REVERT: B 167 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8588 (mp0) REVERT: B 176 MET cc_start: 0.8610 (mtt) cc_final: 0.8256 (mtt) REVERT: B 276 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8307 (mp0) REVERT: B 360 GLN cc_start: 0.8884 (pp30) cc_final: 0.8160 (pp30) REVERT: C 44 MET cc_start: 0.8345 (tpp) cc_final: 0.8020 (tpp) REVERT: C 59 GLN cc_start: 0.8429 (mm-40) cc_final: 0.7617 (tp40) REVERT: C 137 GLN cc_start: 0.8854 (mm-40) cc_final: 0.8544 (mm-40) REVERT: C 191 LYS cc_start: 0.8738 (ttmm) cc_final: 0.8508 (mmtp) REVERT: C 192 ILE cc_start: 0.8626 (tp) cc_final: 0.8359 (pt) REVERT: C 270 GLU cc_start: 0.7639 (mt-10) cc_final: 0.6942 (mp0) REVERT: C 271 SER cc_start: 0.9155 (m) cc_final: 0.8867 (p) REVERT: C 276 GLU cc_start: 0.8352 (mp0) cc_final: 0.8114 (mp0) REVERT: C 314 GLN cc_start: 0.9045 (tp40) cc_final: 0.8512 (tp40) REVERT: D 44 MET cc_start: 0.8075 (mmm) cc_final: 0.7039 (mtt) REVERT: D 47 MET cc_start: 0.1999 (tmm) cc_final: 0.1515 (tmm) REVERT: D 72 GLU cc_start: 0.8047 (pp20) cc_final: 0.7791 (pp20) REVERT: D 82 MET cc_start: 0.8861 (tpp) cc_final: 0.8478 (tmm) REVERT: D 142 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9031 (mp) REVERT: D 192 ILE cc_start: 0.9205 (tp) cc_final: 0.8720 (tp) REVERT: D 280 ASN cc_start: 0.9015 (m-40) cc_final: 0.8721 (m-40) REVERT: E 78 ASN cc_start: 0.8503 (t0) cc_final: 0.7422 (t0) REVERT: E 81 ASP cc_start: 0.8075 (m-30) cc_final: 0.7640 (m-30) REVERT: E 206 ARG cc_start: 0.8606 (mtp-110) cc_final: 0.8359 (ttm-80) REVERT: E 227 MET cc_start: 0.8743 (mmm) cc_final: 0.8460 (tpp) REVERT: E 276 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: E 305 MET cc_start: 0.8697 (mmm) cc_final: 0.8483 (mmt) outliers start: 57 outliers final: 35 residues processed: 306 average time/residue: 0.1064 time to fit residues: 52.0026 Evaluate side-chains 287 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 246 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 99 optimal weight: 0.9990 chunk 182 optimal weight: 50.0000 chunk 79 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 100 optimal weight: 0.0060 chunk 80 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 200 optimal weight: 40.0000 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.097088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.090211 restraints weight = 54456.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.091991 restraints weight = 28908.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.093072 restraints weight = 17894.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.094017 restraints weight = 13501.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.094610 restraints weight = 10014.948| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16113 Z= 0.176 Angle : 0.694 11.114 21934 Z= 0.338 Chirality : 0.044 0.179 2505 Planarity : 0.004 0.057 2828 Dihedral : 5.808 54.894 2323 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.71 % Favored : 97.02 % Rotamer: Outliers : 4.47 % Allowed : 19.87 % Favored : 75.66 % 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 aren not related in a simple way. whole: 0.41 (0.20), residues: 1810 helix: 0.75 (0.20), residues: 725 sheet: -0.47 (0.27), residues: 320 loop : 0.36 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 290 TYR 0.026 0.001 TYR C 166 PHE 0.020 0.002 PHE C 352 TRP 0.029 0.002 TRP C 340 HIS 0.007 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00398 (16113) covalent geometry : angle 0.69399 (21934) hydrogen bonds : bond 0.03543 ( 971) hydrogen bonds : angle 4.58833 ( 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 327 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 258 time to evaluate : 0.611 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 78 ASN cc_start: 0.8752 (t0) cc_final: 0.7580 (t0) REVERT: A 81 ASP cc_start: 0.9044 (m-30) cc_final: 0.8344 (m-30) REVERT: A 121 GLN cc_start: 0.9279 (tt0) cc_final: 0.8850 (tm-30) REVERT: A 132 MET cc_start: 0.8621 (tmm) cc_final: 0.8405 (tmm) REVERT: B 40 HIS cc_start: 0.7387 (m-70) cc_final: 0.7059 (m90) REVERT: B 47 MET cc_start: 0.1600 (ptm) cc_final: 0.0856 (ttt) REVERT: B 86 TRP cc_start: 0.9055 (OUTLIER) cc_final: 0.8823 (m-10) REVERT: B 88 HIS cc_start: 0.8646 (OUTLIER) cc_final: 0.8004 (t-90) REVERT: B 110 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8819 (tt) REVERT: B 137 GLN cc_start: 0.8586 (mt0) cc_final: 0.8349 (mp10) REVERT: B 167 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8616 (mp0) REVERT: B 176 MET cc_start: 0.8652 (mtt) cc_final: 0.8238 (mtt) REVERT: B 227 MET cc_start: 0.9306 (mmm) cc_final: 0.9067 (mmm) REVERT: B 276 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8338 (mp0) REVERT: B 360 GLN cc_start: 0.8875 (pp30) cc_final: 0.8194 (pp30) REVERT: C 44 MET cc_start: 0.8304 (tpp) cc_final: 0.7967 (tpp) REVERT: C 137 GLN cc_start: 0.8857 (mm-40) cc_final: 0.8475 (mm-40) REVERT: C 192 ILE cc_start: 0.8626 (tp) cc_final: 0.8350 (pt) REVERT: C 270 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6532 (mp0) REVERT: C 271 SER cc_start: 0.9095 (m) cc_final: 0.8809 (p) REVERT: C 276 GLU cc_start: 0.8330 (mp0) cc_final: 0.8115 (mp0) REVERT: C 314 GLN cc_start: 0.9067 (tp40) cc_final: 0.8497 (tp-100) REVERT: D 44 MET cc_start: 0.8023 (mmm) cc_final: 0.6953 (mtt) REVERT: D 47 MET cc_start: 0.2007 (tmm) cc_final: 0.1525 (tmm) REVERT: D 72 GLU cc_start: 0.8075 (pp20) cc_final: 0.7778 (pp20) REVERT: D 142 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9031 (mp) REVERT: D 192 ILE cc_start: 0.9208 (tp) cc_final: 0.8753 (tp) REVERT: D 227 MET cc_start: 0.8714 (mmm) cc_final: 0.8506 (mmm) REVERT: D 280 ASN cc_start: 0.9005 (m-40) cc_final: 0.8756 (m-40) REVERT: E 78 ASN cc_start: 0.8553 (t0) cc_final: 0.7404 (t0) REVERT: E 81 ASP cc_start: 0.8143 (m-30) cc_final: 0.7625 (m-30) REVERT: E 162 ASN cc_start: 0.8869 (t0) cc_final: 0.8514 (t0) REVERT: E 206 ARG cc_start: 0.8656 (mtp-110) cc_final: 0.8323 (ttm-80) REVERT: E 227 MET cc_start: 0.8793 (mmm) cc_final: 0.8436 (tpp) REVERT: E 276 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7209 (mp0) REVERT: E 314 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8521 (tm-30) outliers start: 69 outliers final: 43 residues processed: 307 average time/residue: 0.0994 time to fit residues: 49.7732 Evaluate side-chains 287 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 237 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 178 optimal weight: 0.9990 chunk 104 optimal weight: 0.4980 chunk 96 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 186 optimal weight: 30.0000 chunk 26 optimal weight: 0.6980 chunk 114 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 167 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 280 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.096543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.090207 restraints weight = 51746.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.091851 restraints weight = 28400.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.092705 restraints weight = 18194.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.093466 restraints weight = 13996.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.094075 restraints weight = 11236.161| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16113 Z= 0.138 Angle : 0.682 10.570 21934 Z= 0.334 Chirality : 0.043 0.224 2505 Planarity : 0.004 0.060 2828 Dihedral : 5.690 50.712 2323 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.76 % Favored : 96.96 % Rotamer: Outliers : 3.62 % Allowed : 21.17 % Favored : 75.21 % 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 aren not related in a simple way. whole: 0.50 (0.20), residues: 1810 helix: 0.85 (0.20), residues: 725 sheet: -0.38 (0.27), residues: 320 loop : 0.36 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 290 TYR 0.021 0.001 TYR C 166 PHE 0.012 0.001 PHE C 352 TRP 0.058 0.002 TRP C 340 HIS 0.005 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00312 (16113) covalent geometry : angle 0.68228 (21934) hydrogen bonds : bond 0.03447 ( 971) hydrogen bonds : angle 4.55296 ( 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 310 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 254 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8765 (t0) cc_final: 0.7633 (t0) REVERT: A 81 ASP cc_start: 0.9061 (m-30) cc_final: 0.8322 (m-30) REVERT: A 107 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7639 (tm-30) REVERT: A 121 GLN cc_start: 0.9200 (tt0) cc_final: 0.8940 (tm-30) REVERT: A 128 ASN cc_start: 0.8437 (m-40) cc_final: 0.8136 (m-40) REVERT: A 132 MET cc_start: 0.8638 (tmm) cc_final: 0.8402 (tmm) REVERT: A 360 GLN cc_start: 0.8875 (pp30) cc_final: 0.8557 (pp30) REVERT: B 40 HIS cc_start: 0.7306 (m-70) cc_final: 0.6946 (m90) REVERT: B 47 MET cc_start: 0.1522 (ptm) cc_final: 0.0765 (ttt) REVERT: B 88 HIS cc_start: 0.8647 (OUTLIER) cc_final: 0.8159 (t-90) REVERT: B 110 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8849 (tt) REVERT: B 137 GLN cc_start: 0.8537 (mt0) cc_final: 0.8267 (mp10) REVERT: B 167 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8586 (mp0) REVERT: B 175 ILE cc_start: 0.9487 (mt) cc_final: 0.9278 (mt) REVERT: B 176 MET cc_start: 0.8643 (mtt) cc_final: 0.8175 (mtt) REVERT: B 276 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8302 (mp0) REVERT: B 325 MET cc_start: 0.7714 (ppp) cc_final: 0.7489 (ptm) REVERT: C 44 MET cc_start: 0.8338 (tpp) cc_final: 0.8042 (tpp) REVERT: C 137 GLN cc_start: 0.8843 (mm-40) cc_final: 0.8642 (mm-40) REVERT: C 187 ASP cc_start: 0.8519 (m-30) cc_final: 0.8216 (t70) REVERT: C 270 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6577 (mp0) REVERT: C 271 SER cc_start: 0.9029 (m) cc_final: 0.8738 (p) REVERT: C 314 GLN cc_start: 0.9057 (tp40) cc_final: 0.8496 (tp-100) REVERT: D 44 MET cc_start: 0.8174 (mmm) cc_final: 0.7094 (mtt) REVERT: D 47 MET cc_start: 0.2126 (tmm) cc_final: 0.1647 (tmm) REVERT: D 72 GLU cc_start: 0.8029 (pp20) cc_final: 0.7768 (pp20) REVERT: D 82 MET cc_start: 0.9086 (tpp) cc_final: 0.8541 (tmm) REVERT: D 142 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9025 (mp) REVERT: D 192 ILE cc_start: 0.9141 (tp) cc_final: 0.8660 (tp) REVERT: D 276 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8419 (mp0) REVERT: D 280 ASN cc_start: 0.8993 (m-40) cc_final: 0.8732 (m-40) REVERT: E 78 ASN cc_start: 0.8509 (t0) cc_final: 0.7291 (t0) REVERT: E 81 ASP cc_start: 0.8152 (m-30) cc_final: 0.7641 (m-30) REVERT: E 162 ASN cc_start: 0.8766 (t0) cc_final: 0.8413 (t0) REVERT: E 206 ARG cc_start: 0.8628 (mtp-110) cc_final: 0.8370 (ttm-80) REVERT: E 227 MET cc_start: 0.8872 (mmm) cc_final: 0.8492 (tpp) REVERT: E 276 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7260 (mp0) REVERT: E 314 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8457 (tm-30) outliers start: 56 outliers final: 39 residues processed: 292 average time/residue: 0.1039 time to fit residues: 49.1510 Evaluate side-chains 280 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 235 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 143 optimal weight: 8.9990 chunk 59 optimal weight: 0.0470 chunk 195 optimal weight: 30.0000 chunk 164 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 172 optimal weight: 0.5980 chunk 102 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 181 optimal weight: 50.0000 chunk 7 optimal weight: 2.9990 overall best weight: 1.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN B 12 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.099214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.092987 restraints weight = 53653.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.094563 restraints weight = 28955.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.095499 restraints weight = 18276.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.096014 restraints weight = 13480.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.096713 restraints weight = 11057.781| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 16113 Z= 0.151 Angle : 0.696 11.963 21934 Z= 0.339 Chirality : 0.044 0.180 2505 Planarity : 0.004 0.059 2828 Dihedral : 5.610 49.223 2323 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.98 % Favored : 96.74 % Rotamer: Outliers : 3.24 % Allowed : 21.81 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.20), residues: 1810 helix: 0.80 (0.20), residues: 725 sheet: -0.32 (0.28), residues: 320 loop : 0.47 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 290 TYR 0.033 0.001 TYR C 166 PHE 0.011 0.001 PHE C 352 TRP 0.069 0.002 TRP C 340 HIS 0.006 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00349 (16113) covalent geometry : angle 0.69560 (21934) hydrogen bonds : bond 0.03430 ( 971) hydrogen bonds : angle 4.53425 ( 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 296 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 246 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8686 (t0) cc_final: 0.8456 (t0) REVERT: A 121 GLN cc_start: 0.9190 (tt0) cc_final: 0.8967 (tm-30) REVERT: B 40 HIS cc_start: 0.7437 (m-70) cc_final: 0.7098 (m90) REVERT: B 47 MET cc_start: 0.1365 (ptm) cc_final: 0.0666 (ttt) REVERT: B 88 HIS cc_start: 0.8598 (OUTLIER) cc_final: 0.8138 (t-90) REVERT: B 110 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8904 (tt) REVERT: B 137 GLN cc_start: 0.8496 (mt0) cc_final: 0.8121 (mp10) REVERT: B 167 GLU cc_start: 0.9150 (mm-30) cc_final: 0.8614 (mp0) REVERT: B 176 MET cc_start: 0.8544 (mtt) cc_final: 0.8211 (mtt) REVERT: B 222 ASP cc_start: 0.8597 (OUTLIER) cc_final: 0.8319 (p0) REVERT: B 227 MET cc_start: 0.9205 (mmm) cc_final: 0.8992 (mmm) REVERT: B 276 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8368 (mp0) REVERT: B 325 MET cc_start: 0.7702 (ppp) cc_final: 0.7457 (ptm) REVERT: C 44 MET cc_start: 0.8378 (tpp) cc_final: 0.8136 (tpp) REVERT: C 59 GLN cc_start: 0.8456 (tp40) cc_final: 0.8117 (tp40) REVERT: C 65 LEU cc_start: 0.9286 (mt) cc_final: 0.8965 (mt) REVERT: C 187 ASP cc_start: 0.8378 (m-30) cc_final: 0.8145 (t70) REVERT: C 263 GLN cc_start: 0.9034 (mm110) cc_final: 0.8826 (mm-40) REVERT: C 270 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6599 (mp0) REVERT: C 271 SER cc_start: 0.9143 (m) cc_final: 0.8881 (p) REVERT: C 290 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.7979 (mtp85) REVERT: C 314 GLN cc_start: 0.9056 (tp40) cc_final: 0.8495 (tp-100) REVERT: D 44 MET cc_start: 0.7994 (mmm) cc_final: 0.7360 (mtt) REVERT: D 47 MET cc_start: 0.1557 (tmm) cc_final: 0.1192 (tmm) REVERT: D 72 GLU cc_start: 0.7985 (pp20) cc_final: 0.7765 (pp20) REVERT: D 82 MET cc_start: 0.8948 (tpp) cc_final: 0.8487 (tmm) REVERT: D 87 HIS cc_start: 0.8447 (t-90) cc_final: 0.8113 (t-90) REVERT: D 142 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9011 (mp) REVERT: D 192 ILE cc_start: 0.9261 (tp) cc_final: 0.8791 (tp) REVERT: D 280 ASN cc_start: 0.8992 (m-40) cc_final: 0.8746 (m-40) REVERT: E 78 ASN cc_start: 0.8379 (t0) cc_final: 0.7213 (t0) REVERT: E 81 ASP cc_start: 0.7921 (m-30) cc_final: 0.7455 (m-30) REVERT: E 162 ASN cc_start: 0.8815 (t0) cc_final: 0.8465 (t0) REVERT: E 206 ARG cc_start: 0.8626 (mtp-110) cc_final: 0.8378 (ttm-80) REVERT: E 227 MET cc_start: 0.8799 (mmm) cc_final: 0.8513 (tpp) REVERT: E 276 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7174 (mp0) REVERT: E 314 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8469 (tm-30) outliers start: 50 outliers final: 37 residues processed: 283 average time/residue: 0.1040 time to fit residues: 47.5944 Evaluate side-chains 278 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 233 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 36 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 201 optimal weight: 50.0000 chunk 204 optimal weight: 30.0000 chunk 151 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 200 optimal weight: 30.0000 chunk 144 optimal weight: 10.0000 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN A 280 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 GLN ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.097251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.090981 restraints weight = 54291.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.092582 restraints weight = 29323.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.093730 restraints weight = 18318.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.094331 restraints weight = 13013.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.094634 restraints weight = 10188.746| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.5134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 16113 Z= 0.223 Angle : 0.752 11.512 21934 Z= 0.371 Chirality : 0.045 0.211 2505 Planarity : 0.004 0.057 2828 Dihedral : 5.679 50.490 2323 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.15 % Favored : 96.57 % Rotamer: Outliers : 3.17 % Allowed : 22.20 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.20), residues: 1810 helix: 0.72 (0.19), residues: 725 sheet: -0.56 (0.28), residues: 325 loop : 0.35 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 290 TYR 0.030 0.001 TYR B 279 PHE 0.012 0.002 PHE C 352 TRP 0.070 0.002 TRP C 340 HIS 0.006 0.001 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00500 (16113) covalent geometry : angle 0.75214 (21934) hydrogen bonds : bond 0.03567 ( 971) hydrogen bonds : angle 4.56927 ( 2583) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 240 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8683 (t0) cc_final: 0.7514 (t0) REVERT: A 81 ASP cc_start: 0.8904 (m-30) cc_final: 0.8208 (m-30) REVERT: A 107 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7762 (tm-30) REVERT: A 121 GLN cc_start: 0.9178 (tt0) cc_final: 0.8884 (tm-30) REVERT: B 40 HIS cc_start: 0.7573 (m-70) cc_final: 0.7226 (m90) REVERT: B 47 MET cc_start: 0.1447 (ptm) cc_final: 0.0798 (ttt) REVERT: B 86 TRP cc_start: 0.9042 (OUTLIER) cc_final: 0.8796 (m-10) REVERT: B 88 HIS cc_start: 0.8565 (OUTLIER) cc_final: 0.8006 (t-90) REVERT: B 110 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8907 (tt) REVERT: B 176 MET cc_start: 0.8590 (mtt) cc_final: 0.8261 (mtt) REVERT: B 222 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.8373 (p0) REVERT: B 276 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8368 (mp0) REVERT: B 305 MET cc_start: 0.9140 (mmm) cc_final: 0.8747 (mmm) REVERT: C 44 MET cc_start: 0.8345 (tpp) cc_final: 0.8063 (tpp) REVERT: C 59 GLN cc_start: 0.8431 (tp40) cc_final: 0.8170 (tp40) REVERT: C 270 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6522 (mp0) REVERT: C 271 SER cc_start: 0.9115 (m) cc_final: 0.8895 (p) REVERT: C 283 MET cc_start: 0.9003 (mmp) cc_final: 0.8619 (mmt) REVERT: C 314 GLN cc_start: 0.8980 (tp40) cc_final: 0.8617 (tp-100) REVERT: D 44 MET cc_start: 0.7966 (mmm) cc_final: 0.7183 (mtt) REVERT: D 47 MET cc_start: 0.1555 (tmm) cc_final: 0.1127 (tmm) REVERT: D 82 MET cc_start: 0.8950 (tpp) cc_final: 0.8271 (tmm) REVERT: D 87 HIS cc_start: 0.8475 (t-90) cc_final: 0.8165 (t-90) REVERT: D 142 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9055 (mp) REVERT: D 192 ILE cc_start: 0.9318 (tp) cc_final: 0.8904 (tp) REVERT: D 280 ASN cc_start: 0.9007 (m-40) cc_final: 0.8770 (m-40) REVERT: E 78 ASN cc_start: 0.8413 (t0) cc_final: 0.7218 (t0) REVERT: E 81 ASP cc_start: 0.7903 (m-30) cc_final: 0.7474 (m-30) REVERT: E 162 ASN cc_start: 0.8877 (t0) cc_final: 0.8532 (t0) REVERT: E 206 ARG cc_start: 0.8722 (mtp-110) cc_final: 0.8490 (ttm-80) REVERT: E 227 MET cc_start: 0.8836 (mmm) cc_final: 0.8535 (tpp) REVERT: E 276 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7159 (mp0) REVERT: E 314 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8531 (tm-30) outliers start: 49 outliers final: 35 residues processed: 277 average time/residue: 0.1031 time to fit residues: 46.5857 Evaluate side-chains 269 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 226 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 124 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 139 optimal weight: 0.3980 chunk 133 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 197 optimal weight: 40.0000 chunk 201 optimal weight: 50.0000 chunk 106 optimal weight: 8.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN A 280 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.098647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.092239 restraints weight = 53634.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.093937 restraints weight = 29250.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.094831 restraints weight = 18870.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.095583 restraints weight = 14164.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.096053 restraints weight = 10764.003| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16113 Z= 0.148 Angle : 0.739 15.561 21934 Z= 0.360 Chirality : 0.045 0.241 2505 Planarity : 0.004 0.059 2828 Dihedral : 5.604 55.684 2323 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.04 % Favored : 96.69 % Rotamer: Outliers : 3.04 % Allowed : 22.65 % 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 aren not related in a simple way. whole: 0.43 (0.20), residues: 1810 helix: 0.79 (0.20), residues: 725 sheet: -0.53 (0.27), residues: 350 loop : 0.44 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 290 TYR 0.018 0.001 TYR C 166 PHE 0.040 0.001 PHE A 352 TRP 0.066 0.002 TRP C 340 HIS 0.005 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00338 (16113) covalent geometry : angle 0.73921 (21934) hydrogen bonds : bond 0.03421 ( 971) hydrogen bonds : angle 4.53777 ( 2583) =============================================================================== Job complete usr+sys time: 2328.26 seconds wall clock time: 41 minutes 27.43 seconds (2487.43 seconds total)