Starting phenix.real_space_refine on Thu Sep 18 09:10:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5jlf_8163/09_2025/5jlf_8163.cif Found real_map, /net/cci-nas-00/data/ceres_data/5jlf_8163/09_2025/5jlf_8163.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5jlf_8163/09_2025/5jlf_8163.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5jlf_8163/09_2025/5jlf_8163.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5jlf_8163/09_2025/5jlf_8163.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5jlf_8163/09_2025/5jlf_8163.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 100 5.16 5 C 9925 2.51 5 N 2700 2.21 5 O 3060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s 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: 3.84, per 1000 atoms: 0.24 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: 1.37 Conformation dependent library (CDL) restraints added in 513.2 milliseconds Enol-peptide restraints added in 715.3 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: 0.83 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: 2.95 Time building geometry restraints manager: 1.63 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: 1.160 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.640 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 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 537 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 517 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.9202 (m-40) cc_final: 0.8679 (m-40) REVERT: A 78 ASN cc_start: 0.8865 (t0) cc_final: 0.8179 (t0) REVERT: A 81 ASP cc_start: 0.8846 (m-30) cc_final: 0.8426 (m-30) REVERT: A 121 GLN cc_start: 0.9204 (tt0) cc_final: 0.8797 (tm-30) REVERT: A 225 ASN cc_start: 0.8899 (m-40) cc_final: 0.8699 (m-40) REVERT: A 313 MET cc_start: 0.8545 (mmm) cc_final: 0.8152 (mmm) REVERT: A 351 THR cc_start: 0.8723 (p) cc_final: 0.8510 (p) REVERT: B 40 HIS cc_start: 0.7813 (m-70) cc_final: 0.7605 (m-70) REVERT: B 47 MET cc_start: 0.1557 (ptm) cc_final: 0.0880 (ttt) REVERT: B 69 TYR cc_start: 0.9114 (m-10) cc_final: 0.8896 (m-10) REVERT: B 115 ASN cc_start: 0.8348 (m-40) cc_final: 0.8089 (m110) REVERT: B 160 THR cc_start: 0.8978 (m) cc_final: 0.8759 (m) REVERT: B 242 LEU cc_start: 0.9076 (mp) cc_final: 0.8868 (mt) REVERT: B 247 VAL cc_start: 0.9393 (t) cc_final: 0.8873 (p) REVERT: B 279 TYR cc_start: 0.9151 (t80) cc_final: 0.8939 (t80) REVERT: C 123 MET cc_start: 0.8732 (mmt) cc_final: 0.8515 (tpp) REVERT: C 162 ASN cc_start: 0.8216 (m-40) cc_final: 0.7944 (m-40) REVERT: C 186 THR cc_start: 0.9443 (OUTLIER) cc_final: 0.9229 (t) REVERT: C 187 ASP cc_start: 0.8681 (m-30) cc_final: 0.8435 (t0) REVERT: C 191 LYS cc_start: 0.8824 (ptmt) cc_final: 0.8248 (mtpp) REVERT: D 10 CYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8859 (t) REVERT: D 12 ASN cc_start: 0.8786 (m-40) cc_final: 0.8573 (m110) REVERT: D 44 MET cc_start: 0.8117 (mmm) cc_final: 0.7083 (mtt) REVERT: D 78 ASN cc_start: 0.8796 (t0) cc_final: 0.8394 (t0) REVERT: D 81 ASP cc_start: 0.8984 (m-30) cc_final: 0.8667 (m-30) REVERT: D 110 LEU cc_start: 0.9215 (tp) cc_final: 0.8975 (tt) REVERT: D 160 THR cc_start: 0.9399 (m) cc_final: 0.9071 (p) REVERT: D 192 ILE cc_start: 0.9089 (tp) cc_final: 0.8636 (tp) REVERT: D 237 GLU cc_start: 0.8599 (pt0) cc_final: 0.8357 (pm20) REVERT: D 353 GLN cc_start: 0.8727 (mt0) cc_final: 0.8511 (tm-30) REVERT: D 355 MET cc_start: 0.8730 (mtt) cc_final: 0.8302 (tpt) REVERT: E 12 ASN cc_start: 0.9247 (m-40) cc_final: 0.8670 (p0) REVERT: E 78 ASN cc_start: 0.8864 (t0) cc_final: 0.8617 (t0) REVERT: E 157 ASP cc_start: 0.8753 (t0) cc_final: 0.8498 (t0) REVERT: E 162 ASN cc_start: 0.8491 (m-40) cc_final: 0.8134 (m-40) REVERT: E 283 MET cc_start: 0.9321 (mmp) cc_final: 0.9007 (mmt) REVERT: E 327 ILE cc_start: 0.8874 (mt) cc_final: 0.8653 (mp) outliers start: 20 outliers final: 2 residues processed: 532 average time/residue: 0.1376 time to fit residues: 106.3532 Evaluate side-chains 275 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 271 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain E residue 186 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 40.0000 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 30.0000 chunk 77 optimal weight: 0.0770 chunk 122 optimal weight: 0.8980 overall best weight: 0.7940 ------------------------------------------------------------------------------- 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 162 ASN A 246 GLN A 280 ASN A 296 ASN B 12 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN B 280 ASN B 296 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 HIS C 92 ASN C 121 GLN C 296 ASN D 12 ASN D 88 HIS D 92 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN E 59 GLN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN E 246 GLN E 297 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.096630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.076448 restraints weight = 39913.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.078954 restraints weight = 18894.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.080597 restraints weight = 10867.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.081730 restraints weight = 7131.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.082516 restraints weight = 5125.939| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16113 Z= 0.175 Angle : 0.754 11.011 21934 Z= 0.383 Chirality : 0.046 0.242 2505 Planarity : 0.005 0.093 2828 Dihedral : 7.221 68.280 2327 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.93 % Favored : 97.79 % Rotamer: Outliers : 3.56 % Allowed : 14.56 % Favored : 81.88 % 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: -0.02 (0.19), residues: 1810 helix: 0.17 (0.19), residues: 725 sheet: -0.31 (0.27), residues: 285 loop : 0.14 (0.22), residues: 800 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 0.035 0.002 TRP C 340 HIS 0.008 0.002 HIS E 101 Details of bonding type rmsd covalent geometry : bond 0.00387 (16113) covalent geometry : angle 0.75429 (21934) hydrogen bonds : bond 0.04994 ( 971) hydrogen bonds : angle 5.49922 ( 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 375 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 320 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8571 (t0) cc_final: 0.7366 (t0) REVERT: A 81 ASP cc_start: 0.8625 (m-30) cc_final: 0.8260 (m-30) REVERT: A 132 MET cc_start: 0.8375 (ptm) cc_final: 0.8128 (ppp) REVERT: A 325 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.6998 (ptm) REVERT: B 44 MET cc_start: 0.7637 (mpp) cc_final: 0.7087 (mpp) REVERT: B 65 LEU cc_start: 0.8739 (mt) cc_final: 0.8528 (mt) REVERT: B 82 MET cc_start: 0.9048 (tpp) cc_final: 0.8789 (tpp) REVERT: B 325 MET cc_start: 0.6975 (ptm) cc_final: 0.6658 (ttp) REVERT: C 105 LEU cc_start: 0.8851 (mt) cc_final: 0.8492 (mt) REVERT: C 137 GLN cc_start: 0.8696 (mm-40) cc_final: 0.8388 (mm-40) REVERT: C 162 ASN cc_start: 0.8242 (m-40) cc_final: 0.8034 (m-40) REVERT: C 190 MET cc_start: 0.8409 (mmm) cc_final: 0.8066 (mtp) REVERT: C 263 GLN cc_start: 0.8749 (mm110) cc_final: 0.8352 (mt0) REVERT: D 47 MET cc_start: 0.1563 (ppp) cc_final: 0.0055 (ttt) REVERT: D 82 MET cc_start: 0.8941 (tpt) cc_final: 0.8698 (tpt) REVERT: D 110 LEU cc_start: 0.9158 (tp) cc_final: 0.8774 (tt) REVERT: D 142 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8866 (mp) REVERT: D 192 ILE cc_start: 0.9184 (tp) cc_final: 0.8694 (tp) REVERT: E 162 ASN cc_start: 0.8311 (m-40) cc_final: 0.8083 (m-40) REVERT: E 190 MET cc_start: 0.8395 (tpp) cc_final: 0.8186 (mmm) REVERT: E 191 LYS cc_start: 0.8818 (ptmt) cc_final: 0.8476 (ptpt) outliers start: 55 outliers final: 26 residues processed: 358 average time/residue: 0.1163 time to fit residues: 63.7237 Evaluate side-chains 261 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 233 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 297 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 56 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 67 optimal weight: 0.0470 chunk 148 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 123 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 176 optimal weight: 0.3980 chunk 122 optimal weight: 0.9990 overall best weight: 0.6884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN ** E 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.099751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.079304 restraints weight = 40098.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.081816 restraints weight = 18771.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.083511 restraints weight = 10842.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.084550 restraints weight = 7084.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.085371 restraints weight = 5206.366| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16113 Z= 0.148 Angle : 0.682 7.769 21934 Z= 0.342 Chirality : 0.045 0.224 2505 Planarity : 0.004 0.046 2828 Dihedral : 6.546 60.442 2324 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.04 % Favored : 97.68 % Rotamer: Outliers : 3.56 % Allowed : 16.83 % Favored : 79.61 % 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: 0.00 (0.19), residues: 1810 helix: 0.21 (0.19), residues: 755 sheet: -0.19 (0.27), residues: 320 loop : 0.11 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 95 TYR 0.026 0.001 TYR C 166 PHE 0.013 0.001 PHE C 127 TRP 0.017 0.001 TRP C 340 HIS 0.006 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00320 (16113) covalent geometry : angle 0.68215 (21934) hydrogen bonds : bond 0.04426 ( 971) hydrogen bonds : angle 5.04421 ( 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 334 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 279 time to evaluate : 0.568 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: 0.8498 (t0) cc_final: 0.7333 (t0) REVERT: A 305 MET cc_start: 0.8480 (tpp) cc_final: 0.8142 (mmt) REVERT: B 313 MET cc_start: 0.8073 (mmm) cc_final: 0.7759 (mmm) REVERT: C 137 GLN cc_start: 0.8682 (mm-40) cc_final: 0.8368 (mm-40) REVERT: C 271 SER cc_start: 0.8944 (m) cc_final: 0.8742 (p) REVERT: D 47 MET cc_start: 0.1669 (ppp) cc_final: 0.0967 (tmm) REVERT: D 142 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8718 (mp) REVERT: D 192 ILE cc_start: 0.9175 (tp) cc_final: 0.8641 (tp) REVERT: D 276 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7959 (mm-30) REVERT: D 280 ASN cc_start: 0.8845 (m-40) cc_final: 0.8635 (m-40) REVERT: E 206 ARG cc_start: 0.8464 (mtp-110) cc_final: 0.8024 (ttp-170) outliers start: 55 outliers final: 31 residues processed: 315 average time/residue: 0.1046 time to fit residues: 52.3282 Evaluate side-chains 260 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 228 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 330 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 32 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 180 optimal weight: 40.0000 chunk 163 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 200 optimal weight: 40.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN D 115 ASN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN ** E 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.093956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.073614 restraints weight = 40856.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.075991 restraints weight = 19533.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.077555 restraints weight = 11399.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.078592 restraints weight = 7593.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.079253 restraints weight = 5573.486| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 16113 Z= 0.302 Angle : 0.778 10.062 21934 Z= 0.391 Chirality : 0.048 0.186 2505 Planarity : 0.005 0.046 2828 Dihedral : 6.630 63.966 2324 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.93 % Favored : 96.80 % Rotamer: Outliers : 4.66 % Allowed : 17.09 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.19), residues: 1810 helix: 0.20 (0.19), residues: 725 sheet: -0.59 (0.27), residues: 325 loop : 0.19 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 290 TYR 0.023 0.002 TYR C 166 PHE 0.020 0.002 PHE A 352 TRP 0.014 0.002 TRP C 340 HIS 0.007 0.002 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00676 (16113) covalent geometry : angle 0.77787 (21934) hydrogen bonds : bond 0.04449 ( 971) hydrogen bonds : angle 4.99692 ( 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 294 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 222 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7563 (tt0) cc_final: 0.6792 (tt0) REVERT: A 132 MET cc_start: 0.8622 (ppp) cc_final: 0.8419 (ppp) REVERT: A 211 ASP cc_start: 0.8303 (t0) cc_final: 0.8101 (t0) REVERT: A 227 MET cc_start: 0.8702 (mmm) cc_final: 0.8310 (mmt) REVERT: A 241 GLU cc_start: 0.7446 (pm20) cc_final: 0.7231 (pm20) REVERT: A 305 MET cc_start: 0.8689 (tpp) cc_final: 0.8362 (mmt) REVERT: B 82 MET cc_start: 0.9122 (tpp) cc_final: 0.8918 (tpt) REVERT: D 142 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.8965 (mp) REVERT: D 192 ILE cc_start: 0.9278 (tp) cc_final: 0.8836 (tp) outliers start: 72 outliers final: 48 residues processed: 280 average time/residue: 0.1015 time to fit residues: 46.7582 Evaluate side-chains 250 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 201 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 66 optimal weight: 6.9990 chunk 170 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 193 optimal weight: 50.0000 chunk 17 optimal weight: 1.9990 chunk 200 optimal weight: 40.0000 chunk 172 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 194 optimal weight: 40.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 ASN E 360 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.097005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.076930 restraints weight = 40414.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.079358 restraints weight = 19161.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.080939 restraints weight = 11075.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.082017 restraints weight = 7331.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.082684 restraints weight = 5308.303| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16113 Z= 0.145 Angle : 0.668 11.830 21934 Z= 0.329 Chirality : 0.045 0.228 2505 Planarity : 0.004 0.054 2828 Dihedral : 6.095 56.265 2323 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.98 % Favored : 96.74 % Rotamer: Outliers : 3.24 % Allowed : 19.74 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.20), residues: 1810 helix: 0.49 (0.19), residues: 725 sheet: -0.47 (0.28), residues: 320 loop : 0.22 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 62 TYR 0.025 0.001 TYR C 166 PHE 0.016 0.001 PHE A 352 TRP 0.014 0.001 TRP C 340 HIS 0.004 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00322 (16113) covalent geometry : angle 0.66819 (21934) hydrogen bonds : bond 0.03830 ( 971) hydrogen bonds : angle 4.76902 ( 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 303 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 253 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7528 (tt0) cc_final: 0.6682 (tt0) REVERT: A 121 GLN cc_start: 0.8993 (tt0) cc_final: 0.8754 (tm-30) REVERT: A 211 ASP cc_start: 0.8201 (t0) cc_final: 0.7993 (t0) REVERT: A 227 MET cc_start: 0.8705 (mmm) cc_final: 0.8305 (mmt) REVERT: A 241 GLU cc_start: 0.7441 (pm20) cc_final: 0.7170 (pm20) REVERT: B 80 ASP cc_start: 0.7889 (p0) cc_final: 0.7654 (p0) REVERT: B 82 MET cc_start: 0.8995 (tpp) cc_final: 0.8740 (tpt) REVERT: B 88 HIS cc_start: 0.8203 (OUTLIER) cc_final: 0.7519 (t-90) REVERT: B 169 TYR cc_start: 0.8361 (m-80) cc_final: 0.8143 (m-80) REVERT: C 137 GLN cc_start: 0.8784 (mm-40) cc_final: 0.8437 (mm-40) REVERT: D 142 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8837 (mp) REVERT: D 192 ILE cc_start: 0.9224 (tp) cc_final: 0.8724 (tp) REVERT: D 276 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7975 (mm-30) REVERT: E 128 ASN cc_start: 0.8613 (m-40) cc_final: 0.8357 (m-40) REVERT: E 206 ARG cc_start: 0.8549 (mtp-110) cc_final: 0.8310 (ttp-170) outliers start: 50 outliers final: 30 residues processed: 293 average time/residue: 0.1121 time to fit residues: 51.5550 Evaluate side-chains 247 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 215 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 297 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN B 353 GLN D 59 GLN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN ** E 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.096948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.076852 restraints weight = 40422.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.079244 restraints weight = 19141.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.080858 restraints weight = 11083.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.081884 restraints weight = 7244.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.082593 restraints weight = 5264.108| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4720 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= 0.147 Angle : 0.665 11.286 21934 Z= 0.326 Chirality : 0.044 0.246 2505 Planarity : 0.004 0.067 2828 Dihedral : 5.896 53.417 2323 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.76 % Favored : 96.96 % Rotamer: Outliers : 3.82 % Allowed : 20.58 % Favored : 75.60 % 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: 0.28 (0.20), residues: 1810 helix: 0.61 (0.19), residues: 730 sheet: -0.46 (0.28), residues: 320 loop : 0.28 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 62 TYR 0.022 0.001 TYR C 166 PHE 0.035 0.001 PHE A 352 TRP 0.047 0.002 TRP C 340 HIS 0.004 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00330 (16113) covalent geometry : angle 0.66456 (21934) hydrogen bonds : bond 0.03720 ( 971) hydrogen bonds : angle 4.67265 ( 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 286 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 227 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7618 (tt0) cc_final: 0.6798 (tt0) REVERT: A 211 ASP cc_start: 0.8194 (t0) cc_final: 0.7990 (t0) REVERT: A 241 GLU cc_start: 0.7416 (pm20) cc_final: 0.7112 (pm20) REVERT: A 305 MET cc_start: 0.8541 (tpp) cc_final: 0.8198 (mmt) REVERT: B 88 HIS cc_start: 0.8174 (OUTLIER) cc_final: 0.7530 (t-90) REVERT: C 44 MET cc_start: 0.8087 (tpp) cc_final: 0.7690 (tpp) REVERT: C 104 LEU cc_start: 0.8947 (tt) cc_final: 0.8632 (tp) REVERT: C 116 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7856 (mmm-85) REVERT: D 142 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8804 (mp) REVERT: D 176 MET cc_start: 0.8280 (mmm) cc_final: 0.8029 (mtp) REVERT: D 192 ILE cc_start: 0.9183 (tp) cc_final: 0.8681 (tp) REVERT: D 349 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8081 (mp) REVERT: E 128 ASN cc_start: 0.8657 (m-40) cc_final: 0.8366 (m-40) REVERT: E 180 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9014 (tt) REVERT: E 206 ARG cc_start: 0.8428 (mtp-110) cc_final: 0.8072 (ttt90) outliers start: 59 outliers final: 39 residues processed: 276 average time/residue: 0.1136 time to fit residues: 49.5567 Evaluate side-chains 262 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 218 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 116 ARG Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 358 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 99 optimal weight: 6.9990 chunk 182 optimal weight: 50.0000 chunk 79 optimal weight: 9.9990 chunk 23 optimal weight: 0.1980 chunk 87 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 200 optimal weight: 40.0000 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN E 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.096393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.076304 restraints weight = 40368.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.078703 restraints weight = 18975.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.080316 restraints weight = 10932.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.081349 restraints weight = 7155.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.081985 restraints weight = 5177.535| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16113 Z= 0.161 Angle : 0.674 10.903 21934 Z= 0.330 Chirality : 0.044 0.196 2505 Planarity : 0.004 0.060 2828 Dihedral : 5.748 51.172 2323 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.98 % Favored : 96.74 % Rotamer: Outliers : 3.56 % Allowed : 21.10 % Favored : 75.34 % 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: 0.27 (0.20), residues: 1810 helix: 0.61 (0.19), residues: 735 sheet: -0.42 (0.28), residues: 320 loop : 0.25 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 62 TYR 0.025 0.001 TYR C 166 PHE 0.025 0.002 PHE C 352 TRP 0.071 0.002 TRP C 340 HIS 0.004 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00362 (16113) covalent geometry : angle 0.67358 (21934) hydrogen bonds : bond 0.03619 ( 971) hydrogen bonds : angle 4.63219 ( 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 282 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 227 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7765 (tt0) cc_final: 0.6790 (tt0) REVERT: A 227 MET cc_start: 0.8771 (mmm) cc_final: 0.8366 (mmt) REVERT: A 241 GLU cc_start: 0.7418 (pm20) cc_final: 0.7105 (pm20) REVERT: A 305 MET cc_start: 0.8547 (tpp) cc_final: 0.8206 (mmt) REVERT: B 80 ASP cc_start: 0.7988 (p0) cc_final: 0.7778 (p0) REVERT: B 88 HIS cc_start: 0.8264 (OUTLIER) cc_final: 0.7607 (t-90) REVERT: C 44 MET cc_start: 0.8100 (tpp) cc_final: 0.7698 (tpp) REVERT: C 104 LEU cc_start: 0.8987 (tt) cc_final: 0.8590 (tp) REVERT: C 116 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7814 (mmm-85) REVERT: C 137 GLN cc_start: 0.8852 (mm-40) cc_final: 0.8624 (mm110) REVERT: C 340 TRP cc_start: 0.8088 (t60) cc_final: 0.7071 (t60) REVERT: D 142 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8808 (mp) REVERT: D 176 MET cc_start: 0.8291 (mmm) cc_final: 0.8046 (mtp) REVERT: D 192 ILE cc_start: 0.9164 (tp) cc_final: 0.8669 (tp) REVERT: D 349 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8083 (mp) REVERT: E 78 ASN cc_start: 0.8332 (t0) cc_final: 0.8032 (p0) REVERT: E 128 ASN cc_start: 0.8675 (m-40) cc_final: 0.8398 (m-40) REVERT: E 180 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9033 (tt) REVERT: E 206 ARG cc_start: 0.8462 (mtp-110) cc_final: 0.8237 (ttm-80) outliers start: 55 outliers final: 41 residues processed: 268 average time/residue: 0.1061 time to fit residues: 45.6283 Evaluate side-chains 264 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 218 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 116 ARG Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 297 ASN 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: 2.9990 chunk 104 optimal weight: 0.3980 chunk 96 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 186 optimal weight: 30.0000 chunk 26 optimal weight: 0.3980 chunk 114 optimal weight: 7.9990 chunk 118 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 137 GLN ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN E 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.096860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.076802 restraints weight = 40712.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.079250 restraints weight = 19124.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.080859 restraints weight = 10966.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.081901 restraints weight = 7172.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.082617 restraints weight = 5187.545| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.5008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16113 Z= 0.150 Angle : 0.672 10.475 21934 Z= 0.327 Chirality : 0.044 0.217 2505 Planarity : 0.004 0.061 2828 Dihedral : 5.651 49.096 2323 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.93 % Favored : 96.80 % Rotamer: Outliers : 3.75 % Allowed : 20.65 % Favored : 75.60 % 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: 0.34 (0.20), residues: 1810 helix: 0.67 (0.19), residues: 735 sheet: -0.36 (0.28), residues: 320 loop : 0.27 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 290 TYR 0.024 0.001 TYR C 166 PHE 0.046 0.001 PHE C 352 TRP 0.066 0.002 TRP C 340 HIS 0.005 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00339 (16113) covalent geometry : angle 0.67191 (21934) hydrogen bonds : bond 0.03508 ( 971) hydrogen bonds : angle 4.60535 ( 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 284 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 226 time to evaluate : 0.536 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 107 GLU cc_start: 0.7760 (tt0) cc_final: 0.6824 (tt0) REVERT: A 227 MET cc_start: 0.8780 (mmm) cc_final: 0.8361 (mmt) REVERT: A 241 GLU cc_start: 0.7415 (pm20) cc_final: 0.7091 (pm20) REVERT: A 305 MET cc_start: 0.8586 (tpp) cc_final: 0.8266 (mmt) REVERT: B 80 ASP cc_start: 0.7987 (p0) cc_final: 0.7767 (p0) REVERT: B 88 HIS cc_start: 0.8291 (OUTLIER) cc_final: 0.7678 (t-90) REVERT: C 44 MET cc_start: 0.8172 (tpp) cc_final: 0.7810 (tpp) REVERT: C 104 LEU cc_start: 0.8963 (tt) cc_final: 0.8601 (tp) REVERT: C 116 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7788 (mmm-85) REVERT: C 137 GLN cc_start: 0.8866 (mm-40) cc_final: 0.8594 (mm110) REVERT: C 340 TRP cc_start: 0.8072 (t60) cc_final: 0.7650 (t60) REVERT: D 72 GLU cc_start: 0.7794 (pp20) cc_final: 0.7580 (pp20) REVERT: D 82 MET cc_start: 0.8885 (tpp) cc_final: 0.8412 (tmm) REVERT: D 142 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8824 (mp) REVERT: D 192 ILE cc_start: 0.9164 (tp) cc_final: 0.8670 (tp) REVERT: D 349 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8101 (mp) REVERT: E 128 ASN cc_start: 0.8631 (m-40) cc_final: 0.8374 (m-40) REVERT: E 180 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9104 (tt) REVERT: E 206 ARG cc_start: 0.8452 (mtp-110) cc_final: 0.8081 (ttm-80) outliers start: 58 outliers final: 46 residues processed: 271 average time/residue: 0.1046 time to fit residues: 45.7693 Evaluate side-chains 267 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 216 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 116 ARG Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 143 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 195 optimal weight: 50.0000 chunk 164 optimal weight: 0.9990 chunk 118 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 172 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 181 optimal weight: 50.0000 chunk 7 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 137 GLN B 263 GLN B 314 GLN C 59 GLN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN E 297 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.096563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.076875 restraints weight = 40698.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.079309 restraints weight = 18938.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.080887 restraints weight = 10828.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.081881 restraints weight = 7065.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.082626 restraints weight = 5140.555| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16113 Z= 0.156 Angle : 0.678 10.718 21934 Z= 0.330 Chirality : 0.044 0.194 2505 Planarity : 0.004 0.062 2828 Dihedral : 5.579 47.084 2323 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.87 % Favored : 96.85 % Rotamer: Outliers : 3.69 % Allowed : 20.97 % Favored : 75.34 % 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: 0.33 (0.20), residues: 1810 helix: 0.69 (0.19), residues: 735 sheet: -0.43 (0.28), residues: 325 loop : 0.27 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 290 TYR 0.025 0.001 TYR C 166 PHE 0.040 0.001 PHE C 352 TRP 0.059 0.002 TRP C 340 HIS 0.005 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00353 (16113) covalent geometry : angle 0.67769 (21934) hydrogen bonds : bond 0.03496 ( 971) hydrogen bonds : angle 4.57236 ( 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 276 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 219 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7770 (tt0) cc_final: 0.6870 (tt0) REVERT: A 227 MET cc_start: 0.8811 (mmm) cc_final: 0.8408 (mmt) REVERT: A 241 GLU cc_start: 0.7427 (pm20) cc_final: 0.7104 (pm20) REVERT: A 305 MET cc_start: 0.8595 (tpp) cc_final: 0.8234 (mmt) REVERT: A 313 MET cc_start: 0.8230 (mmm) cc_final: 0.7829 (mtp) REVERT: B 80 ASP cc_start: 0.7970 (p0) cc_final: 0.7736 (p0) REVERT: B 88 HIS cc_start: 0.8274 (OUTLIER) cc_final: 0.7690 (t-90) REVERT: C 44 MET cc_start: 0.8161 (tpp) cc_final: 0.7813 (tpp) REVERT: C 104 LEU cc_start: 0.8959 (tt) cc_final: 0.8615 (tp) REVERT: C 116 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7913 (tpp80) REVERT: C 313 MET cc_start: 0.8893 (tpp) cc_final: 0.8689 (mmm) REVERT: D 47 MET cc_start: 0.4318 (tmm) cc_final: -0.0006 (ttt) REVERT: D 72 GLU cc_start: 0.7780 (pp20) cc_final: 0.7553 (pp20) REVERT: D 82 MET cc_start: 0.8863 (tpp) cc_final: 0.8404 (tmm) REVERT: D 142 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8831 (mp) REVERT: D 192 ILE cc_start: 0.9165 (tp) cc_final: 0.8675 (tp) REVERT: D 349 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8080 (mp) REVERT: E 128 ASN cc_start: 0.8627 (m-40) cc_final: 0.8379 (m-40) REVERT: E 206 ARG cc_start: 0.8497 (mtp-110) cc_final: 0.8115 (ttm-80) outliers start: 57 outliers final: 48 residues processed: 264 average time/residue: 0.1043 time to fit residues: 44.3384 Evaluate side-chains 266 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 214 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 47 MET Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 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 160 THR Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 116 ARG Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 358 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 36 optimal weight: 10.0000 chunk 46 optimal weight: 0.3980 chunk 59 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 201 optimal weight: 30.0000 chunk 204 optimal weight: 50.0000 chunk 151 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 200 optimal weight: 30.0000 chunk 144 optimal weight: 10.0000 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN D 78 ASN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN E 297 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.093888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.073912 restraints weight = 40962.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.076302 restraints weight = 19451.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.077895 restraints weight = 11296.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.078871 restraints weight = 7433.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.079601 restraints weight = 5469.965| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 16113 Z= 0.278 Angle : 0.767 11.479 21934 Z= 0.380 Chirality : 0.047 0.217 2505 Planarity : 0.004 0.060 2828 Dihedral : 5.824 50.201 2323 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.37 % Favored : 96.35 % Rotamer: Outliers : 3.69 % Allowed : 21.17 % Favored : 75.15 % 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: 0.10 (0.20), residues: 1810 helix: 0.53 (0.19), residues: 730 sheet: -0.65 (0.28), residues: 325 loop : 0.16 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 290 TYR 0.027 0.002 TYR C 143 PHE 0.045 0.002 PHE C 352 TRP 0.103 0.003 TRP C 340 HIS 0.009 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00620 (16113) covalent geometry : angle 0.76734 (21934) hydrogen bonds : bond 0.03824 ( 971) hydrogen bonds : angle 4.72900 ( 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 271 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 214 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7821 (tt0) cc_final: 0.6881 (tt0) REVERT: B 44 MET cc_start: 0.8074 (tpp) cc_final: 0.7842 (tpp) REVERT: B 80 ASP cc_start: 0.8003 (p0) cc_final: 0.7788 (p0) REVERT: B 88 HIS cc_start: 0.8340 (OUTLIER) cc_final: 0.7697 (t-90) REVERT: C 44 MET cc_start: 0.8199 (tpp) cc_final: 0.7808 (tpp) REVERT: C 104 LEU cc_start: 0.9014 (tt) cc_final: 0.8721 (tp) REVERT: C 116 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.8001 (tpp80) REVERT: C 340 TRP cc_start: 0.7681 (t60) cc_final: 0.6984 (t60) REVERT: D 142 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.8986 (mp) REVERT: D 192 ILE cc_start: 0.9232 (tp) cc_final: 0.8786 (tp) REVERT: D 349 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8122 (mp) REVERT: E 128 ASN cc_start: 0.8668 (m-40) cc_final: 0.8420 (m-40) outliers start: 57 outliers final: 47 residues processed: 260 average time/residue: 0.1075 time to fit residues: 44.8106 Evaluate side-chains 252 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 201 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 116 ARG Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 358 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 124 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 197 optimal weight: 40.0000 chunk 201 optimal weight: 30.0000 chunk 106 optimal weight: 7.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN D 78 ASN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN E 297 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.096761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.076727 restraints weight = 40407.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.079177 restraints weight = 19001.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.080760 restraints weight = 10916.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.081815 restraints weight = 7182.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.082469 restraints weight = 5198.228| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 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 0.048 16113 Z= 0.146 Angle : 0.695 11.460 21934 Z= 0.340 Chirality : 0.044 0.193 2505 Planarity : 0.004 0.062 2828 Dihedral : 5.670 53.750 2323 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.04 % Favored : 96.69 % Rotamer: Outliers : 3.24 % Allowed : 22.07 % Favored : 74.69 % 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: 0.28 (0.20), residues: 1810 helix: 0.68 (0.20), residues: 730 sheet: -0.50 (0.28), residues: 320 loop : 0.23 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 206 TYR 0.032 0.001 TYR A 166 PHE 0.031 0.001 PHE C 352 TRP 0.099 0.003 TRP C 340 HIS 0.010 0.001 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00330 (16113) covalent geometry : angle 0.69516 (21934) hydrogen bonds : bond 0.03487 ( 971) hydrogen bonds : angle 4.61316 ( 2583) =============================================================================== Job complete usr+sys time: 2538.32 seconds wall clock time: 44 minutes 51.62 seconds (2691.62 seconds total)