Starting phenix.real_space_refine on Thu Jan 16 00:37:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uz0_42829/01_2025/8uz0_42829_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uz0_42829/01_2025/8uz0_42829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uz0_42829/01_2025/8uz0_42829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uz0_42829/01_2025/8uz0_42829.map" model { file = "/net/cci-nas-00/data/ceres_data/8uz0_42829/01_2025/8uz0_42829_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uz0_42829/01_2025/8uz0_42829_trim.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.117 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: 7 Type Number sf(0) Gaussians P 18 5.49 5 Mg 9 5.21 5 S 189 5.16 5 C 16668 2.51 5 N 4455 2.21 5 O 5094 1.98 5 H 25938 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 170 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 52371 Number of models: 1 Model: "" Number of chains: 18 Chain: "J" Number of atoms: 5791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5791 Classifications: {'peptide': 372} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: "K" Number of atoms: 5791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5791 Classifications: {'peptide': 372} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: "L" Number of atoms: 5791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5791 Classifications: {'peptide': 372} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: "M" Number of atoms: 5791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5791 Classifications: {'peptide': 372} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: "N" Number of atoms: 5791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5791 Classifications: {'peptide': 372} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: "O" Number of atoms: 5791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5791 Classifications: {'peptide': 372} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: "P" Number of atoms: 5791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5791 Classifications: {'peptide': 372} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: "Q" Number of atoms: 5791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5791 Classifications: {'peptide': 372} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: "R" Number of atoms: 5791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5791 Classifications: {'peptide': 372} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: "J" 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: "K" 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: "L" 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: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: 19.15, per 1000 atoms: 0.37 Number of scatterers: 52371 At special positions: 0 Unit cell: (92.874, 100.95, 302.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 189 16.00 P 18 15.00 Mg 9 11.99 O 5094 8.00 N 4455 7.00 C 16668 6.00 H 25938 1.00 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: 11.08 Conformation dependent library (CDL) restraints added in 3.2 seconds 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6192 Finding SS restraints... Secondary structure from input PDB file: 193 helices and 54 sheets defined 50.2% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.07 Creating SS restraints... Processing helix chain 'J' and resid 55 through 62 Processing helix chain 'J' and resid 78 through 92 removed outlier: 4.301A pdb=" N LYS J 84 " --> pdb=" O ASP J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 101 removed outlier: 3.542A pdb=" N HIS J 101 " --> pdb=" O PRO J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 126 removed outlier: 3.837A pdb=" N ARG J 116 " --> pdb=" O PRO J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 137 through 146 removed outlier: 3.556A pdb=" N LEU J 142 " --> pdb=" O ALA J 138 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR J 143 " --> pdb=" O VAL J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 194 Processing helix chain 'J' and resid 195 through 197 No H-bonds generated for 'chain 'J' and resid 195 through 197' Processing helix chain 'J' and resid 202 through 217 Processing helix chain 'J' and resid 222 through 230 Processing helix chain 'J' and resid 252 through 257 Processing helix chain 'J' and resid 258 through 262 Processing helix chain 'J' and resid 263 through 268 Processing helix chain 'J' and resid 273 through 285 removed outlier: 3.590A pdb=" N CYS J 285 " --> pdb=" O SER J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 288 No H-bonds generated for 'chain 'J' and resid 286 through 288' Processing helix chain 'J' and resid 289 through 296 Processing helix chain 'J' and resid 301 through 306 removed outlier: 4.445A pdb=" N TYR J 306 " --> pdb=" O THR J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 308 through 321 Processing helix chain 'J' and resid 332 through 336 removed outlier: 4.449A pdb=" N LYS J 336 " --> pdb=" O PRO J 333 " (cutoff:3.500A) Processing helix chain 'J' and resid 337 through 349 Processing helix chain 'J' and resid 350 through 356 removed outlier: 4.459A pdb=" N GLN J 354 " --> pdb=" O THR J 351 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TRP J 356 " --> pdb=" O GLN J 353 " (cutoff:3.500A) Processing helix chain 'J' and resid 359 through 363 Processing helix chain 'J' and resid 366 through 373 removed outlier: 3.582A pdb=" N HIS J 371 " --> pdb=" O SER J 368 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 62 Processing helix chain 'K' and resid 78 through 92 removed outlier: 3.836A pdb=" N LYS K 84 " --> pdb=" O ASP K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 126 removed outlier: 3.947A pdb=" N ARG K 116 " --> pdb=" O PRO K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 146 removed outlier: 3.776A pdb=" N LEU K 142 " --> pdb=" O ALA K 138 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR K 143 " --> pdb=" O VAL K 139 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA K 144 " --> pdb=" O LEU K 140 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER K 145 " --> pdb=" O SER K 141 " (cutoff:3.500A) Processing helix chain 'K' and resid 172 through 175 Processing helix chain 'K' and resid 181 through 196 removed outlier: 4.042A pdb=" N GLU K 195 " --> pdb=" O LYS K 191 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG K 196 " --> pdb=" O ILE K 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 202 through 217 removed outlier: 3.809A pdb=" N GLU K 207 " --> pdb=" O THR K 203 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE K 208 " --> pdb=" O ALA K 204 " (cutoff:3.500A) Processing helix chain 'K' and resid 222 through 232 removed outlier: 3.637A pdb=" N SER K 232 " --> pdb=" O ALA K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 257 Processing helix chain 'K' and resid 258 through 262 Processing helix chain 'K' and resid 263 through 268 Processing helix chain 'K' and resid 273 through 285 Processing helix chain 'K' and resid 286 through 288 No H-bonds generated for 'chain 'K' and resid 286 through 288' Processing helix chain 'K' and resid 289 through 296 removed outlier: 3.541A pdb=" N ALA K 295 " --> pdb=" O LYS K 291 " (cutoff:3.500A) Processing helix chain 'K' and resid 301 through 305 Processing helix chain 'K' and resid 308 through 321 Processing helix chain 'K' and resid 337 through 347 Processing helix chain 'K' and resid 348 through 355 removed outlier: 6.029A pdb=" N THR K 351 " --> pdb=" O SER K 348 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN K 353 " --> pdb=" O SER K 350 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLN K 354 " --> pdb=" O THR K 351 " (cutoff:3.500A) Processing helix chain 'K' and resid 359 through 363 Processing helix chain 'K' and resid 368 through 374 removed outlier: 4.163A pdb=" N ARG K 372 " --> pdb=" O SER K 368 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 62 Processing helix chain 'L' and resid 78 through 92 removed outlier: 3.971A pdb=" N LYS L 84 " --> pdb=" O ASP L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 101 Processing helix chain 'L' and resid 112 through 126 removed outlier: 3.896A pdb=" N ARG L 116 " --> pdb=" O PRO L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 146 Processing helix chain 'L' and resid 172 through 175 removed outlier: 3.516A pdb=" N ILE L 175 " --> pdb=" O PRO L 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 172 through 175' Processing helix chain 'L' and resid 181 through 195 removed outlier: 3.813A pdb=" N GLU L 195 " --> pdb=" O LYS L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 202 through 217 removed outlier: 3.753A pdb=" N GLU L 207 " --> pdb=" O THR L 203 " (cutoff:3.500A) Processing helix chain 'L' and resid 222 through 232 Processing helix chain 'L' and resid 252 through 257 removed outlier: 3.550A pdb=" N CYS L 257 " --> pdb=" O GLU L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 258 through 262 Processing helix chain 'L' and resid 263 through 268 Processing helix chain 'L' and resid 273 through 285 Processing helix chain 'L' and resid 286 through 288 No H-bonds generated for 'chain 'L' and resid 286 through 288' Processing helix chain 'L' and resid 289 through 295 Processing helix chain 'L' and resid 301 through 305 Processing helix chain 'L' and resid 308 through 321 Processing helix chain 'L' and resid 334 through 336 No H-bonds generated for 'chain 'L' and resid 334 through 336' Processing helix chain 'L' and resid 337 through 349 Processing helix chain 'L' and resid 350 through 353 Processing helix chain 'L' and resid 359 through 363 Processing helix chain 'L' and resid 366 through 368 No H-bonds generated for 'chain 'L' and resid 366 through 368' Processing helix chain 'L' and resid 369 through 374 removed outlier: 3.766A pdb=" N CYS L 374 " --> pdb=" O VAL L 370 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 62 Processing helix chain 'M' and resid 78 through 92 removed outlier: 3.650A pdb=" N LYS M 84 " --> pdb=" O ASP M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 126 removed outlier: 4.006A pdb=" N ARG M 116 " --> pdb=" O PRO M 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 137 through 146 removed outlier: 3.704A pdb=" N LEU M 142 " --> pdb=" O ALA M 138 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR M 143 " --> pdb=" O VAL M 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 181 through 194 removed outlier: 3.569A pdb=" N THR M 194 " --> pdb=" O MET M 190 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 197 No H-bonds generated for 'chain 'M' and resid 195 through 197' Processing helix chain 'M' and resid 202 through 217 removed outlier: 3.693A pdb=" N GLU M 207 " --> pdb=" O THR M 203 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE M 208 " --> pdb=" O ALA M 204 " (cutoff:3.500A) Processing helix chain 'M' and resid 222 through 232 removed outlier: 3.622A pdb=" N SER M 232 " --> pdb=" O ALA M 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 252 through 257 Processing helix chain 'M' and resid 258 through 262 Processing helix chain 'M' and resid 263 through 268 Processing helix chain 'M' and resid 273 through 285 Processing helix chain 'M' and resid 289 through 295 Processing helix chain 'M' and resid 301 through 305 Processing helix chain 'M' and resid 308 through 321 Processing helix chain 'M' and resid 337 through 347 Processing helix chain 'M' and resid 348 through 353 removed outlier: 6.186A pdb=" N THR M 351 " --> pdb=" O SER M 348 " (cutoff:3.500A) Processing helix chain 'M' and resid 359 through 363 Processing helix chain 'M' and resid 364 through 365 No H-bonds generated for 'chain 'M' and resid 364 through 365' Processing helix chain 'M' and resid 366 through 368 No H-bonds generated for 'chain 'M' and resid 366 through 368' Processing helix chain 'M' and resid 369 through 374 removed outlier: 3.542A pdb=" N CYS M 374 " --> pdb=" O VAL M 370 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 61 Processing helix chain 'N' and resid 78 through 92 removed outlier: 3.957A pdb=" N LYS N 84 " --> pdb=" O ASP N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 112 through 126 removed outlier: 3.916A pdb=" N ARG N 116 " --> pdb=" O PRO N 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 146 removed outlier: 3.603A pdb=" N LEU N 142 " --> pdb=" O ALA N 138 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR N 143 " --> pdb=" O VAL N 139 " (cutoff:3.500A) Processing helix chain 'N' and resid 172 through 175 removed outlier: 3.534A pdb=" N ILE N 175 " --> pdb=" O PRO N 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 172 through 175' Processing helix chain 'N' and resid 181 through 194 removed outlier: 3.548A pdb=" N THR N 194 " --> pdb=" O MET N 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 195 through 197 No H-bonds generated for 'chain 'N' and resid 195 through 197' Processing helix chain 'N' and resid 202 through 217 removed outlier: 3.783A pdb=" N GLU N 207 " --> pdb=" O THR N 203 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE N 208 " --> pdb=" O ALA N 204 " (cutoff:3.500A) Processing helix chain 'N' and resid 222 through 232 Processing helix chain 'N' and resid 252 through 257 Processing helix chain 'N' and resid 258 through 262 Processing helix chain 'N' and resid 263 through 268 Processing helix chain 'N' and resid 273 through 285 removed outlier: 3.504A pdb=" N CYS N 285 " --> pdb=" O SER N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 286 through 288 No H-bonds generated for 'chain 'N' and resid 286 through 288' Processing helix chain 'N' and resid 289 through 295 Processing helix chain 'N' and resid 301 through 305 Processing helix chain 'N' and resid 308 through 321 Processing helix chain 'N' and resid 334 through 336 No H-bonds generated for 'chain 'N' and resid 334 through 336' Processing helix chain 'N' and resid 337 through 347 Processing helix chain 'N' and resid 348 through 353 removed outlier: 6.208A pdb=" N THR N 351 " --> pdb=" O SER N 348 " (cutoff:3.500A) Processing helix chain 'N' and resid 359 through 363 Processing helix chain 'N' and resid 368 through 374 removed outlier: 4.338A pdb=" N ARG N 372 " --> pdb=" O SER N 368 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 62 Processing helix chain 'O' and resid 78 through 92 removed outlier: 3.959A pdb=" N LYS O 84 " --> pdb=" O ASP O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 112 through 126 removed outlier: 3.959A pdb=" N ARG O 116 " --> pdb=" O PRO O 112 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 146 removed outlier: 3.522A pdb=" N LEU O 142 " --> pdb=" O ALA O 138 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR O 143 " --> pdb=" O VAL O 139 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA O 144 " --> pdb=" O LEU O 140 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER O 145 " --> pdb=" O SER O 141 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 175 Processing helix chain 'O' and resid 181 through 194 removed outlier: 3.585A pdb=" N THR O 194 " --> pdb=" O MET O 190 " (cutoff:3.500A) Processing helix chain 'O' and resid 195 through 197 No H-bonds generated for 'chain 'O' and resid 195 through 197' Processing helix chain 'O' and resid 202 through 217 removed outlier: 3.704A pdb=" N GLU O 207 " --> pdb=" O THR O 203 " (cutoff:3.500A) Processing helix chain 'O' and resid 222 through 232 removed outlier: 3.679A pdb=" N SER O 232 " --> pdb=" O ALA O 228 " (cutoff:3.500A) Processing helix chain 'O' and resid 252 through 257 Processing helix chain 'O' and resid 258 through 262 Processing helix chain 'O' and resid 263 through 268 Processing helix chain 'O' and resid 273 through 284 Processing helix chain 'O' and resid 289 through 295 Processing helix chain 'O' and resid 301 through 306 removed outlier: 4.376A pdb=" N TYR O 306 " --> pdb=" O THR O 303 " (cutoff:3.500A) Processing helix chain 'O' and resid 308 through 321 Processing helix chain 'O' and resid 334 through 336 No H-bonds generated for 'chain 'O' and resid 334 through 336' Processing helix chain 'O' and resid 337 through 349 Processing helix chain 'O' and resid 350 through 353 Processing helix chain 'O' and resid 359 through 364 Processing helix chain 'O' and resid 366 through 368 No H-bonds generated for 'chain 'O' and resid 366 through 368' Processing helix chain 'O' and resid 369 through 374 Processing helix chain 'P' and resid 55 through 61 Processing helix chain 'P' and resid 78 through 92 removed outlier: 3.615A pdb=" N LYS P 84 " --> pdb=" O ASP P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 112 through 126 removed outlier: 3.983A pdb=" N ARG P 116 " --> pdb=" O PRO P 112 " (cutoff:3.500A) Processing helix chain 'P' and resid 137 through 146 removed outlier: 3.648A pdb=" N TYR P 143 " --> pdb=" O VAL P 139 " (cutoff:3.500A) Processing helix chain 'P' and resid 172 through 175 Processing helix chain 'P' and resid 181 through 194 removed outlier: 3.820A pdb=" N THR P 194 " --> pdb=" O MET P 190 " (cutoff:3.500A) Processing helix chain 'P' and resid 195 through 197 No H-bonds generated for 'chain 'P' and resid 195 through 197' Processing helix chain 'P' and resid 204 through 217 removed outlier: 3.669A pdb=" N ILE P 208 " --> pdb=" O ALA P 204 " (cutoff:3.500A) Processing helix chain 'P' and resid 222 through 232 removed outlier: 3.591A pdb=" N SER P 232 " --> pdb=" O ALA P 228 " (cutoff:3.500A) Processing helix chain 'P' and resid 252 through 257 Processing helix chain 'P' and resid 258 through 262 Processing helix chain 'P' and resid 263 through 268 Processing helix chain 'P' and resid 273 through 285 Processing helix chain 'P' and resid 286 through 288 No H-bonds generated for 'chain 'P' and resid 286 through 288' Processing helix chain 'P' and resid 289 through 295 Processing helix chain 'P' and resid 301 through 305 Processing helix chain 'P' and resid 308 through 321 Processing helix chain 'P' and resid 337 through 349 Processing helix chain 'P' and resid 350 through 353 removed outlier: 3.539A pdb=" N GLN P 353 " --> pdb=" O SER P 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 350 through 353' Processing helix chain 'P' and resid 359 through 363 Processing helix chain 'P' and resid 368 through 374 removed outlier: 4.136A pdb=" N ARG P 372 " --> pdb=" O SER P 368 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 62 Processing helix chain 'Q' and resid 78 through 92 removed outlier: 3.985A pdb=" N LYS Q 84 " --> pdb=" O ASP Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 112 through 126 removed outlier: 3.858A pdb=" N ARG Q 116 " --> pdb=" O PRO Q 112 " (cutoff:3.500A) Processing helix chain 'Q' and resid 137 through 146 removed outlier: 3.505A pdb=" N LEU Q 142 " --> pdb=" O ALA Q 138 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR Q 143 " --> pdb=" O VAL Q 139 " (cutoff:3.500A) Processing helix chain 'Q' and resid 181 through 194 removed outlier: 3.704A pdb=" N THR Q 194 " --> pdb=" O MET Q 190 " (cutoff:3.500A) Processing helix chain 'Q' and resid 195 through 197 No H-bonds generated for 'chain 'Q' and resid 195 through 197' Processing helix chain 'Q' and resid 202 through 217 removed outlier: 3.528A pdb=" N ILE Q 208 " --> pdb=" O ALA Q 204 " (cutoff:3.500A) Processing helix chain 'Q' and resid 222 through 232 Processing helix chain 'Q' and resid 252 through 257 Processing helix chain 'Q' and resid 258 through 262 Processing helix chain 'Q' and resid 263 through 268 Processing helix chain 'Q' and resid 273 through 285 removed outlier: 3.685A pdb=" N CYS Q 285 " --> pdb=" O SER Q 281 " (cutoff:3.500A) Processing helix chain 'Q' and resid 286 through 296 removed outlier: 3.529A pdb=" N ARG Q 290 " --> pdb=" O ASP Q 286 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYS Q 291 " --> pdb=" O ILE Q 287 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ASP Q 292 " --> pdb=" O ASP Q 288 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA Q 295 " --> pdb=" O LYS Q 291 " (cutoff:3.500A) Processing helix chain 'Q' and resid 301 through 306 removed outlier: 4.338A pdb=" N TYR Q 306 " --> pdb=" O THR Q 303 " (cutoff:3.500A) Processing helix chain 'Q' and resid 308 through 321 Processing helix chain 'Q' and resid 337 through 347 Processing helix chain 'Q' and resid 348 through 349 No H-bonds generated for 'chain 'Q' and resid 348 through 349' Processing helix chain 'Q' and resid 350 through 355 removed outlier: 4.165A pdb=" N GLN Q 354 " --> pdb=" O THR Q 351 " (cutoff:3.500A) Processing helix chain 'Q' and resid 359 through 363 Processing helix chain 'Q' and resid 366 through 368 No H-bonds generated for 'chain 'Q' and resid 366 through 368' Processing helix chain 'Q' and resid 369 through 374 removed outlier: 3.553A pdb=" N LYS Q 373 " --> pdb=" O ILE Q 369 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 62 Processing helix chain 'R' and resid 78 through 92 removed outlier: 4.195A pdb=" N LYS R 84 " --> pdb=" O ASP R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 126 removed outlier: 3.728A pdb=" N ARG R 116 " --> pdb=" O PRO R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 146 removed outlier: 3.846A pdb=" N LEU R 142 " --> pdb=" O ALA R 138 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N TYR R 143 " --> pdb=" O VAL R 139 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA R 144 " --> pdb=" O LEU R 140 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 175 removed outlier: 3.579A pdb=" N ILE R 175 " --> pdb=" O PRO R 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 172 through 175' Processing helix chain 'R' and resid 181 through 195 removed outlier: 4.027A pdb=" N GLU R 195 " --> pdb=" O LYS R 191 " (cutoff:3.500A) Processing helix chain 'R' and resid 202 through 217 removed outlier: 3.699A pdb=" N GLU R 207 " --> pdb=" O THR R 203 " (cutoff:3.500A) Processing helix chain 'R' and resid 222 through 232 Processing helix chain 'R' and resid 252 through 257 Processing helix chain 'R' and resid 258 through 262 Processing helix chain 'R' and resid 263 through 268 Processing helix chain 'R' and resid 273 through 284 Processing helix chain 'R' and resid 286 through 294 removed outlier: 3.696A pdb=" N ARG R 290 " --> pdb=" O ASP R 286 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LYS R 291 " --> pdb=" O ILE R 287 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ASP R 292 " --> pdb=" O ASP R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 301 through 305 Processing helix chain 'R' and resid 308 through 321 Processing helix chain 'R' and resid 332 through 336 removed outlier: 4.502A pdb=" N LYS R 336 " --> pdb=" O PRO R 333 " (cutoff:3.500A) Processing helix chain 'R' and resid 337 through 349 Processing helix chain 'R' and resid 350 through 355 removed outlier: 4.260A pdb=" N GLN R 354 " --> pdb=" O THR R 351 " (cutoff:3.500A) Processing helix chain 'R' and resid 359 through 363 Processing helix chain 'R' and resid 366 through 368 No H-bonds generated for 'chain 'R' and resid 366 through 368' Processing helix chain 'R' and resid 369 through 374 removed outlier: 3.663A pdb=" N LYS R 373 " --> pdb=" O ILE R 369 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 29 through 32 removed outlier: 6.735A pdb=" N LEU J 8 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N THR J 106 " --> pdb=" O LEU J 8 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N CYS J 10 " --> pdb=" O THR J 106 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR J 103 " --> pdb=" O TYR J 133 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ALA J 135 " --> pdb=" O THR J 103 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU J 105 " --> pdb=" O ALA J 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'J' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'J' and resid 176 through 178 removed outlier: 6.424A pdb=" N ASN J 297 " --> pdb=" O ILE J 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 176 through 178 removed outlier: 4.048A pdb=" N GLN L 41 " --> pdb=" O ALA J 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'K' and resid 29 through 32 removed outlier: 3.547A pdb=" N THR K 106 " --> pdb=" O CYS K 10 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'K' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'K' and resid 176 through 178 removed outlier: 6.490A pdb=" N ASN K 297 " --> pdb=" O ILE K 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 176 through 178 removed outlier: 3.851A pdb=" N GLN M 41 " --> pdb=" O ALA K 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'L' and resid 29 through 32 removed outlier: 3.911A pdb=" N THR L 106 " --> pdb=" O CYS L 10 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ASN L 12 " --> pdb=" O THR L 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'L' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'L' and resid 176 through 178 removed outlier: 6.319A pdb=" N ASN L 297 " --> pdb=" O ILE L 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 176 through 178 removed outlier: 3.891A pdb=" N GLN N 41 " --> pdb=" O ALA L 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'M' and resid 29 through 32 removed outlier: 3.569A pdb=" N THR M 106 " --> pdb=" O CYS M 10 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ASN M 12 " --> pdb=" O THR M 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'M' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'M' and resid 176 through 178 Processing sheet with id=AC5, first strand: chain 'M' and resid 176 through 178 removed outlier: 3.747A pdb=" N GLN O 41 " --> pdb=" O ALA M 170 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'N' and resid 29 through 32 removed outlier: 6.447A pdb=" N LEU N 8 " --> pdb=" O LEU N 104 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N THR N 106 " --> pdb=" O LEU N 8 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N CYS N 10 " --> pdb=" O THR N 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'N' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'N' and resid 176 through 178 removed outlier: 6.336A pdb=" N ASN N 297 " --> pdb=" O ILE N 330 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 176 through 178 removed outlier: 3.681A pdb=" N GLN P 41 " --> pdb=" O ALA N 170 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 238 through 241 Processing sheet with id=AD4, first strand: chain 'O' and resid 29 through 33 removed outlier: 4.197A pdb=" N GLY O 15 " --> pdb=" O SER O 33 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU O 8 " --> pdb=" O LEU O 104 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N THR O 106 " --> pdb=" O LEU O 8 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N CYS O 10 " --> pdb=" O THR O 106 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 53 through 54 Processing sheet with id=AD6, first strand: chain 'O' and resid 71 through 72 Processing sheet with id=AD7, first strand: chain 'O' and resid 176 through 178 removed outlier: 6.502A pdb=" N ILE O 151 " --> pdb=" O VAL O 298 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N SER O 300 " --> pdb=" O ILE O 151 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU O 153 " --> pdb=" O SER O 300 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASN O 297 " --> pdb=" O ILE O 330 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'O' and resid 176 through 178 removed outlier: 3.769A pdb=" N GLN Q 41 " --> pdb=" O ALA O 170 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 238 through 241 Processing sheet with id=AE1, first strand: chain 'P' and resid 29 through 32 removed outlier: 6.549A pdb=" N LEU P 8 " --> pdb=" O LEU P 104 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N THR P 106 " --> pdb=" O LEU P 8 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N CYS P 10 " --> pdb=" O THR P 106 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 53 through 54 Processing sheet with id=AE3, first strand: chain 'P' and resid 71 through 72 Processing sheet with id=AE4, first strand: chain 'P' and resid 176 through 178 Processing sheet with id=AE5, first strand: chain 'P' and resid 176 through 178 removed outlier: 3.764A pdb=" N GLN R 41 " --> pdb=" O ALA P 170 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'P' and resid 238 through 241 Processing sheet with id=AE7, first strand: chain 'Q' and resid 29 through 32 removed outlier: 3.704A pdb=" N THR Q 106 " --> pdb=" O CYS Q 10 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 53 through 54 Processing sheet with id=AE9, first strand: chain 'Q' and resid 71 through 72 Processing sheet with id=AF1, first strand: chain 'Q' and resid 169 through 170 Processing sheet with id=AF2, first strand: chain 'Q' and resid 169 through 170 removed outlier: 6.334A pdb=" N ASN Q 297 " --> pdb=" O ILE Q 330 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Q' and resid 238 through 241 Processing sheet with id=AF4, first strand: chain 'R' and resid 29 through 32 removed outlier: 3.589A pdb=" N THR R 106 " --> pdb=" O CYS R 10 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'R' and resid 53 through 54 Processing sheet with id=AF6, first strand: chain 'R' and resid 71 through 72 Processing sheet with id=AF7, first strand: chain 'R' and resid 169 through 170 Processing sheet with id=AF8, first strand: chain 'R' and resid 169 through 170 removed outlier: 6.328A pdb=" N ASN R 297 " --> pdb=" O ILE R 330 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'R' and resid 238 through 241 1311 hydrogen bonds defined for protein. 3324 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: 20.37 Time building geometry restraints manager: 13.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.92 - 1.10: 25893 1.10 - 1.28: 4410 1.28 - 1.46: 8663 1.46 - 1.64: 13648 1.64 - 1.82: 333 Bond restraints: 52947 Sorted by residual: bond pdb=" N MET R 47 " pdb=" H MET R 47 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N ALA R 108 " pdb=" H ALA R 108 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NE2 HIS R 371 " pdb=" HE2 HIS R 371 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CD1 TYR P 169 " pdb=" HD1 TYR P 169 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CE1 HIS R 161 " pdb=" HE1 HIS R 161 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 52942 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 81413 2.76 - 5.52: 11376 5.52 - 8.27: 2791 8.27 - 11.03: 106 11.03 - 13.79: 29 Bond angle restraints: 95715 Sorted by residual: angle pdb=" CA ASP P 244 " pdb=" CB ASP P 244 " pdb=" CG ASP P 244 " ideal model delta sigma weight residual 112.60 119.26 -6.66 1.00e+00 1.00e+00 4.43e+01 angle pdb=" CA ASP R 244 " pdb=" CB ASP R 244 " pdb=" CG ASP R 244 " ideal model delta sigma weight residual 112.60 119.17 -6.57 1.00e+00 1.00e+00 4.32e+01 angle pdb=" CA ASP L 244 " pdb=" CB ASP L 244 " pdb=" CG ASP L 244 " ideal model delta sigma weight residual 112.60 118.92 -6.32 1.00e+00 1.00e+00 3.99e+01 angle pdb=" C ILE M 330 " pdb=" CA ILE M 330 " pdb=" CB ILE M 330 " ideal model delta sigma weight residual 111.53 119.74 -8.21 1.30e+00 5.92e-01 3.98e+01 angle pdb=" CA ASP O 244 " pdb=" CB ASP O 244 " pdb=" CG ASP O 244 " ideal model delta sigma weight residual 112.60 118.89 -6.29 1.00e+00 1.00e+00 3.95e+01 ... (remaining 95710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.64: 23800 33.64 - 67.27: 1057 67.27 - 100.91: 82 100.91 - 134.55: 9 134.55 - 168.19: 9 Dihedral angle restraints: 24957 sinusoidal: 13734 harmonic: 11223 Sorted by residual: dihedral pdb=" C GLU Q 93 " pdb=" N GLU Q 93 " pdb=" CA GLU Q 93 " pdb=" CB GLU Q 93 " ideal model delta harmonic sigma weight residual -122.60 -142.81 20.21 0 2.50e+00 1.60e-01 6.53e+01 dihedral pdb=" C GLU L 93 " pdb=" N GLU L 93 " pdb=" CA GLU L 93 " pdb=" CB GLU L 93 " ideal model delta harmonic sigma weight residual -122.60 -142.05 19.45 0 2.50e+00 1.60e-01 6.05e+01 dihedral pdb=" N GLU Q 93 " pdb=" C GLU Q 93 " pdb=" CA GLU Q 93 " pdb=" CB GLU Q 93 " ideal model delta harmonic sigma weight residual 122.80 141.69 -18.89 0 2.50e+00 1.60e-01 5.71e+01 ... (remaining 24954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 3587 0.161 - 0.322: 429 0.322 - 0.483: 38 0.483 - 0.644: 10 0.644 - 0.805: 4 Chirality restraints: 4068 Sorted by residual: chirality pdb=" CA GLU Q 93 " pdb=" N GLU Q 93 " pdb=" C GLU Q 93 " pdb=" CB GLU Q 93 " both_signs ideal model delta sigma weight residual False 2.51 1.71 0.81 2.00e-01 2.50e+01 1.62e+01 chirality pdb=" CA GLU L 93 " pdb=" N GLU L 93 " pdb=" C GLU L 93 " pdb=" CB GLU L 93 " both_signs ideal model delta sigma weight residual False 2.51 1.72 0.79 2.00e-01 2.50e+01 1.56e+01 chirality pdb=" CA GLU N 93 " pdb=" N GLU N 93 " pdb=" C GLU N 93 " pdb=" CB GLU N 93 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.44e+01 ... (remaining 4065 not shown) Planarity restraints: 7857 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP J 340 " 0.308 2.00e-02 2.50e+03 1.17e-01 5.49e+02 pdb=" CG TRP J 340 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TRP J 340 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP J 340 " -0.115 2.00e-02 2.50e+03 pdb=" NE1 TRP J 340 " -0.128 2.00e-02 2.50e+03 pdb=" CE2 TRP J 340 " -0.092 2.00e-02 2.50e+03 pdb=" CE3 TRP J 340 " -0.122 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 340 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 340 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP J 340 " 0.061 2.00e-02 2.50e+03 pdb=" HD1 TRP J 340 " 0.079 2.00e-02 2.50e+03 pdb=" HE1 TRP J 340 " -0.024 2.00e-02 2.50e+03 pdb=" HE3 TRP J 340 " -0.165 2.00e-02 2.50e+03 pdb=" HZ2 TRP J 340 " 0.058 2.00e-02 2.50e+03 pdb=" HZ3 TRP J 340 " 0.037 2.00e-02 2.50e+03 pdb=" HH2 TRP J 340 " 0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP O 340 " 0.288 2.00e-02 2.50e+03 1.12e-01 5.00e+02 pdb=" CG TRP O 340 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP O 340 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP O 340 " -0.118 2.00e-02 2.50e+03 pdb=" NE1 TRP O 340 " -0.107 2.00e-02 2.50e+03 pdb=" CE2 TRP O 340 " -0.100 2.00e-02 2.50e+03 pdb=" CE3 TRP O 340 " -0.115 2.00e-02 2.50e+03 pdb=" CZ2 TRP O 340 " -0.016 2.00e-02 2.50e+03 pdb=" CZ3 TRP O 340 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP O 340 " 0.058 2.00e-02 2.50e+03 pdb=" HD1 TRP O 340 " 0.085 2.00e-02 2.50e+03 pdb=" HE1 TRP O 340 " -0.014 2.00e-02 2.50e+03 pdb=" HE3 TRP O 340 " -0.152 2.00e-02 2.50e+03 pdb=" HZ2 TRP O 340 " 0.047 2.00e-02 2.50e+03 pdb=" HZ3 TRP O 340 " 0.048 2.00e-02 2.50e+03 pdb=" HH2 TRP O 340 " 0.165 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP P 340 " 0.297 2.00e-02 2.50e+03 1.08e-01 4.70e+02 pdb=" CG TRP P 340 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TRP P 340 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 TRP P 340 " -0.080 2.00e-02 2.50e+03 pdb=" NE1 TRP P 340 " -0.128 2.00e-02 2.50e+03 pdb=" CE2 TRP P 340 " -0.082 2.00e-02 2.50e+03 pdb=" CE3 TRP P 340 " -0.099 2.00e-02 2.50e+03 pdb=" CZ2 TRP P 340 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP P 340 " -0.021 2.00e-02 2.50e+03 pdb=" CH2 TRP P 340 " 0.062 2.00e-02 2.50e+03 pdb=" HD1 TRP P 340 " 0.043 2.00e-02 2.50e+03 pdb=" HE1 TRP P 340 " -0.009 2.00e-02 2.50e+03 pdb=" HE3 TRP P 340 " -0.152 2.00e-02 2.50e+03 pdb=" HZ2 TRP P 340 " 0.060 2.00e-02 2.50e+03 pdb=" HZ3 TRP P 340 " 0.007 2.00e-02 2.50e+03 pdb=" HH2 TRP P 340 " 0.155 2.00e-02 2.50e+03 ... (remaining 7854 not shown) Histogram of nonbonded interaction distances: 1.31 - 1.97: 1141 1.97 - 2.62: 57613 2.62 - 3.28: 164190 3.28 - 3.94: 219331 3.94 - 4.60: 332181 Nonbonded interactions: 774456 Sorted by model distance: nonbonded pdb=" H GLY R 302 " pdb=" O2A ADP R 401 " model vdw 1.308 2.450 nonbonded pdb=" H GLY J 302 " pdb=" O2A ADP J 401 " model vdw 1.322 2.450 nonbonded pdb=" H GLY K 302 " pdb=" O2A ADP K 401 " model vdw 1.372 2.450 nonbonded pdb=" H GLY P 302 " pdb=" O2A ADP P 401 " model vdw 1.416 2.450 nonbonded pdb=" H GLY O 302 " pdb=" O2A ADP O 401 " model vdw 1.452 2.450 ... (remaining 774451 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.680 Extract box with map and model: 1.430 Check model and map are aligned: 0.300 Set scattering table: 0.390 Process input model: 87.290 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.160 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: 0.010 Load rotamer database and sin/cos tables:10.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 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 : 0.012 0.091 27009 Z= 0.770 Angle : 1.890 9.531 36657 Z= 1.253 Chirality : 0.112 0.805 4068 Planarity : 0.017 0.187 4689 Dihedral : 15.935 168.186 10053 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 0.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.69 % Favored : 96.25 % Rotamer: Outliers : 3.11 % Allowed : 5.17 % Favored : 91.72 % Cbeta Deviations : 1.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.13), residues: 3303 helix: -1.72 (0.12), residues: 1305 sheet: 0.40 (0.23), residues: 360 loop : -0.22 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.206 0.034 TRP J 340 HIS 0.014 0.004 HIS L 275 PHE 0.067 0.013 PHE Q 262 TYR 0.132 0.019 TYR N 69 ARG 0.021 0.002 ARG P 210 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 528 time to evaluate : 3.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 82 MET cc_start: 0.7861 (tpt) cc_final: 0.7603 (tpt) REVERT: J 195 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6571 (tt0) REVERT: J 244 ASP cc_start: 0.4099 (OUTLIER) cc_final: 0.2269 (m-30) REVERT: J 283 MET cc_start: 0.9226 (mmm) cc_final: 0.8840 (mmm) REVERT: J 326 LYS cc_start: 0.8230 (pttt) cc_final: 0.7980 (ptmt) REVERT: J 330 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8102 (mt) REVERT: K 227 MET cc_start: 0.8943 (mmm) cc_final: 0.8620 (mmm) REVERT: K 269 MET cc_start: 0.8857 (ptp) cc_final: 0.8586 (ptp) REVERT: L 17 VAL cc_start: 0.8538 (OUTLIER) cc_final: 0.8296 (p) REVERT: L 82 MET cc_start: 0.8743 (tpt) cc_final: 0.8531 (tpp) REVERT: L 277 THR cc_start: 0.9091 (OUTLIER) cc_final: 0.8884 (m) REVERT: M 54 VAL cc_start: 0.9148 (OUTLIER) cc_final: 0.8841 (t) REVERT: M 111 ASN cc_start: 0.9272 (OUTLIER) cc_final: 0.8836 (t0) REVERT: M 326 LYS cc_start: 0.7655 (pttt) cc_final: 0.7223 (mmtm) REVERT: M 361 GLU cc_start: 0.8250 (tt0) cc_final: 0.7993 (tt0) REVERT: N 50 LYS cc_start: 0.8165 (tttt) cc_final: 0.7962 (ttmt) REVERT: N 119 MET cc_start: 0.8852 (ttm) cc_final: 0.8565 (ttp) REVERT: N 132 MET cc_start: 0.9476 (OUTLIER) cc_final: 0.9252 (ppp) REVERT: N 176 MET cc_start: 0.9081 (mmm) cc_final: 0.8849 (mmm) REVERT: N 225 ASN cc_start: 0.8314 (t0) cc_final: 0.7900 (t0) REVERT: N 227 MET cc_start: 0.8379 (mmm) cc_final: 0.8098 (mmm) REVERT: N 269 MET cc_start: 0.8948 (ptp) cc_final: 0.8452 (ptm) REVERT: N 328 LYS cc_start: 0.8419 (ttpm) cc_final: 0.8210 (tttt) REVERT: O 17 VAL cc_start: 0.8391 (OUTLIER) cc_final: 0.8154 (p) REVERT: O 47 MET cc_start: 0.7254 (ttp) cc_final: 0.6985 (ttp) REVERT: O 82 MET cc_start: 0.9254 (tpt) cc_final: 0.8962 (tpt) REVERT: O 123 MET cc_start: 0.9015 (tpp) cc_final: 0.8785 (tpp) REVERT: O 190 MET cc_start: 0.9218 (mtm) cc_final: 0.9016 (mtp) REVERT: O 227 MET cc_start: 0.9070 (mmm) cc_final: 0.8689 (mmm) REVERT: O 283 MET cc_start: 0.9135 (mmt) cc_final: 0.8731 (mmm) REVERT: P 17 VAL cc_start: 0.8665 (OUTLIER) cc_final: 0.8272 (p) REVERT: P 41 GLN cc_start: 0.7851 (tt0) cc_final: 0.7365 (tp-100) REVERT: P 225 ASN cc_start: 0.8165 (OUTLIER) cc_final: 0.7823 (m110) REVERT: P 227 MET cc_start: 0.8964 (mmm) cc_final: 0.8647 (mmm) REVERT: P 269 MET cc_start: 0.9058 (ptp) cc_final: 0.8846 (ptm) REVERT: P 313 MET cc_start: 0.8501 (ttp) cc_final: 0.8273 (mtp) REVERT: Q 80 ASP cc_start: 0.8308 (m-30) cc_final: 0.8079 (m-30) REVERT: R 180 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8929 (tt) REVERT: R 191 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8176 (ttmm) REVERT: R 291 LYS cc_start: 0.7115 (mmtt) cc_final: 0.5954 (mptt) outliers start: 88 outliers final: 18 residues processed: 587 average time/residue: 2.4863 time to fit residues: 1694.7485 Evaluate side-chains 340 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 309 time to evaluate : 3.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain J residue 244 ASP Chi-restraints excluded: chain J residue 330 ILE Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 277 THR Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 111 ASN Chi-restraints excluded: chain M residue 132 MET Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 330 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 132 MET Chi-restraints excluded: chain N residue 211 ASP Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 330 ILE Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 225 ASN Chi-restraints excluded: chain P residue 253 GLU Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 244 ASP Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 191 LYS Chi-restraints excluded: chain R residue 330 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 281 optimal weight: 0.8980 chunk 252 optimal weight: 0.7980 chunk 140 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 170 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 158 optimal weight: 0.7980 chunk 194 optimal weight: 0.9980 chunk 302 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 162 ASN ** J 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 GLN K 225 ASN L 162 ASN M 162 ASN O 41 GLN O 137 GLN O 161 HIS P 162 ASN Q 137 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.125203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.093447 restraints weight = 92998.067| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.66 r_work: 0.3026 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27009 Z= 0.210 Angle : 0.694 7.368 36657 Z= 0.351 Chirality : 0.045 0.165 4068 Planarity : 0.005 0.063 4689 Dihedral : 12.595 151.279 3818 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.11 % Allowed : 12.10 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.15), residues: 3303 helix: -0.28 (0.14), residues: 1296 sheet: -0.27 (0.22), residues: 531 loop : 0.59 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP Q 356 HIS 0.005 0.001 HIS N 161 PHE 0.016 0.002 PHE J 90 TYR 0.015 0.001 TYR N 294 ARG 0.005 0.001 ARG J 372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 357 time to evaluate : 3.104 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: J 81 ASP cc_start: 0.7081 (m-30) cc_final: 0.6832 (m-30) REVERT: J 82 MET cc_start: 0.7567 (tpt) cc_final: 0.7097 (tpt) REVERT: J 227 MET cc_start: 0.7493 (mmm) cc_final: 0.7157 (tpp) REVERT: J 283 MET cc_start: 0.8209 (mmm) cc_final: 0.7927 (mmm) REVERT: J 326 LYS cc_start: 0.8524 (pttt) cc_final: 0.7661 (pttt) REVERT: J 336 LYS cc_start: 0.8073 (tptm) cc_final: 0.7663 (ttmt) REVERT: J 355 MET cc_start: 0.8219 (mtm) cc_final: 0.7890 (mtp) REVERT: K 59 GLN cc_start: 0.8713 (tp40) cc_final: 0.8469 (tp-100) REVERT: K 176 MET cc_start: 0.8607 (mmp) cc_final: 0.8324 (mmt) REVERT: K 190 MET cc_start: 0.7747 (mtm) cc_final: 0.7519 (mtm) REVERT: K 227 MET cc_start: 0.7999 (mmm) cc_final: 0.7754 (mmm) REVERT: K 269 MET cc_start: 0.8717 (ptp) cc_final: 0.8383 (ptp) REVERT: L 17 VAL cc_start: 0.8374 (OUTLIER) cc_final: 0.8148 (p) REVERT: L 72 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7337 (mt-10) REVERT: L 82 MET cc_start: 0.8853 (tpt) cc_final: 0.8356 (tpp) REVERT: L 83 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7260 (tm-30) REVERT: L 277 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8518 (m) REVERT: M 61 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7363 (mttt) REVERT: M 72 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7160 (tm-30) REVERT: M 95 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7421 (ptp90) REVERT: M 118 LYS cc_start: 0.8301 (tptm) cc_final: 0.7412 (mtmt) REVERT: M 226 GLU cc_start: 0.8620 (tp30) cc_final: 0.8214 (tp30) REVERT: M 326 LYS cc_start: 0.7668 (pttt) cc_final: 0.7415 (pptt) REVERT: M 361 GLU cc_start: 0.8034 (tt0) cc_final: 0.7724 (tt0) REVERT: N 9 VAL cc_start: 0.8698 (p) cc_final: 0.8388 (m) REVERT: N 132 MET cc_start: 0.9329 (OUTLIER) cc_final: 0.9026 (ppp) REVERT: N 225 ASN cc_start: 0.8277 (t0) cc_final: 0.7890 (t0) REVERT: N 328 LYS cc_start: 0.8535 (ttpm) cc_final: 0.8042 (tttt) REVERT: N 336 LYS cc_start: 0.8022 (tptm) cc_final: 0.7525 (ttpt) REVERT: N 363 ASP cc_start: 0.7713 (p0) cc_final: 0.7304 (p0) REVERT: O 17 VAL cc_start: 0.8386 (OUTLIER) cc_final: 0.8148 (p) REVERT: O 82 MET cc_start: 0.9037 (tpt) cc_final: 0.8608 (tpt) REVERT: O 123 MET cc_start: 0.9097 (tpp) cc_final: 0.8830 (mmm) REVERT: O 137 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8179 (mt0) REVERT: O 225 ASN cc_start: 0.8163 (t0) cc_final: 0.7952 (t160) REVERT: O 227 MET cc_start: 0.8632 (mmm) cc_final: 0.8303 (mmm) REVERT: O 283 MET cc_start: 0.8929 (mmt) cc_final: 0.8506 (mmm) REVERT: O 326 LYS cc_start: 0.8315 (pttt) cc_final: 0.7871 (pttp) REVERT: O 348 SER cc_start: 0.8504 (t) cc_final: 0.8254 (m) REVERT: O 355 MET cc_start: 0.9007 (mtt) cc_final: 0.8620 (mtt) REVERT: O 363 ASP cc_start: 0.7641 (p0) cc_final: 0.7125 (p0) REVERT: P 17 VAL cc_start: 0.8336 (OUTLIER) cc_final: 0.8036 (p) REVERT: P 44 MET cc_start: 0.8499 (mmm) cc_final: 0.8249 (mmt) REVERT: P 57 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8184 (mm-30) REVERT: P 123 MET cc_start: 0.8820 (mmp) cc_final: 0.8615 (mmp) REVERT: P 180 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8703 (tp) REVERT: P 225 ASN cc_start: 0.7935 (OUTLIER) cc_final: 0.7468 (m110) REVERT: P 227 MET cc_start: 0.8567 (mmm) cc_final: 0.8172 (mmm) REVERT: P 269 MET cc_start: 0.8903 (ptp) cc_final: 0.8666 (ptm) REVERT: P 313 MET cc_start: 0.8526 (ttp) cc_final: 0.8206 (mtp) REVERT: P 329 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8845 (mp) REVERT: P 354 GLN cc_start: 0.8317 (mm110) cc_final: 0.7660 (mt0) REVERT: P 360 GLN cc_start: 0.8455 (tp40) cc_final: 0.8184 (tp-100) REVERT: Q 72 GLU cc_start: 0.8154 (tp30) cc_final: 0.7487 (mp0) REVERT: Q 95 ARG cc_start: 0.7679 (mtm-85) cc_final: 0.7452 (mtp-110) REVERT: Q 137 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7907 (mt0) REVERT: Q 179 ASP cc_start: 0.8716 (m-30) cc_final: 0.8460 (m-30) REVERT: Q 241 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8226 (tt0) REVERT: Q 244 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7716 (p0) REVERT: Q 360 GLN cc_start: 0.8630 (tm-30) cc_final: 0.8014 (tm130) REVERT: R 54 VAL cc_start: 0.8724 (OUTLIER) cc_final: 0.8507 (t) REVERT: R 72 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7677 (mp0) REVERT: R 83 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7462 (tm-30) REVERT: R 180 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8591 (tt) REVERT: R 191 LYS cc_start: 0.8064 (ttmt) cc_final: 0.7535 (tttt) REVERT: R 227 MET cc_start: 0.8300 (mmm) cc_final: 0.7778 (mmt) REVERT: R 291 LYS cc_start: 0.5329 (mmtt) cc_final: 0.4426 (mptt) outliers start: 88 outliers final: 29 residues processed: 417 average time/residue: 2.3676 time to fit residues: 1157.1662 Evaluate side-chains 359 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 311 time to evaluate : 3.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 95 ARG Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 199 SER Chi-restraints excluded: chain L residue 277 THR Chi-restraints excluded: chain L residue 324 THR Chi-restraints excluded: chain L residue 350 SER Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 61 LYS Chi-restraints excluded: chain M residue 72 GLU Chi-restraints excluded: chain M residue 95 ARG Chi-restraints excluded: chain M residue 132 MET Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 253 GLU Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 132 MET Chi-restraints excluded: chain N residue 232 SER Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 137 GLN Chi-restraints excluded: chain O residue 211 ASP Chi-restraints excluded: chain O residue 330 ILE Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 122 ILE Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 225 ASN Chi-restraints excluded: chain P residue 253 GLU Chi-restraints excluded: chain P residue 329 ILE Chi-restraints excluded: chain Q residue 49 GLN Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 83 GLU Chi-restraints excluded: chain Q residue 137 GLN Chi-restraints excluded: chain Q residue 241 GLU Chi-restraints excluded: chain Q residue 244 ASP Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 236 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 127 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 319 optimal weight: 1.9990 chunk 311 optimal weight: 8.9990 chunk 252 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 35 optimal weight: 8.9990 chunk 152 optimal weight: 5.9990 chunk 191 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 225 ASN J 263 GLN J 297 ASN K 297 ASN L 121 GLN L 225 ASN O 41 GLN O 137 GLN P 40 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.122979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.091232 restraints weight = 94054.728| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.64 r_work: 0.2982 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27009 Z= 0.276 Angle : 0.660 7.311 36657 Z= 0.328 Chirality : 0.045 0.161 4068 Planarity : 0.005 0.051 4689 Dihedral : 11.868 155.397 3794 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.40 % Allowed : 13.41 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.15), residues: 3303 helix: 0.04 (0.14), residues: 1314 sheet: -0.12 (0.23), residues: 522 loop : 0.52 (0.17), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP N 340 HIS 0.004 0.001 HIS M 161 PHE 0.012 0.001 PHE L 262 TYR 0.013 0.001 TYR N 294 ARG 0.005 0.000 ARG J 372 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 330 time to evaluate : 3.279 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: J 81 ASP cc_start: 0.7228 (m-30) cc_final: 0.6936 (m-30) REVERT: J 82 MET cc_start: 0.7692 (tpt) cc_final: 0.7267 (tpt) REVERT: J 176 MET cc_start: 0.8854 (mmt) cc_final: 0.8613 (mmt) REVERT: J 227 MET cc_start: 0.7456 (mmm) cc_final: 0.7216 (tpp) REVERT: J 283 MET cc_start: 0.8246 (mmm) cc_final: 0.7865 (mmm) REVERT: J 326 LYS cc_start: 0.8588 (pttt) cc_final: 0.7706 (pttt) REVERT: J 336 LYS cc_start: 0.8140 (tptm) cc_final: 0.7721 (ttmt) REVERT: J 355 MET cc_start: 0.8172 (mtm) cc_final: 0.7825 (mtt) REVERT: K 328 LYS cc_start: 0.8068 (tttt) cc_final: 0.7454 (ttmp) REVERT: L 17 VAL cc_start: 0.8360 (OUTLIER) cc_final: 0.8157 (p) REVERT: L 57 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8168 (mm-30) REVERT: L 72 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7907 (mm-30) REVERT: L 83 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7258 (tm-30) REVERT: L 119 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8148 (ttp) REVERT: L 241 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7747 (mm-30) REVERT: L 277 THR cc_start: 0.8767 (OUTLIER) cc_final: 0.8558 (m) REVERT: M 61 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7537 (mttt) REVERT: M 72 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7246 (tm-30) REVERT: M 95 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7568 (ptp90) REVERT: M 118 LYS cc_start: 0.8310 (tptm) cc_final: 0.7375 (mtmt) REVERT: M 122 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7872 (mp) REVERT: M 361 GLU cc_start: 0.8245 (tt0) cc_final: 0.7903 (tt0) REVERT: N 132 MET cc_start: 0.9214 (OUTLIER) cc_final: 0.8890 (ppp) REVERT: N 225 ASN cc_start: 0.8271 (t0) cc_final: 0.7919 (t0) REVERT: N 253 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8264 (pm20) REVERT: N 336 LYS cc_start: 0.8431 (tptm) cc_final: 0.7933 (tttt) REVERT: N 372 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8355 (ptp90) REVERT: O 17 VAL cc_start: 0.8474 (OUTLIER) cc_final: 0.8263 (p) REVERT: O 82 MET cc_start: 0.9016 (tpt) cc_final: 0.8574 (tpt) REVERT: O 106 THR cc_start: 0.9011 (m) cc_final: 0.8678 (m) REVERT: O 225 ASN cc_start: 0.8436 (t0) cc_final: 0.7801 (m110) REVERT: O 227 MET cc_start: 0.8735 (mmm) cc_final: 0.8532 (mmm) REVERT: O 234 SER cc_start: 0.8194 (m) cc_final: 0.7338 (t) REVERT: O 244 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.8015 (p0) REVERT: O 270 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.8000 (tt0) REVERT: O 283 MET cc_start: 0.8992 (mmt) cc_final: 0.8627 (mmm) REVERT: O 326 LYS cc_start: 0.8379 (pttt) cc_final: 0.7948 (pttp) REVERT: O 328 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8306 (ttmm) REVERT: O 348 SER cc_start: 0.8431 (t) cc_final: 0.8185 (m) REVERT: O 355 MET cc_start: 0.9041 (mtt) cc_final: 0.8565 (mtt) REVERT: O 363 ASP cc_start: 0.7457 (p0) cc_final: 0.7075 (p0) REVERT: P 17 VAL cc_start: 0.8369 (OUTLIER) cc_final: 0.8061 (p) REVERT: P 57 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8152 (mm-30) REVERT: P 211 ASP cc_start: 0.8676 (OUTLIER) cc_final: 0.8222 (t70) REVERT: P 225 ASN cc_start: 0.7968 (OUTLIER) cc_final: 0.7525 (m110) REVERT: P 227 MET cc_start: 0.8609 (mmm) cc_final: 0.8215 (mmm) REVERT: P 269 MET cc_start: 0.8798 (ptp) cc_final: 0.8533 (ptm) REVERT: P 313 MET cc_start: 0.8589 (ttp) cc_final: 0.8239 (mtp) REVERT: P 360 GLN cc_start: 0.8381 (tp40) cc_final: 0.8162 (tp-100) REVERT: Q 59 GLN cc_start: 0.8711 (tp-100) cc_final: 0.8366 (mm-40) REVERT: Q 72 GLU cc_start: 0.8179 (tp30) cc_final: 0.7552 (mt-10) REVERT: Q 95 ARG cc_start: 0.7889 (mtm-85) cc_final: 0.7681 (mtp-110) REVERT: Q 360 GLN cc_start: 0.8570 (tm-30) cc_final: 0.7951 (tm130) REVERT: R 83 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7467 (tm-30) REVERT: R 180 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8657 (tt) REVERT: R 191 LYS cc_start: 0.7862 (ttmt) cc_final: 0.7415 (tttt) REVERT: R 227 MET cc_start: 0.8279 (mmm) cc_final: 0.8068 (mmt) REVERT: R 269 MET cc_start: 0.8404 (ptp) cc_final: 0.7943 (ptp) REVERT: R 291 LYS cc_start: 0.5196 (mmtt) cc_final: 0.4407 (mptt) outliers start: 96 outliers final: 39 residues processed: 392 average time/residue: 2.4925 time to fit residues: 1162.9384 Evaluate side-chains 363 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 302 time to evaluate : 3.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 95 ARG Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 95 ARG Chi-restraints excluded: chain L residue 119 MET Chi-restraints excluded: chain L residue 199 SER Chi-restraints excluded: chain L residue 241 GLU Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain L residue 277 THR Chi-restraints excluded: chain L residue 324 THR Chi-restraints excluded: chain L residue 350 SER Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 61 LYS Chi-restraints excluded: chain M residue 72 GLU Chi-restraints excluded: chain M residue 95 ARG Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 132 MET Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 253 GLU Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain N residue 128 ASN Chi-restraints excluded: chain N residue 132 MET Chi-restraints excluded: chain N residue 253 GLU Chi-restraints excluded: chain N residue 348 SER Chi-restraints excluded: chain N residue 372 ARG Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 211 ASP Chi-restraints excluded: chain O residue 244 ASP Chi-restraints excluded: chain O residue 270 GLU Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 328 LYS Chi-restraints excluded: chain O residue 329 ILE Chi-restraints excluded: chain O residue 330 ILE Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 95 ARG Chi-restraints excluded: chain P residue 211 ASP Chi-restraints excluded: chain P residue 225 ASN Chi-restraints excluded: chain P residue 232 SER Chi-restraints excluded: chain P residue 253 GLU Chi-restraints excluded: chain P residue 257 CYS Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 49 GLN Chi-restraints excluded: chain Q residue 83 GLU Chi-restraints excluded: chain Q residue 232 SER Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 338 SER Chi-restraints excluded: chain R residue 360 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 185 optimal weight: 4.9990 chunk 239 optimal weight: 3.9990 chunk 244 optimal weight: 0.7980 chunk 236 optimal weight: 1.9990 chunk 308 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 227 optimal weight: 0.7980 chunk 305 optimal weight: 3.9990 chunk 283 optimal weight: 3.9990 chunk 281 optimal weight: 0.6980 chunk 158 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 297 ASN K 297 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.123562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.091746 restraints weight = 93764.449| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.64 r_work: 0.2910 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27009 Z= 0.225 Angle : 0.618 6.764 36657 Z= 0.302 Chirality : 0.044 0.152 4068 Planarity : 0.005 0.118 4689 Dihedral : 11.526 169.710 3788 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.22 % Allowed : 14.58 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.15), residues: 3303 helix: 0.36 (0.14), residues: 1314 sheet: 0.01 (0.22), residues: 567 loop : 0.53 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP O 356 HIS 0.004 0.001 HIS L 275 PHE 0.010 0.001 PHE O 31 TYR 0.010 0.001 TYR P 69 ARG 0.008 0.000 ARG J 372 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 319 time to evaluate : 3.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 44 MET cc_start: 0.2964 (mmm) cc_final: 0.2652 (mmm) REVERT: J 80 ASP cc_start: 0.7946 (m-30) cc_final: 0.7549 (m-30) REVERT: J 81 ASP cc_start: 0.7274 (m-30) cc_final: 0.6981 (m-30) REVERT: J 82 MET cc_start: 0.7728 (tpt) cc_final: 0.7287 (tpt) REVERT: J 83 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7500 (tp30) REVERT: J 176 MET cc_start: 0.8834 (mmt) cc_final: 0.8581 (mmt) REVERT: J 227 MET cc_start: 0.7354 (mmm) cc_final: 0.7137 (tpp) REVERT: J 326 LYS cc_start: 0.8518 (pttt) cc_final: 0.7612 (pttt) REVERT: J 336 LYS cc_start: 0.8107 (tptm) cc_final: 0.7719 (ttmt) REVERT: J 355 MET cc_start: 0.8121 (mtm) cc_final: 0.7827 (mtt) REVERT: K 269 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8296 (ptp) REVERT: K 328 LYS cc_start: 0.8002 (tttt) cc_final: 0.7625 (tttp) REVERT: L 57 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8132 (mm-30) REVERT: L 72 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7911 (mm-30) REVERT: L 83 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7225 (tm-30) REVERT: L 95 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7346 (ptp-170) REVERT: L 206 ARG cc_start: 0.7767 (ttm-80) cc_final: 0.7443 (ttp-170) REVERT: L 241 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7777 (mm-30) REVERT: M 61 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7446 (mttt) REVERT: M 72 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7311 (tm-30) REVERT: M 95 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7623 (ptp90) REVERT: M 118 LYS cc_start: 0.8188 (tptm) cc_final: 0.7267 (mtmt) REVERT: M 122 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7749 (mp) REVERT: M 326 LYS cc_start: 0.7689 (pptt) cc_final: 0.6414 (mmtm) REVERT: M 361 GLU cc_start: 0.8283 (tt0) cc_final: 0.8034 (tt0) REVERT: M 372 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.8083 (ptp90) REVERT: N 225 ASN cc_start: 0.8214 (t0) cc_final: 0.7887 (t0) REVERT: N 253 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8165 (pm20) REVERT: N 336 LYS cc_start: 0.8438 (tptm) cc_final: 0.7977 (tttt) REVERT: N 372 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8270 (ptp90) REVERT: O 17 VAL cc_start: 0.8411 (OUTLIER) cc_final: 0.8190 (p) REVERT: O 41 GLN cc_start: 0.7191 (tt0) cc_final: 0.6246 (tp40) REVERT: O 225 ASN cc_start: 0.8443 (t0) cc_final: 0.7765 (m110) REVERT: O 227 MET cc_start: 0.8642 (mmm) cc_final: 0.8395 (mmm) REVERT: O 244 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7776 (p0) REVERT: O 269 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8675 (ptm) REVERT: O 270 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.8032 (tt0) REVERT: O 283 MET cc_start: 0.8836 (mmt) cc_final: 0.8470 (mmm) REVERT: O 326 LYS cc_start: 0.8263 (pttt) cc_final: 0.7880 (pttp) REVERT: O 328 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8275 (ttmm) REVERT: O 348 SER cc_start: 0.8244 (t) cc_final: 0.7994 (m) REVERT: O 363 ASP cc_start: 0.7267 (p0) cc_final: 0.6947 (p0) REVERT: P 17 VAL cc_start: 0.8316 (OUTLIER) cc_final: 0.8008 (p) REVERT: P 57 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8194 (mm-30) REVERT: P 66 THR cc_start: 0.8908 (t) cc_final: 0.8554 (m) REVERT: P 180 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8745 (tt) REVERT: P 211 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8133 (t70) REVERT: P 225 ASN cc_start: 0.7977 (OUTLIER) cc_final: 0.7483 (m110) REVERT: P 227 MET cc_start: 0.8529 (mmm) cc_final: 0.8141 (mmm) REVERT: P 269 MET cc_start: 0.8709 (ptp) cc_final: 0.8465 (ptm) REVERT: P 313 MET cc_start: 0.8451 (ttp) cc_final: 0.8203 (mtp) REVERT: Q 72 GLU cc_start: 0.8019 (tp30) cc_final: 0.7526 (mt-10) REVERT: Q 95 ARG cc_start: 0.7934 (mtm-85) cc_final: 0.7710 (mtp-110) REVERT: Q 355 MET cc_start: 0.8668 (mtp) cc_final: 0.8423 (mpp) REVERT: Q 360 GLN cc_start: 0.8409 (tm-30) cc_final: 0.7653 (tm130) REVERT: R 83 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7456 (tm-30) REVERT: R 180 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8610 (tt) REVERT: R 191 LYS cc_start: 0.7756 (ttmt) cc_final: 0.7313 (tttt) REVERT: R 227 MET cc_start: 0.8168 (mmm) cc_final: 0.7945 (mmt) REVERT: R 269 MET cc_start: 0.8366 (ptp) cc_final: 0.7917 (ptp) REVERT: R 291 LYS cc_start: 0.4990 (mmtt) cc_final: 0.4471 (mptt) REVERT: R 325 MET cc_start: 0.6950 (ptm) cc_final: 0.6744 (ptm) outliers start: 91 outliers final: 36 residues processed: 379 average time/residue: 2.3916 time to fit residues: 1060.4069 Evaluate side-chains 362 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 302 time to evaluate : 3.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 83 GLU Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain J residue 299 MET Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 95 ARG Chi-restraints excluded: chain L residue 241 GLU Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain L residue 324 THR Chi-restraints excluded: chain L residue 350 SER Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 61 LYS Chi-restraints excluded: chain M residue 72 GLU Chi-restraints excluded: chain M residue 95 ARG Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 132 MET Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 253 GLU Chi-restraints excluded: chain M residue 372 ARG Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain N residue 232 SER Chi-restraints excluded: chain N residue 253 GLU Chi-restraints excluded: chain N residue 372 ARG Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 47 MET Chi-restraints excluded: chain O residue 211 ASP Chi-restraints excluded: chain O residue 244 ASP Chi-restraints excluded: chain O residue 269 MET Chi-restraints excluded: chain O residue 270 GLU Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 328 LYS Chi-restraints excluded: chain O residue 329 ILE Chi-restraints excluded: chain O residue 330 ILE Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 95 ARG Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 211 ASP Chi-restraints excluded: chain P residue 225 ASN Chi-restraints excluded: chain P residue 232 SER Chi-restraints excluded: chain P residue 253 GLU Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 49 GLN Chi-restraints excluded: chain Q residue 83 GLU Chi-restraints excluded: chain Q residue 269 MET Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 257 CYS Chi-restraints excluded: chain R residue 338 SER Chi-restraints excluded: chain R residue 360 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 199 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 275 optimal weight: 0.8980 chunk 208 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 263 GLN K 297 ASN N 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.120866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.089095 restraints weight = 94281.271| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.62 r_work: 0.2921 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 27009 Z= 0.278 Angle : 0.628 6.966 36657 Z= 0.308 Chirality : 0.045 0.160 4068 Planarity : 0.005 0.057 4689 Dihedral : 11.292 172.727 3781 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.47 % Allowed : 14.61 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.15), residues: 3303 helix: 0.65 (0.15), residues: 1260 sheet: 0.07 (0.22), residues: 567 loop : 0.51 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP N 340 HIS 0.004 0.001 HIS P 88 PHE 0.015 0.001 PHE O 31 TYR 0.012 0.001 TYR P 69 ARG 0.007 0.000 ARG J 372 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 311 time to evaluate : 3.157 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: J 44 MET cc_start: 0.2978 (mmm) cc_final: 0.2637 (mmm) REVERT: J 80 ASP cc_start: 0.7926 (m-30) cc_final: 0.7515 (m-30) REVERT: J 81 ASP cc_start: 0.7354 (m-30) cc_final: 0.6985 (m-30) REVERT: J 82 MET cc_start: 0.7735 (tpt) cc_final: 0.7311 (tpt) REVERT: J 83 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7479 (tp30) REVERT: J 176 MET cc_start: 0.8859 (mmt) cc_final: 0.8370 (mmt) REVERT: J 227 MET cc_start: 0.7165 (mmm) cc_final: 0.6963 (tpp) REVERT: J 283 MET cc_start: 0.8273 (mmm) cc_final: 0.7936 (mmm) REVERT: J 336 LYS cc_start: 0.8076 (tptm) cc_final: 0.7771 (ttmt) REVERT: J 355 MET cc_start: 0.8094 (mtm) cc_final: 0.7837 (mtm) REVERT: K 72 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7213 (mt-10) REVERT: K 269 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8186 (ptp) REVERT: K 328 LYS cc_start: 0.7780 (tttt) cc_final: 0.7427 (tttm) REVERT: L 72 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7899 (mm-30) REVERT: L 83 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7171 (tm-30) REVERT: L 95 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.7342 (ptp-170) REVERT: L 206 ARG cc_start: 0.7812 (ttm-80) cc_final: 0.7496 (ttp-170) REVERT: L 241 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8103 (tt0) REVERT: L 246 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7708 (mt0) REVERT: L 328 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8299 (ttpt) REVERT: M 61 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7439 (mttp) REVERT: M 72 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7295 (tm-30) REVERT: M 95 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7708 (ptp90) REVERT: M 118 LYS cc_start: 0.8036 (tptm) cc_final: 0.7055 (mtmt) REVERT: M 122 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7660 (mp) REVERT: M 283 MET cc_start: 0.8583 (mmp) cc_final: 0.8131 (mmm) REVERT: M 326 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.6582 (mmtm) REVERT: M 361 GLU cc_start: 0.8215 (tt0) cc_final: 0.7877 (tt0) REVERT: N 137 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8336 (mt0) REVERT: N 225 ASN cc_start: 0.8081 (t0) cc_final: 0.7410 (m110) REVERT: N 253 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8121 (pm20) REVERT: N 336 LYS cc_start: 0.8595 (tptm) cc_final: 0.8199 (tttt) REVERT: N 372 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8252 (ptp90) REVERT: O 17 VAL cc_start: 0.8317 (OUTLIER) cc_final: 0.8093 (p) REVERT: O 41 GLN cc_start: 0.7137 (tt0) cc_final: 0.6216 (tp40) REVERT: O 225 ASN cc_start: 0.8443 (t0) cc_final: 0.7778 (m110) REVERT: O 227 MET cc_start: 0.8600 (mmm) cc_final: 0.8344 (mmm) REVERT: O 244 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7940 (p0) REVERT: O 269 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8603 (ptm) REVERT: O 270 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7809 (tt0) REVERT: O 283 MET cc_start: 0.8802 (mmt) cc_final: 0.8460 (mmm) REVERT: O 326 LYS cc_start: 0.8267 (pttt) cc_final: 0.7860 (pttp) REVERT: O 328 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8259 (ttmm) REVERT: O 363 ASP cc_start: 0.7508 (p0) cc_final: 0.7217 (p0) REVERT: P 17 VAL cc_start: 0.8293 (OUTLIER) cc_final: 0.7982 (p) REVERT: P 57 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8285 (mm-30) REVERT: P 72 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7364 (mm-30) REVERT: P 211 ASP cc_start: 0.8646 (OUTLIER) cc_final: 0.8146 (t70) REVERT: P 225 ASN cc_start: 0.7969 (OUTLIER) cc_final: 0.7457 (m110) REVERT: P 227 MET cc_start: 0.8508 (mmm) cc_final: 0.8107 (mmm) REVERT: P 269 MET cc_start: 0.8682 (ptp) cc_final: 0.8416 (ptm) REVERT: P 313 MET cc_start: 0.8427 (ttp) cc_final: 0.8122 (tpp) REVERT: Q 72 GLU cc_start: 0.7998 (tp30) cc_final: 0.7505 (mt-10) REVERT: Q 122 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8018 (mt) REVERT: Q 149 THR cc_start: 0.8632 (t) cc_final: 0.8197 (m) REVERT: Q 355 MET cc_start: 0.8327 (mtp) cc_final: 0.8027 (mpp) REVERT: R 83 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7372 (tm-30) REVERT: R 191 LYS cc_start: 0.7768 (ttmt) cc_final: 0.7362 (ttmm) REVERT: R 227 MET cc_start: 0.8114 (mmm) cc_final: 0.7818 (mmt) REVERT: R 269 MET cc_start: 0.8304 (ptp) cc_final: 0.7856 (ptp) REVERT: R 291 LYS cc_start: 0.4917 (mmtt) cc_final: 0.4402 (mptt) REVERT: R 325 MET cc_start: 0.6838 (ptm) cc_final: 0.6472 (ptm) outliers start: 98 outliers final: 46 residues processed: 376 average time/residue: 2.4839 time to fit residues: 1090.4775 Evaluate side-chains 370 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 297 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 83 GLU Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain J residue 299 MET Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 128 ASN Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 95 ARG Chi-restraints excluded: chain L residue 199 SER Chi-restraints excluded: chain L residue 241 GLU Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain L residue 269 MET Chi-restraints excluded: chain L residue 324 THR Chi-restraints excluded: chain L residue 328 LYS Chi-restraints excluded: chain L residue 350 SER Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 61 LYS Chi-restraints excluded: chain M residue 72 GLU Chi-restraints excluded: chain M residue 95 ARG Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 132 MET Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 253 GLU Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 326 LYS Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 128 ASN Chi-restraints excluded: chain N residue 137 GLN Chi-restraints excluded: chain N residue 232 SER Chi-restraints excluded: chain N residue 238 LYS Chi-restraints excluded: chain N residue 253 GLU Chi-restraints excluded: chain N residue 372 ARG Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 47 MET Chi-restraints excluded: chain O residue 149 THR Chi-restraints excluded: chain O residue 211 ASP Chi-restraints excluded: chain O residue 244 ASP Chi-restraints excluded: chain O residue 269 MET Chi-restraints excluded: chain O residue 270 GLU Chi-restraints excluded: chain O residue 328 LYS Chi-restraints excluded: chain O residue 329 ILE Chi-restraints excluded: chain O residue 330 ILE Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 72 GLU Chi-restraints excluded: chain P residue 95 ARG Chi-restraints excluded: chain P residue 211 ASP Chi-restraints excluded: chain P residue 225 ASN Chi-restraints excluded: chain P residue 232 SER Chi-restraints excluded: chain P residue 253 GLU Chi-restraints excluded: chain P residue 257 CYS Chi-restraints excluded: chain P residue 344 SER Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 49 GLN Chi-restraints excluded: chain Q residue 52 SER Chi-restraints excluded: chain Q residue 83 GLU Chi-restraints excluded: chain Q residue 122 ILE Chi-restraints excluded: chain Q residue 269 MET Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 95 ARG Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 257 CYS Chi-restraints excluded: chain R residue 338 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 118 optimal weight: 2.9990 chunk 245 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 253 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 329 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 328 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 196 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 263 GLN N 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.120892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.089135 restraints weight = 94057.789| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.61 r_work: 0.2959 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 27009 Z= 0.380 Angle : 0.659 7.459 36657 Z= 0.327 Chirality : 0.046 0.163 4068 Planarity : 0.005 0.054 4689 Dihedral : 11.375 179.790 3779 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.61 % Allowed : 14.86 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.15), residues: 3303 helix: 0.56 (0.15), residues: 1260 sheet: 0.10 (0.22), residues: 567 loop : 0.39 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP N 340 HIS 0.005 0.001 HIS P 88 PHE 0.011 0.001 PHE L 31 TYR 0.014 0.001 TYR P 69 ARG 0.010 0.001 ARG J 372 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 306 time to evaluate : 3.282 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: J 44 MET cc_start: 0.2961 (mmm) cc_final: 0.2634 (mmm) REVERT: J 80 ASP cc_start: 0.7868 (m-30) cc_final: 0.7467 (m-30) REVERT: J 81 ASP cc_start: 0.7431 (m-30) cc_final: 0.7054 (m-30) REVERT: J 82 MET cc_start: 0.7831 (tpt) cc_final: 0.7414 (tpt) REVERT: J 83 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7512 (tp30) REVERT: J 176 MET cc_start: 0.8913 (mmt) cc_final: 0.8463 (mmt) REVERT: J 289 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8150 (pt) REVERT: J 336 LYS cc_start: 0.8294 (tptm) cc_final: 0.7973 (ttmt) REVERT: J 355 MET cc_start: 0.8158 (mtm) cc_final: 0.7815 (mtt) REVERT: K 72 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7249 (mt-10) REVERT: K 269 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8266 (ptp) REVERT: K 328 LYS cc_start: 0.7780 (tttt) cc_final: 0.7443 (tttm) REVERT: K 360 GLN cc_start: 0.8586 (tm-30) cc_final: 0.7950 (tp-100) REVERT: L 72 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7905 (mm-30) REVERT: L 83 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7240 (tm-30) REVERT: L 95 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.7416 (ptp-170) REVERT: L 119 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.7955 (ttp) REVERT: L 206 ARG cc_start: 0.7835 (ttm-80) cc_final: 0.7529 (ttp-170) REVERT: L 246 GLN cc_start: 0.8134 (mt0) cc_final: 0.7924 (mt0) REVERT: L 328 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8181 (ttpp) REVERT: M 61 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7524 (mttp) REVERT: M 95 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7382 (mtt-85) REVERT: M 122 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7807 (mp) REVERT: M 283 MET cc_start: 0.8630 (mmp) cc_final: 0.8221 (mmm) REVERT: M 326 LYS cc_start: 0.7862 (pptt) cc_final: 0.6741 (mmtm) REVERT: M 361 GLU cc_start: 0.8236 (tt0) cc_final: 0.7847 (tt0) REVERT: M 372 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7947 (ptp90) REVERT: N 225 ASN cc_start: 0.8119 (t0) cc_final: 0.7459 (m110) REVERT: N 253 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8313 (pm20) REVERT: N 336 LYS cc_start: 0.8618 (tptm) cc_final: 0.8264 (ttmt) REVERT: N 372 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8231 (ptp90) REVERT: O 33 SER cc_start: 0.8964 (OUTLIER) cc_final: 0.8365 (t) REVERT: O 41 GLN cc_start: 0.7116 (tt0) cc_final: 0.6266 (tp40) REVERT: O 225 ASN cc_start: 0.8501 (t0) cc_final: 0.7866 (m110) REVERT: O 227 MET cc_start: 0.8656 (mmm) cc_final: 0.8396 (mmm) REVERT: O 244 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7981 (p0) REVERT: O 270 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7840 (tt0) REVERT: O 283 MET cc_start: 0.8877 (mmt) cc_final: 0.8589 (mmm) REVERT: O 326 LYS cc_start: 0.8300 (pttt) cc_final: 0.7911 (pttp) REVERT: O 328 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8259 (ttmm) REVERT: O 355 MET cc_start: 0.8977 (mtt) cc_final: 0.8738 (mtt) REVERT: O 363 ASP cc_start: 0.7600 (p0) cc_final: 0.7289 (p0) REVERT: P 17 VAL cc_start: 0.8371 (OUTLIER) cc_final: 0.8048 (p) REVERT: P 57 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8256 (mm-30) REVERT: P 72 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7313 (mm-30) REVERT: P 211 ASP cc_start: 0.8737 (OUTLIER) cc_final: 0.8254 (t70) REVERT: P 225 ASN cc_start: 0.8098 (m-40) cc_final: 0.7578 (m110) REVERT: P 227 MET cc_start: 0.8598 (mmm) cc_final: 0.8312 (mmm) REVERT: P 269 MET cc_start: 0.8754 (ptp) cc_final: 0.8522 (ptm) REVERT: P 313 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8157 (mtp) REVERT: Q 72 GLU cc_start: 0.8008 (tp30) cc_final: 0.7550 (mt-10) REVERT: Q 122 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8152 (mt) REVERT: Q 149 THR cc_start: 0.8671 (t) cc_final: 0.8361 (m) REVERT: Q 355 MET cc_start: 0.8405 (mtp) cc_final: 0.8090 (mpp) REVERT: Q 360 GLN cc_start: 0.8517 (tm-30) cc_final: 0.7871 (tm-30) REVERT: R 83 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7460 (tm-30) REVERT: R 191 LYS cc_start: 0.7818 (ttmt) cc_final: 0.7417 (ttmm) REVERT: R 227 MET cc_start: 0.8180 (mmm) cc_final: 0.7790 (mmt) REVERT: R 269 MET cc_start: 0.8381 (ptp) cc_final: 0.8038 (ptp) REVERT: R 283 MET cc_start: 0.8061 (mmt) cc_final: 0.7702 (tpp) REVERT: R 286 ASP cc_start: 0.6814 (t70) cc_final: 0.6384 (m-30) REVERT: R 291 LYS cc_start: 0.4885 (mmtt) cc_final: 0.4345 (mptt) REVERT: R 325 MET cc_start: 0.7124 (ptm) cc_final: 0.6729 (ptm) outliers start: 102 outliers final: 50 residues processed: 375 average time/residue: 2.5065 time to fit residues: 1112.6807 Evaluate side-chains 370 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 296 time to evaluate : 3.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 83 GLU Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain J residue 289 ILE Chi-restraints excluded: chain J residue 299 MET Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 353 GLN Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 128 ASN Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 95 ARG Chi-restraints excluded: chain L residue 119 MET Chi-restraints excluded: chain L residue 199 SER Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain L residue 269 MET Chi-restraints excluded: chain L residue 324 THR Chi-restraints excluded: chain L residue 328 LYS Chi-restraints excluded: chain L residue 350 SER Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 61 LYS Chi-restraints excluded: chain M residue 72 GLU Chi-restraints excluded: chain M residue 95 ARG Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 132 MET Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 253 GLU Chi-restraints excluded: chain M residue 372 ARG Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 128 ASN Chi-restraints excluded: chain N residue 232 SER Chi-restraints excluded: chain N residue 253 GLU Chi-restraints excluded: chain N residue 348 SER Chi-restraints excluded: chain N residue 363 ASP Chi-restraints excluded: chain N residue 372 ARG Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 47 MET Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 149 THR Chi-restraints excluded: chain O residue 211 ASP Chi-restraints excluded: chain O residue 244 ASP Chi-restraints excluded: chain O residue 270 GLU Chi-restraints excluded: chain O residue 328 LYS Chi-restraints excluded: chain O residue 329 ILE Chi-restraints excluded: chain O residue 330 ILE Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 72 GLU Chi-restraints excluded: chain P residue 95 ARG Chi-restraints excluded: chain P residue 211 ASP Chi-restraints excluded: chain P residue 232 SER Chi-restraints excluded: chain P residue 253 GLU Chi-restraints excluded: chain P residue 257 CYS Chi-restraints excluded: chain P residue 313 MET Chi-restraints excluded: chain P residue 344 SER Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 52 SER Chi-restraints excluded: chain Q residue 83 GLU Chi-restraints excluded: chain Q residue 122 ILE Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 269 MET Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 257 CYS Chi-restraints excluded: chain R residue 338 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 298 optimal weight: 0.7980 chunk 323 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 277 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 276 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 263 GLN N 12 ASN P 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.122074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.090420 restraints weight = 93458.941| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.61 r_work: 0.2976 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 27009 Z= 0.278 Angle : 0.618 6.797 36657 Z= 0.303 Chirality : 0.045 0.150 4068 Planarity : 0.004 0.049 4689 Dihedral : 10.999 176.410 3776 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.18 % Allowed : 15.64 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.15), residues: 3303 helix: 0.72 (0.15), residues: 1260 sheet: 0.14 (0.22), residues: 567 loop : 0.41 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP N 340 HIS 0.005 0.001 HIS P 88 PHE 0.011 0.001 PHE L 31 TYR 0.011 0.001 TYR P 69 ARG 0.010 0.001 ARG J 372 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 305 time to evaluate : 3.167 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: J 44 MET cc_start: 0.2905 (mmm) cc_final: 0.2586 (mmm) REVERT: J 80 ASP cc_start: 0.7854 (m-30) cc_final: 0.7454 (m-30) REVERT: J 81 ASP cc_start: 0.7448 (m-30) cc_final: 0.7029 (m-30) REVERT: J 82 MET cc_start: 0.7852 (tpt) cc_final: 0.7456 (tpt) REVERT: J 83 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7516 (tp30) REVERT: J 176 MET cc_start: 0.8927 (mmt) cc_final: 0.8457 (mmt) REVERT: J 283 MET cc_start: 0.8208 (mmm) cc_final: 0.7803 (mmm) REVERT: J 336 LYS cc_start: 0.8242 (tptm) cc_final: 0.7976 (ttmt) REVERT: J 355 MET cc_start: 0.8119 (mtm) cc_final: 0.7819 (mtm) REVERT: K 72 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7228 (mt-10) REVERT: K 205 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.7050 (mt-10) REVERT: K 269 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8176 (ptp) REVERT: K 328 LYS cc_start: 0.7847 (tttt) cc_final: 0.7522 (tttp) REVERT: K 360 GLN cc_start: 0.8583 (tm-30) cc_final: 0.7954 (tp-100) REVERT: L 72 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7910 (mm-30) REVERT: L 83 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7306 (tm-30) REVERT: L 119 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8346 (mtp) REVERT: L 206 ARG cc_start: 0.7793 (ttm-80) cc_final: 0.7506 (ttp-170) REVERT: L 241 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8173 (tt0) REVERT: L 246 GLN cc_start: 0.8102 (mt0) cc_final: 0.7839 (mt0) REVERT: L 328 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8221 (ttpp) REVERT: M 61 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7533 (mttp) REVERT: M 95 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7515 (mtt-85) REVERT: M 283 MET cc_start: 0.8629 (mmp) cc_final: 0.8218 (mmm) REVERT: M 326 LYS cc_start: 0.7825 (pptt) cc_final: 0.6709 (mmtm) REVERT: M 361 GLU cc_start: 0.8204 (tt0) cc_final: 0.7828 (tt0) REVERT: M 372 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.8065 (ptp90) REVERT: N 137 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8549 (mt0) REVERT: N 225 ASN cc_start: 0.8070 (t0) cc_final: 0.7506 (m110) REVERT: N 253 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8185 (pm20) REVERT: N 336 LYS cc_start: 0.8594 (tptm) cc_final: 0.8326 (ttpt) REVERT: N 344 SER cc_start: 0.8560 (OUTLIER) cc_final: 0.8326 (p) REVERT: N 372 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8241 (ptp90) REVERT: O 33 SER cc_start: 0.8978 (OUTLIER) cc_final: 0.8395 (t) REVERT: O 41 GLN cc_start: 0.7121 (tt0) cc_final: 0.6284 (tp40) REVERT: O 225 ASN cc_start: 0.8490 (t0) cc_final: 0.7886 (m110) REVERT: O 227 MET cc_start: 0.8666 (mmm) cc_final: 0.8381 (mmm) REVERT: O 238 LYS cc_start: 0.8565 (mmmm) cc_final: 0.8194 (mmtp) REVERT: O 244 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7925 (p0) REVERT: O 270 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7811 (tt0) REVERT: O 283 MET cc_start: 0.8871 (mmt) cc_final: 0.8578 (mmm) REVERT: O 326 LYS cc_start: 0.8250 (pttt) cc_final: 0.7848 (pttp) REVERT: O 328 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8268 (ttmm) REVERT: O 355 MET cc_start: 0.9022 (mtt) cc_final: 0.8566 (mtm) REVERT: O 363 ASP cc_start: 0.7531 (p0) cc_final: 0.7218 (p0) REVERT: P 17 VAL cc_start: 0.8335 (OUTLIER) cc_final: 0.8009 (p) REVERT: P 47 MET cc_start: 0.6679 (mtp) cc_final: 0.5392 (ptt) REVERT: P 57 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8274 (mm-30) REVERT: P 211 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8174 (t70) REVERT: P 225 ASN cc_start: 0.8047 (m-40) cc_final: 0.7542 (m110) REVERT: P 227 MET cc_start: 0.8590 (mmm) cc_final: 0.8169 (mmm) REVERT: P 269 MET cc_start: 0.8728 (ptp) cc_final: 0.8493 (ptm) REVERT: P 360 GLN cc_start: 0.8103 (tm-30) cc_final: 0.6944 (mp10) REVERT: Q 72 GLU cc_start: 0.8012 (tp30) cc_final: 0.7546 (mt-10) REVERT: Q 149 THR cc_start: 0.8661 (t) cc_final: 0.8347 (m) REVERT: Q 355 MET cc_start: 0.8408 (mtp) cc_final: 0.8094 (mpp) REVERT: Q 360 GLN cc_start: 0.8469 (tm-30) cc_final: 0.7817 (tm-30) REVERT: R 83 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7434 (tm-30) REVERT: R 191 LYS cc_start: 0.7826 (ttmt) cc_final: 0.7376 (tttt) REVERT: R 269 MET cc_start: 0.8319 (ptp) cc_final: 0.7926 (ptp) REVERT: R 283 MET cc_start: 0.8160 (mmt) cc_final: 0.7809 (tpp) REVERT: R 286 ASP cc_start: 0.6812 (t70) cc_final: 0.6402 (m-30) REVERT: R 291 LYS cc_start: 0.4883 (mmtt) cc_final: 0.4316 (mptt) outliers start: 90 outliers final: 49 residues processed: 370 average time/residue: 2.3792 time to fit residues: 1031.2911 Evaluate side-chains 374 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 303 time to evaluate : 3.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 83 GLU Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain J residue 299 MET Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 353 GLN Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 128 ASN Chi-restraints excluded: chain K residue 205 GLU Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 119 MET Chi-restraints excluded: chain L residue 199 SER Chi-restraints excluded: chain L residue 241 GLU Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain L residue 324 THR Chi-restraints excluded: chain L residue 328 LYS Chi-restraints excluded: chain L residue 350 SER Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 61 LYS Chi-restraints excluded: chain M residue 72 GLU Chi-restraints excluded: chain M residue 95 ARG Chi-restraints excluded: chain M residue 132 MET Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 253 GLU Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 372 ARG Chi-restraints excluded: chain N residue 12 ASN Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 128 ASN Chi-restraints excluded: chain N residue 137 GLN Chi-restraints excluded: chain N residue 232 SER Chi-restraints excluded: chain N residue 253 GLU Chi-restraints excluded: chain N residue 344 SER Chi-restraints excluded: chain N residue 348 SER Chi-restraints excluded: chain N residue 363 ASP Chi-restraints excluded: chain N residue 372 ARG Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 47 MET Chi-restraints excluded: chain O residue 149 THR Chi-restraints excluded: chain O residue 211 ASP Chi-restraints excluded: chain O residue 244 ASP Chi-restraints excluded: chain O residue 270 GLU Chi-restraints excluded: chain O residue 328 LYS Chi-restraints excluded: chain O residue 329 ILE Chi-restraints excluded: chain O residue 330 ILE Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 95 ARG Chi-restraints excluded: chain P residue 211 ASP Chi-restraints excluded: chain P residue 232 SER Chi-restraints excluded: chain P residue 253 GLU Chi-restraints excluded: chain P residue 257 CYS Chi-restraints excluded: chain P residue 344 SER Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 52 SER Chi-restraints excluded: chain Q residue 83 GLU Chi-restraints excluded: chain Q residue 234 SER Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 95 ARG Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 257 CYS Chi-restraints excluded: chain R residue 338 SER Chi-restraints excluded: chain R residue 360 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 277 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 298 optimal weight: 0.9980 chunk 185 optimal weight: 4.9990 chunk 145 optimal weight: 0.1980 chunk 30 optimal weight: 10.0000 chunk 326 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 229 optimal weight: 0.5980 chunk 299 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 263 GLN J 297 ASN K 12 ASN N 12 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.121935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.090378 restraints weight = 94087.512| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.62 r_work: 0.2920 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 27009 Z= 0.179 Angle : 0.587 6.703 36657 Z= 0.285 Chirality : 0.043 0.146 4068 Planarity : 0.004 0.052 4689 Dihedral : 10.496 161.539 3776 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.65 % Allowed : 16.21 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.15), residues: 3303 helix: 0.98 (0.15), residues: 1260 sheet: 0.21 (0.22), residues: 567 loop : 0.47 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 340 HIS 0.004 0.001 HIS P 88 PHE 0.010 0.001 PHE O 31 TYR 0.008 0.001 TYR P 69 ARG 0.011 0.000 ARG J 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 316 time to evaluate : 3.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 44 MET cc_start: 0.2895 (mmm) cc_final: 0.2599 (mmm) REVERT: J 80 ASP cc_start: 0.7784 (m-30) cc_final: 0.7387 (m-30) REVERT: J 81 ASP cc_start: 0.7413 (m-30) cc_final: 0.7014 (m-30) REVERT: J 82 MET cc_start: 0.7688 (tpt) cc_final: 0.7305 (tpt) REVERT: J 176 MET cc_start: 0.8877 (mmt) cc_final: 0.8376 (mmt) REVERT: J 283 MET cc_start: 0.8194 (mmm) cc_final: 0.7781 (mmm) REVERT: J 286 ASP cc_start: 0.7370 (t0) cc_final: 0.6880 (m-30) REVERT: J 336 LYS cc_start: 0.8176 (tptm) cc_final: 0.7904 (ttmt) REVERT: J 355 MET cc_start: 0.8052 (mtm) cc_final: 0.7799 (mtm) REVERT: K 64 ILE cc_start: 0.8443 (pt) cc_final: 0.8232 (pp) REVERT: K 269 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8072 (ptp) REVERT: K 328 LYS cc_start: 0.7766 (tttt) cc_final: 0.7431 (tttm) REVERT: K 360 GLN cc_start: 0.8579 (tm-30) cc_final: 0.7925 (tp-100) REVERT: L 72 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: L 83 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7178 (tm-30) REVERT: L 119 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8245 (mtp) REVERT: L 206 ARG cc_start: 0.7528 (ttm-80) cc_final: 0.7202 (ttp-170) REVERT: L 246 GLN cc_start: 0.8003 (mt0) cc_final: 0.7696 (mt0) REVERT: L 328 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8302 (ttpt) REVERT: M 61 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7357 (mttp) REVERT: M 95 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7511 (mtt-85) REVERT: M 283 MET cc_start: 0.8544 (mmp) cc_final: 0.8088 (mmm) REVERT: M 326 LYS cc_start: 0.7728 (pptt) cc_final: 0.6575 (mmtm) REVERT: M 361 GLU cc_start: 0.8141 (tt0) cc_final: 0.7831 (tt0) REVERT: N 225 ASN cc_start: 0.7987 (t0) cc_final: 0.7440 (m110) REVERT: N 253 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8242 (pm20) REVERT: N 336 LYS cc_start: 0.8523 (tptm) cc_final: 0.8269 (ttpt) REVERT: N 372 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8210 (ptp90) REVERT: O 33 SER cc_start: 0.8907 (OUTLIER) cc_final: 0.8335 (t) REVERT: O 41 GLN cc_start: 0.7040 (tt0) cc_final: 0.6160 (tp40) REVERT: O 93 GLU cc_start: 0.7206 (pt0) cc_final: 0.6903 (pt0) REVERT: O 225 ASN cc_start: 0.8385 (t0) cc_final: 0.7813 (m110) REVERT: O 227 MET cc_start: 0.8554 (mmm) cc_final: 0.8285 (mmm) REVERT: O 238 LYS cc_start: 0.8492 (mmmm) cc_final: 0.8115 (mmtp) REVERT: O 244 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7884 (p0) REVERT: O 270 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8054 (tt0) REVERT: O 283 MET cc_start: 0.8775 (mmt) cc_final: 0.8464 (mmm) REVERT: O 326 LYS cc_start: 0.8211 (pttt) cc_final: 0.7754 (pttp) REVERT: O 328 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8217 (ttmm) REVERT: O 355 MET cc_start: 0.8964 (mtt) cc_final: 0.8536 (mtm) REVERT: O 360 GLN cc_start: 0.7109 (tt0) cc_final: 0.6482 (pm20) REVERT: O 363 ASP cc_start: 0.7365 (p0) cc_final: 0.6883 (p0) REVERT: P 17 VAL cc_start: 0.8199 (OUTLIER) cc_final: 0.7880 (p) REVERT: P 47 MET cc_start: 0.6691 (mtp) cc_final: 0.5427 (ptt) REVERT: P 57 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8256 (mm-30) REVERT: P 95 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7655 (mtt-85) REVERT: P 176 MET cc_start: 0.9053 (mmm) cc_final: 0.8715 (mmm) REVERT: P 211 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.8101 (t70) REVERT: P 225 ASN cc_start: 0.7950 (m-40) cc_final: 0.7448 (m110) REVERT: P 227 MET cc_start: 0.8466 (mmm) cc_final: 0.8067 (mmm) REVERT: P 269 MET cc_start: 0.8638 (ptp) cc_final: 0.8410 (ptm) REVERT: P 336 LYS cc_start: 0.8464 (tptm) cc_final: 0.7849 (ttpt) REVERT: P 360 GLN cc_start: 0.8081 (tm-30) cc_final: 0.6854 (mp10) REVERT: Q 72 GLU cc_start: 0.7934 (tp30) cc_final: 0.7425 (mt-10) REVERT: Q 83 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7323 (tm-30) REVERT: Q 149 THR cc_start: 0.8602 (t) cc_final: 0.8268 (m) REVERT: Q 355 MET cc_start: 0.8341 (mtp) cc_final: 0.8028 (mpp) REVERT: Q 360 GLN cc_start: 0.8312 (tm-30) cc_final: 0.7620 (tm-30) REVERT: R 34 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8634 (mm) REVERT: R 83 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7363 (tm-30) REVERT: R 191 LYS cc_start: 0.7730 (ttmt) cc_final: 0.7341 (ttmm) REVERT: R 269 MET cc_start: 0.8236 (ptp) cc_final: 0.7824 (ptp) REVERT: R 283 MET cc_start: 0.8053 (mmt) cc_final: 0.7722 (tpp) REVERT: R 286 ASP cc_start: 0.6642 (t70) cc_final: 0.6251 (m-30) REVERT: R 291 LYS cc_start: 0.4788 (mmtt) cc_final: 0.4301 (mptt) REVERT: R 325 MET cc_start: 0.6825 (ptm) cc_final: 0.6563 (ptm) outliers start: 75 outliers final: 39 residues processed: 368 average time/residue: 2.4765 time to fit residues: 1070.4627 Evaluate side-chains 363 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 306 time to evaluate : 3.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain J residue 299 MET Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 353 GLN Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 119 MET Chi-restraints excluded: chain L residue 199 SER Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain L residue 324 THR Chi-restraints excluded: chain L residue 328 LYS Chi-restraints excluded: chain L residue 350 SER Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 61 LYS Chi-restraints excluded: chain M residue 95 ARG Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 253 GLU Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain N residue 12 ASN Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 137 GLN Chi-restraints excluded: chain N residue 253 GLU Chi-restraints excluded: chain N residue 372 ARG Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 47 MET Chi-restraints excluded: chain O residue 149 THR Chi-restraints excluded: chain O residue 211 ASP Chi-restraints excluded: chain O residue 244 ASP Chi-restraints excluded: chain O residue 270 GLU Chi-restraints excluded: chain O residue 328 LYS Chi-restraints excluded: chain O residue 330 ILE Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 95 ARG Chi-restraints excluded: chain P residue 211 ASP Chi-restraints excluded: chain P residue 232 SER Chi-restraints excluded: chain P residue 253 GLU Chi-restraints excluded: chain P residue 257 CYS Chi-restraints excluded: chain P residue 344 SER Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 52 SER Chi-restraints excluded: chain Q residue 83 GLU Chi-restraints excluded: chain Q residue 234 SER Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 95 ARG Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 257 CYS Chi-restraints excluded: chain R residue 338 SER Chi-restraints excluded: chain R residue 360 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 323 optimal weight: 7.9990 chunk 321 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 chunk 77 optimal weight: 0.1980 chunk 100 optimal weight: 0.7980 chunk 271 optimal weight: 0.9990 chunk 264 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 chunk 178 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 297 ASN K 137 GLN K 297 ASN L 225 ASN N 12 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.122840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.091310 restraints weight = 93711.368| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.62 r_work: 0.2958 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 27009 Z= 0.160 Angle : 0.577 6.630 36657 Z= 0.277 Chirality : 0.043 0.159 4068 Planarity : 0.004 0.055 4689 Dihedral : 10.041 159.309 3773 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.09 % Allowed : 17.16 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.15), residues: 3303 helix: 1.17 (0.15), residues: 1260 sheet: 0.25 (0.22), residues: 567 loop : 0.55 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 340 HIS 0.004 0.001 HIS N 161 PHE 0.010 0.001 PHE O 31 TYR 0.008 0.001 TYR N 294 ARG 0.013 0.000 ARG J 372 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 325 time to evaluate : 3.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 80 ASP cc_start: 0.7782 (m-30) cc_final: 0.7384 (m-30) REVERT: J 81 ASP cc_start: 0.7450 (m-30) cc_final: 0.7014 (m-30) REVERT: J 82 MET cc_start: 0.7734 (tpt) cc_final: 0.7253 (tpt) REVERT: J 176 MET cc_start: 0.8895 (mmt) cc_final: 0.8402 (mmt) REVERT: J 283 MET cc_start: 0.8226 (mmm) cc_final: 0.7814 (mmm) REVERT: J 286 ASP cc_start: 0.7328 (t0) cc_final: 0.6873 (m-30) REVERT: J 324 THR cc_start: 0.8608 (OUTLIER) cc_final: 0.8230 (t) REVERT: J 336 LYS cc_start: 0.8187 (tptm) cc_final: 0.7927 (ttmt) REVERT: J 355 MET cc_start: 0.8089 (mtm) cc_final: 0.7844 (mtm) REVERT: K 269 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8056 (ptp) REVERT: K 328 LYS cc_start: 0.7776 (tttt) cc_final: 0.7440 (tttp) REVERT: K 360 GLN cc_start: 0.8537 (tm-30) cc_final: 0.7876 (tp-100) REVERT: L 72 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: L 83 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7207 (tm-30) REVERT: L 119 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8284 (mtp) REVERT: L 206 ARG cc_start: 0.7594 (ttm-80) cc_final: 0.7242 (ttp-170) REVERT: L 246 GLN cc_start: 0.8050 (mt0) cc_final: 0.7682 (mt0) REVERT: L 328 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8316 (ttpt) REVERT: L 348 SER cc_start: 0.8301 (t) cc_final: 0.7995 (p) REVERT: M 61 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7402 (mttp) REVERT: M 95 ARG cc_start: 0.8050 (ptp90) cc_final: 0.7585 (mtt-85) REVERT: M 118 LYS cc_start: 0.7979 (tptm) cc_final: 0.7155 (mtmt) REVERT: M 283 MET cc_start: 0.8576 (mmp) cc_final: 0.8158 (mmm) REVERT: M 326 LYS cc_start: 0.7810 (pptt) cc_final: 0.6612 (mmtm) REVERT: M 361 GLU cc_start: 0.8156 (tt0) cc_final: 0.7849 (tt0) REVERT: M 363 ASP cc_start: 0.7616 (p0) cc_final: 0.7372 (p0) REVERT: N 225 ASN cc_start: 0.8017 (t0) cc_final: 0.7516 (m110) REVERT: N 253 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8103 (pm20) REVERT: N 336 LYS cc_start: 0.8514 (tptm) cc_final: 0.8294 (ttpt) REVERT: N 372 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8244 (ptp90) REVERT: O 41 GLN cc_start: 0.7091 (tt0) cc_final: 0.6227 (tp40) REVERT: O 93 GLU cc_start: 0.7187 (pt0) cc_final: 0.6892 (pt0) REVERT: O 225 ASN cc_start: 0.8240 (t0) cc_final: 0.7697 (m110) REVERT: O 227 MET cc_start: 0.8573 (mmm) cc_final: 0.8312 (mmm) REVERT: O 238 LYS cc_start: 0.8518 (mmmm) cc_final: 0.8146 (mmtp) REVERT: O 244 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7814 (p0) REVERT: O 270 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8004 (tt0) REVERT: O 283 MET cc_start: 0.8781 (mmt) cc_final: 0.8472 (mmm) REVERT: O 326 LYS cc_start: 0.8187 (pttt) cc_final: 0.7755 (pttp) REVERT: O 328 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8252 (ttmm) REVERT: O 355 MET cc_start: 0.8916 (mtt) cc_final: 0.8541 (mtm) REVERT: O 360 GLN cc_start: 0.7087 (tt0) cc_final: 0.6490 (pm20) REVERT: O 363 ASP cc_start: 0.7342 (p0) cc_final: 0.6837 (p0) REVERT: P 17 VAL cc_start: 0.8214 (OUTLIER) cc_final: 0.7891 (p) REVERT: P 47 MET cc_start: 0.6681 (mtp) cc_final: 0.5483 (ptt) REVERT: P 95 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7749 (mtt-85) REVERT: P 176 MET cc_start: 0.9073 (mmm) cc_final: 0.8732 (mmm) REVERT: P 211 ASP cc_start: 0.8630 (OUTLIER) cc_final: 0.8147 (t70) REVERT: P 225 ASN cc_start: 0.7983 (m-40) cc_final: 0.7467 (m-40) REVERT: P 227 MET cc_start: 0.8491 (mmm) cc_final: 0.8099 (mmm) REVERT: P 336 LYS cc_start: 0.8463 (tptm) cc_final: 0.7864 (ttpt) REVERT: P 360 GLN cc_start: 0.8105 (tm-30) cc_final: 0.6918 (mp10) REVERT: Q 72 GLU cc_start: 0.7982 (tp30) cc_final: 0.7514 (mt-10) REVERT: Q 83 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7352 (tm-30) REVERT: Q 95 ARG cc_start: 0.7809 (mtp-110) cc_final: 0.7586 (mtm110) REVERT: Q 149 THR cc_start: 0.8620 (t) cc_final: 0.8293 (m) REVERT: Q 355 MET cc_start: 0.8374 (mtp) cc_final: 0.8007 (mpp) REVERT: Q 360 GLN cc_start: 0.8313 (tm-30) cc_final: 0.7618 (tm-30) REVERT: R 34 ILE cc_start: 0.9004 (mt) cc_final: 0.8705 (mm) REVERT: R 83 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7379 (tm-30) REVERT: R 191 LYS cc_start: 0.7767 (ttmt) cc_final: 0.7385 (ttmm) REVERT: R 269 MET cc_start: 0.8197 (ptp) cc_final: 0.7828 (ptp) REVERT: R 283 MET cc_start: 0.8043 (mmt) cc_final: 0.7653 (tpp) REVERT: R 286 ASP cc_start: 0.6626 (t70) cc_final: 0.6238 (m-30) REVERT: R 291 LYS cc_start: 0.4823 (mmtt) cc_final: 0.4318 (mptt) REVERT: R 325 MET cc_start: 0.6807 (ptm) cc_final: 0.6560 (ptm) outliers start: 59 outliers final: 31 residues processed: 367 average time/residue: 2.5171 time to fit residues: 1084.2530 Evaluate side-chains 357 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 311 time to evaluate : 3.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 101 HIS Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain J residue 299 MET Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 353 GLN Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 119 MET Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain L residue 324 THR Chi-restraints excluded: chain L residue 328 LYS Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 61 LYS Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 253 GLU Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 137 GLN Chi-restraints excluded: chain N residue 253 GLU Chi-restraints excluded: chain N residue 372 ARG Chi-restraints excluded: chain O residue 47 MET Chi-restraints excluded: chain O residue 149 THR Chi-restraints excluded: chain O residue 211 ASP Chi-restraints excluded: chain O residue 244 ASP Chi-restraints excluded: chain O residue 270 GLU Chi-restraints excluded: chain O residue 328 LYS Chi-restraints excluded: chain O residue 330 ILE Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 95 ARG Chi-restraints excluded: chain P residue 211 ASP Chi-restraints excluded: chain P residue 232 SER Chi-restraints excluded: chain P residue 253 GLU Chi-restraints excluded: chain P residue 257 CYS Chi-restraints excluded: chain P residue 344 SER Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 52 SER Chi-restraints excluded: chain Q residue 83 GLU Chi-restraints excluded: chain Q residue 234 SER Chi-restraints excluded: chain R residue 95 ARG Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 257 CYS Chi-restraints excluded: chain R residue 338 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 77 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 274 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 321 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 263 GLN Q 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.119287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.087482 restraints weight = 94461.318| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.61 r_work: 0.2965 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 27009 Z= 0.390 Angle : 0.651 7.253 36657 Z= 0.321 Chirality : 0.046 0.160 4068 Planarity : 0.005 0.061 4689 Dihedral : 10.306 157.891 3773 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.98 % Allowed : 17.34 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.15), residues: 3303 helix: 0.85 (0.15), residues: 1260 sheet: 0.22 (0.22), residues: 567 loop : 0.42 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP N 340 HIS 0.005 0.001 HIS K 161 PHE 0.011 0.001 PHE P 262 TYR 0.016 0.001 TYR P 69 ARG 0.012 0.001 ARG J 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 307 time to evaluate : 3.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 80 ASP cc_start: 0.7810 (m-30) cc_final: 0.7405 (m-30) REVERT: J 81 ASP cc_start: 0.7501 (m-30) cc_final: 0.7071 (m-30) REVERT: J 82 MET cc_start: 0.7798 (tpt) cc_final: 0.7397 (tpt) REVERT: J 176 MET cc_start: 0.8945 (mmt) cc_final: 0.8673 (mmt) REVERT: J 336 LYS cc_start: 0.8211 (tptm) cc_final: 0.7952 (ttmt) REVERT: K 269 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.8237 (ptp) REVERT: K 328 LYS cc_start: 0.7923 (tttt) cc_final: 0.7585 (tttm) REVERT: K 360 GLN cc_start: 0.8566 (tm-30) cc_final: 0.7958 (tp-100) REVERT: L 72 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7820 (mm-30) REVERT: L 83 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7336 (tm-30) REVERT: L 119 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8388 (mtp) REVERT: L 206 ARG cc_start: 0.7869 (ttm-80) cc_final: 0.7561 (ttp-170) REVERT: L 246 GLN cc_start: 0.8149 (mt0) cc_final: 0.7835 (mt0) REVERT: L 328 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8253 (ttpp) REVERT: L 348 SER cc_start: 0.8385 (t) cc_final: 0.8131 (p) REVERT: M 61 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7611 (mttp) REVERT: M 68 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8186 (mptp) REVERT: M 95 ARG cc_start: 0.8126 (ptp90) cc_final: 0.7643 (mtt-85) REVERT: M 283 MET cc_start: 0.8685 (mmp) cc_final: 0.8323 (mmm) REVERT: M 326 LYS cc_start: 0.7885 (pptt) cc_final: 0.6780 (mmtm) REVERT: M 361 GLU cc_start: 0.8280 (tt0) cc_final: 0.7835 (tt0) REVERT: N 225 ASN cc_start: 0.8103 (t0) cc_final: 0.7624 (m110) REVERT: N 253 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8487 (pm20) REVERT: N 328 LYS cc_start: 0.8222 (ttmt) cc_final: 0.7783 (tttt) REVERT: N 372 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8198 (ptp90) REVERT: O 33 SER cc_start: 0.8984 (OUTLIER) cc_final: 0.8398 (t) REVERT: O 41 GLN cc_start: 0.7125 (tt0) cc_final: 0.6318 (tp40) REVERT: O 93 GLU cc_start: 0.7354 (pt0) cc_final: 0.7020 (pt0) REVERT: O 225 ASN cc_start: 0.8515 (t0) cc_final: 0.7938 (m110) REVERT: O 227 MET cc_start: 0.8673 (mmm) cc_final: 0.8401 (mmm) REVERT: O 238 LYS cc_start: 0.8640 (mmmm) cc_final: 0.8299 (mmtp) REVERT: O 244 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7935 (p0) REVERT: O 270 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7888 (tt0) REVERT: O 283 MET cc_start: 0.8886 (mmt) cc_final: 0.8596 (mmm) REVERT: O 326 LYS cc_start: 0.8255 (pttt) cc_final: 0.7853 (pttp) REVERT: O 328 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8297 (ttmm) REVERT: O 355 MET cc_start: 0.9023 (mtt) cc_final: 0.8552 (mtm) REVERT: O 363 ASP cc_start: 0.7605 (p0) cc_final: 0.7264 (p0) REVERT: P 17 VAL cc_start: 0.8367 (OUTLIER) cc_final: 0.8040 (p) REVERT: P 47 MET cc_start: 0.6716 (mtp) cc_final: 0.5510 (ptt) REVERT: P 157 ASP cc_start: 0.8618 (t0) cc_final: 0.8208 (t0) REVERT: P 211 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.8284 (t70) REVERT: P 225 ASN cc_start: 0.8145 (m-40) cc_final: 0.7611 (m110) REVERT: P 227 MET cc_start: 0.8624 (mmm) cc_final: 0.8329 (mmm) REVERT: P 336 LYS cc_start: 0.8579 (tptm) cc_final: 0.8013 (ttpt) REVERT: P 360 GLN cc_start: 0.8136 (tm-30) cc_final: 0.6979 (mp10) REVERT: Q 72 GLU cc_start: 0.8042 (tp30) cc_final: 0.7643 (mt-10) REVERT: Q 95 ARG cc_start: 0.7860 (mtp-110) cc_final: 0.7630 (mtm110) REVERT: Q 149 THR cc_start: 0.8681 (t) cc_final: 0.8387 (m) REVERT: Q 355 MET cc_start: 0.8430 (mtp) cc_final: 0.8102 (mpp) REVERT: Q 360 GLN cc_start: 0.8465 (tm-30) cc_final: 0.7809 (tm-30) REVERT: R 34 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8774 (mm) REVERT: R 83 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7487 (tm-30) REVERT: R 191 LYS cc_start: 0.7863 (ttmt) cc_final: 0.7495 (ttmm) REVERT: R 269 MET cc_start: 0.8352 (ptp) cc_final: 0.8040 (ptp) REVERT: R 283 MET cc_start: 0.8159 (mmt) cc_final: 0.7724 (tpp) REVERT: R 286 ASP cc_start: 0.6825 (t70) cc_final: 0.6437 (m-30) REVERT: R 291 LYS cc_start: 0.4975 (mmtt) cc_final: 0.4445 (mptt) REVERT: R 325 MET cc_start: 0.6920 (ptm) cc_final: 0.6667 (ptm) outliers start: 56 outliers final: 35 residues processed: 347 average time/residue: 2.5165 time to fit residues: 1015.6764 Evaluate side-chains 353 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 303 time to evaluate : 3.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain J residue 299 MET Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 353 GLN Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 119 MET Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain L residue 324 THR Chi-restraints excluded: chain L residue 328 LYS Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 61 LYS Chi-restraints excluded: chain M residue 68 LYS Chi-restraints excluded: chain M residue 72 GLU Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 253 GLU Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 253 GLU Chi-restraints excluded: chain N residue 372 ARG Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 47 MET Chi-restraints excluded: chain O residue 149 THR Chi-restraints excluded: chain O residue 211 ASP Chi-restraints excluded: chain O residue 244 ASP Chi-restraints excluded: chain O residue 253 GLU Chi-restraints excluded: chain O residue 270 GLU Chi-restraints excluded: chain O residue 328 LYS Chi-restraints excluded: chain O residue 330 ILE Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 95 ARG Chi-restraints excluded: chain P residue 211 ASP Chi-restraints excluded: chain P residue 232 SER Chi-restraints excluded: chain P residue 253 GLU Chi-restraints excluded: chain P residue 257 CYS Chi-restraints excluded: chain P residue 344 SER Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 52 SER Chi-restraints excluded: chain Q residue 83 GLU Chi-restraints excluded: chain Q residue 234 SER Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 95 ARG Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 257 CYS Chi-restraints excluded: chain R residue 338 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 270 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 247 optimal weight: 1.9990 chunk 278 optimal weight: 0.9990 chunk 172 optimal weight: 0.8980 chunk 151 optimal weight: 0.5980 chunk 194 optimal weight: 0.8980 chunk 263 optimal weight: 4.9990 chunk 231 optimal weight: 0.5980 chunk 158 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 297 ASN P 354 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.122337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.090735 restraints weight = 93921.726| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.62 r_work: 0.3018 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27009 Z= 0.164 Angle : 0.579 6.460 36657 Z= 0.278 Chirality : 0.043 0.146 4068 Planarity : 0.004 0.060 4689 Dihedral : 9.926 163.810 3773 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.80 % Allowed : 17.69 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.15), residues: 3303 helix: 1.17 (0.15), residues: 1260 sheet: 0.29 (0.22), residues: 567 loop : 0.54 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 356 HIS 0.003 0.001 HIS P 88 PHE 0.011 0.001 PHE O 31 TYR 0.011 0.001 TYR J 53 ARG 0.013 0.000 ARG J 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28636.05 seconds wall clock time: 487 minutes 43.13 seconds (29263.13 seconds total)