Starting phenix.real_space_refine on Tue Sep 24 19:46:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uz0_42829/09_2024/8uz0_42829_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uz0_42829/09_2024/8uz0_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uz0_42829/09_2024/8uz0_42829.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uz0_42829/09_2024/8uz0_42829.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uz0_42829/09_2024/8uz0_42829_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uz0_42829/09_2024/8uz0_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-5461/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: 19.66, per 1000 atoms: 0.38 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: 10.08 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: 4.20 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: 20.32 Time building geometry restraints manager: 12.37 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: 0.00 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.700 Extract box with map and model: 1.460 Check model and map are aligned: 0.310 Set scattering table: 0.380 Process input model: 88.430 Find NCS groups from input model: 1.360 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:10.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.450 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 88 poor density : 528 time to evaluate : 3.146 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: 2.5472 time to fit residues: 1736.6178 Evaluate side-chains 340 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 309 time to evaluate : 3.157 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2879 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= 0.205 Angle : 0.693 7.379 36657 Z= 0.348 Chirality : 0.045 0.164 4068 Planarity : 0.005 0.063 4689 Dihedral : 12.612 151.061 3818 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.11 % Allowed : 12.17 % Favored : 84.71 % 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 : 0.58 (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 0.015 0.002 PHE J 90 TYR 0.014 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 fitting. rotamer outliers: 88 poor density : 357 time to evaluate : 3.480 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 82 MET cc_start: 0.7993 (tpt) cc_final: 0.7675 (tpt) REVERT: J 227 MET cc_start: 0.8413 (mmm) cc_final: 0.7780 (tpp) REVERT: J 283 MET cc_start: 0.8998 (mmm) cc_final: 0.8783 (mmm) REVERT: J 326 LYS cc_start: 0.8112 (pttt) cc_final: 0.7716 (pttt) REVERT: J 330 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.7982 (mt) REVERT: J 355 MET cc_start: 0.8318 (mtm) cc_final: 0.8060 (mtp) REVERT: K 176 MET cc_start: 0.8694 (mmp) cc_final: 0.8477 (mmt) REVERT: K 190 MET cc_start: 0.8822 (mtm) cc_final: 0.8558 (mtm) REVERT: K 227 MET cc_start: 0.8817 (mmm) cc_final: 0.8573 (mmm) REVERT: K 269 MET cc_start: 0.8858 (ptp) cc_final: 0.8617 (ptp) REVERT: L 17 VAL cc_start: 0.8645 (OUTLIER) cc_final: 0.8360 (p) REVERT: L 82 MET cc_start: 0.8762 (tpt) cc_final: 0.8525 (tpp) REVERT: M 61 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8157 (mttt) REVERT: M 72 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7679 (tm-30) REVERT: M 118 LYS cc_start: 0.8725 (tptm) cc_final: 0.8418 (mtmt) REVERT: M 226 GLU cc_start: 0.8685 (tp30) cc_final: 0.8341 (tp30) REVERT: M 361 GLU cc_start: 0.8268 (tt0) cc_final: 0.8009 (tt0) REVERT: N 225 ASN cc_start: 0.8309 (t0) cc_final: 0.7937 (t0) REVERT: N 328 LYS cc_start: 0.8558 (ttpm) cc_final: 0.8215 (tttt) REVERT: N 336 LYS cc_start: 0.7975 (tptm) cc_final: 0.7745 (ttpt) REVERT: N 363 ASP cc_start: 0.7995 (p0) cc_final: 0.7659 (p0) REVERT: O 17 VAL cc_start: 0.8355 (OUTLIER) cc_final: 0.8113 (p) REVERT: O 82 MET cc_start: 0.9248 (tpt) cc_final: 0.8951 (tpt) REVERT: O 137 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8371 (mt0) REVERT: O 227 MET cc_start: 0.8702 (mmm) cc_final: 0.8393 (mmm) REVERT: O 283 MET cc_start: 0.8945 (mmt) cc_final: 0.8608 (mmm) REVERT: O 326 LYS cc_start: 0.8075 (pttt) cc_final: 0.7857 (pttp) REVERT: O 355 MET cc_start: 0.9076 (mtt) cc_final: 0.8736 (mtt) REVERT: O 363 ASP cc_start: 0.7919 (p0) cc_final: 0.7491 (p0) REVERT: P 17 VAL cc_start: 0.8503 (OUTLIER) cc_final: 0.8175 (p) REVERT: P 44 MET cc_start: 0.8617 (mmm) cc_final: 0.8378 (mmt) REVERT: P 57 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8112 (mm-30) REVERT: P 180 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8932 (tp) REVERT: P 225 ASN cc_start: 0.8060 (OUTLIER) cc_final: 0.7667 (m110) REVERT: P 227 MET cc_start: 0.8659 (mmm) cc_final: 0.8300 (mmm) REVERT: P 269 MET cc_start: 0.9000 (ptp) cc_final: 0.8793 (ptm) REVERT: P 313 MET cc_start: 0.8572 (ttp) cc_final: 0.8358 (mtp) REVERT: P 329 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8876 (mp) REVERT: P 354 GLN cc_start: 0.8226 (mm110) cc_final: 0.7997 (mt0) REVERT: P 360 GLN cc_start: 0.8483 (tp40) cc_final: 0.8171 (tp-100) REVERT: Q 137 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8317 (mt0) REVERT: Q 241 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8247 (tt0) REVERT: Q 360 GLN cc_start: 0.8554 (tm-30) cc_final: 0.8208 (tm130) REVERT: R 72 GLU cc_start: 0.8303 (mm-30) cc_final: 0.8080 (mp0) REVERT: R 180 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8950 (tt) REVERT: R 227 MET cc_start: 0.8813 (mmm) cc_final: 0.8193 (mmt) REVERT: R 291 LYS cc_start: 0.6714 (mmtt) cc_final: 0.5754 (mptt) outliers start: 88 outliers final: 27 residues processed: 416 average time/residue: 2.3883 time to fit residues: 1163.1049 Evaluate side-chains 344 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 303 time to evaluate : 3.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 330 ILE 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 199 SER 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 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 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 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 236 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 168 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 251 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 302 optimal weight: 3.9990 chunk 327 optimal weight: 5.9990 chunk 269 optimal weight: 0.0770 chunk 300 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 243 optimal weight: 2.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 225 ASN L 121 GLN L 225 ASN O 41 GLN O 225 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 27009 Z= 0.331 Angle : 0.680 7.570 36657 Z= 0.341 Chirality : 0.046 0.166 4068 Planarity : 0.005 0.050 4689 Dihedral : 11.833 155.598 3786 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.36 % Allowed : 13.73 % Favored : 82.91 % 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: 0.08 (0.15), residues: 3303 helix: -0.05 (0.14), residues: 1314 sheet: -0.13 (0.23), residues: 522 loop : 0.48 (0.17), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP O 356 HIS 0.004 0.001 HIS J 101 PHE 0.013 0.002 PHE J 90 TYR 0.015 0.001 TYR P 69 ARG 0.006 0.001 ARG O 256 *********************** 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 415 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 320 time to evaluate : 3.158 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 82 MET cc_start: 0.8024 (tpt) cc_final: 0.7737 (tpt) REVERT: J 227 MET cc_start: 0.8407 (mmm) cc_final: 0.7895 (tpp) REVERT: J 326 LYS cc_start: 0.8225 (pttt) cc_final: 0.7813 (pttt) REVERT: J 330 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8015 (mt) REVERT: J 355 MET cc_start: 0.8320 (mtm) cc_final: 0.8097 (mtt) REVERT: K 190 MET cc_start: 0.8835 (mtm) cc_final: 0.8609 (mtm) REVERT: K 227 MET cc_start: 0.8750 (mmm) cc_final: 0.8520 (mmm) REVERT: L 17 VAL cc_start: 0.8665 (OUTLIER) cc_final: 0.8409 (p) REVERT: L 57 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8107 (mm-30) REVERT: L 119 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8416 (ttp) REVERT: L 241 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8143 (mm-30) REVERT: M 61 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8297 (mttp) REVERT: M 72 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7749 (tm-30) REVERT: M 95 ARG cc_start: 0.8231 (ptp90) cc_final: 0.7718 (mtt-85) REVERT: M 118 LYS cc_start: 0.8772 (tptm) cc_final: 0.8391 (mtmt) REVERT: M 326 LYS cc_start: 0.7982 (pptt) cc_final: 0.6904 (mmtm) REVERT: M 361 GLU cc_start: 0.8474 (tt0) cc_final: 0.8229 (tt0) REVERT: N 225 ASN cc_start: 0.8301 (t0) cc_final: 0.7966 (t0) REVERT: N 253 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8374 (pm20) REVERT: N 336 LYS cc_start: 0.8418 (tptm) cc_final: 0.8077 (ttpt) REVERT: N 372 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8269 (ptp90) REVERT: O 17 VAL cc_start: 0.8411 (OUTLIER) cc_final: 0.8209 (p) REVERT: O 227 MET cc_start: 0.8761 (mmm) cc_final: 0.8415 (mmm) REVERT: O 234 SER cc_start: 0.8199 (m) cc_final: 0.7485 (t) REVERT: O 244 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7726 (p0) REVERT: O 283 MET cc_start: 0.9056 (mmt) cc_final: 0.8773 (mmm) REVERT: O 326 LYS cc_start: 0.8182 (pttt) cc_final: 0.7967 (pttp) REVERT: O 355 MET cc_start: 0.9109 (mtt) cc_final: 0.8706 (mtt) REVERT: O 363 ASP cc_start: 0.7807 (p0) cc_final: 0.7501 (p0) REVERT: P 17 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.8229 (p) REVERT: P 57 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8080 (mm-30) REVERT: P 123 MET cc_start: 0.8818 (mmp) cc_final: 0.8561 (mmp) REVERT: P 211 ASP cc_start: 0.8802 (OUTLIER) cc_final: 0.8561 (t70) REVERT: P 225 ASN cc_start: 0.8145 (OUTLIER) cc_final: 0.7762 (m110) REVERT: P 227 MET cc_start: 0.8682 (mmm) cc_final: 0.8296 (mmm) REVERT: P 269 MET cc_start: 0.8927 (ptp) cc_final: 0.8680 (ptm) REVERT: P 313 MET cc_start: 0.8644 (ttp) cc_final: 0.8366 (mtp) REVERT: P 360 GLN cc_start: 0.8422 (tp40) cc_final: 0.8192 (tp-100) REVERT: Q 59 GLN cc_start: 0.8665 (tp-100) cc_final: 0.8357 (mm-40) REVERT: Q 241 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8545 (tt0) REVERT: Q 360 GLN cc_start: 0.8531 (tm-30) cc_final: 0.8195 (tm130) REVERT: R 180 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9059 (tt) REVERT: R 227 MET cc_start: 0.8798 (mmm) cc_final: 0.8563 (mmt) REVERT: R 244 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.8139 (p0) REVERT: R 269 MET cc_start: 0.8365 (ptp) cc_final: 0.8129 (ptp) REVERT: R 291 LYS cc_start: 0.6497 (mmtt) cc_final: 0.5832 (mptt) outliers start: 95 outliers final: 43 residues processed: 383 average time/residue: 2.4050 time to fit residues: 1077.7558 Evaluate side-chains 352 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 291 time to evaluate : 3.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 330 ILE Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 95 ARG Chi-restraints excluded: chain K residue 128 ASN 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 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 269 MET 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 149 THR Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 253 GLU Chi-restraints excluded: chain N residue 9 VAL 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 232 SER 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 324 THR 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 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 49 GLN Chi-restraints excluded: chain Q residue 52 SER Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 83 GLU Chi-restraints excluded: chain Q residue 232 SER Chi-restraints excluded: chain Q residue 241 GLU Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 83 GLU Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 244 ASP 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 299 optimal weight: 5.9990 chunk 227 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 304 optimal weight: 3.9990 chunk 321 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 chunk 288 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 297 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3591 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= 0.254 Angle : 0.626 6.961 36657 Z= 0.308 Chirality : 0.044 0.150 4068 Planarity : 0.004 0.052 4689 Dihedral : 11.593 178.210 3784 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.50 % Allowed : 14.65 % Favored : 81.85 % 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: 0.32 (0.15), residues: 3303 helix: 0.29 (0.14), residues: 1314 sheet: 0.01 (0.22), residues: 567 loop : 0.46 (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 0.011 0.001 PHE O 31 TYR 0.010 0.001 TYR P 69 ARG 0.007 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 404 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 305 time to evaluate : 3.290 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: 0.2620 (mmm) cc_final: 0.2299 (mmm) REVERT: J 82 MET cc_start: 0.8068 (tpt) cc_final: 0.7784 (tpt) REVERT: J 227 MET cc_start: 0.8305 (mmm) cc_final: 0.7774 (tpp) REVERT: J 283 MET cc_start: 0.8996 (mmm) cc_final: 0.8765 (mmm) REVERT: J 326 LYS cc_start: 0.8211 (pttt) cc_final: 0.7776 (pttt) REVERT: J 330 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.7843 (mt) REVERT: K 72 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7937 (mt-10) REVERT: K 227 MET cc_start: 0.8743 (mmm) cc_final: 0.8486 (mmm) REVERT: L 17 VAL cc_start: 0.8615 (OUTLIER) cc_final: 0.8380 (p) REVERT: L 57 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8113 (mm-30) REVERT: L 119 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8445 (ttp) REVERT: L 241 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8227 (mm-30) REVERT: L 328 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8175 (ttpt) REVERT: M 61 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8288 (mttt) REVERT: M 72 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7776 (tm-30) REVERT: M 95 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7922 (mtt-85) REVERT: M 137 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8405 (mm110) REVERT: M 326 LYS cc_start: 0.8061 (pptt) cc_final: 0.6971 (mmtm) REVERT: M 361 GLU cc_start: 0.8455 (tt0) cc_final: 0.8176 (tt0) REVERT: M 372 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.8081 (ptp90) REVERT: N 9 VAL cc_start: 0.9001 (OUTLIER) cc_final: 0.8790 (t) REVERT: N 225 ASN cc_start: 0.8219 (t0) cc_final: 0.7922 (t0) REVERT: N 253 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8277 (pm20) REVERT: N 336 LYS cc_start: 0.8440 (tptm) cc_final: 0.8151 (tttt) REVERT: N 372 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8233 (ptp90) REVERT: O 17 VAL cc_start: 0.8366 (OUTLIER) cc_final: 0.8150 (p) REVERT: O 225 ASN cc_start: 0.8484 (t0) cc_final: 0.8009 (m110) REVERT: O 227 MET cc_start: 0.8760 (mmm) cc_final: 0.8536 (mmm) REVERT: O 244 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7567 (p0) REVERT: O 283 MET cc_start: 0.8988 (mmt) cc_final: 0.8698 (mmm) REVERT: O 355 MET cc_start: 0.9029 (mtt) cc_final: 0.8621 (mtt) REVERT: O 363 ASP cc_start: 0.7948 (p0) cc_final: 0.7661 (p0) REVERT: P 17 VAL cc_start: 0.8556 (OUTLIER) cc_final: 0.8233 (p) REVERT: P 47 MET cc_start: 0.6992 (mtp) cc_final: 0.5845 (ptt) REVERT: P 57 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8127 (mm-30) REVERT: P 72 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7783 (mm-30) REVERT: P 123 MET cc_start: 0.8900 (mmp) cc_final: 0.8648 (mmp) REVERT: P 180 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8485 (tp) REVERT: P 211 ASP cc_start: 0.8792 (OUTLIER) cc_final: 0.8544 (t70) REVERT: P 225 ASN cc_start: 0.8152 (OUTLIER) cc_final: 0.7745 (m110) REVERT: P 227 MET cc_start: 0.8669 (mmm) cc_final: 0.8291 (mmm) REVERT: P 269 MET cc_start: 0.8845 (ptp) cc_final: 0.8628 (ptm) REVERT: Q 54 VAL cc_start: 0.9127 (OUTLIER) cc_final: 0.8893 (t) REVERT: Q 72 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7888 (mt-10) REVERT: Q 241 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8569 (tt0) REVERT: Q 360 GLN cc_start: 0.8476 (tm-30) cc_final: 0.8065 (tm130) REVERT: R 227 MET cc_start: 0.8781 (mmm) cc_final: 0.8440 (mmt) REVERT: R 291 LYS cc_start: 0.6265 (mmtt) cc_final: 0.5770 (mptt) REVERT: R 325 MET cc_start: 0.7015 (ptm) cc_final: 0.6729 (ptm) outliers start: 99 outliers final: 38 residues processed: 370 average time/residue: 2.3908 time to fit residues: 1041.2668 Evaluate side-chains 361 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 297 time to evaluate : 3.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 330 ILE Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 57 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 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 137 GLN 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 9 VAL 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 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 324 THR 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 72 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 49 GLN Chi-restraints excluded: chain Q residue 52 SER Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 72 GLU Chi-restraints excluded: chain Q residue 83 GLU Chi-restraints excluded: chain Q residue 241 GLU 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 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 268 optimal weight: 0.0070 chunk 182 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 239 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 274 optimal weight: 3.9990 chunk 222 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 164 optimal weight: 0.4980 chunk 288 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.7004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 263 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 27009 Z= 0.252 Angle : 0.614 6.877 36657 Z= 0.301 Chirality : 0.044 0.144 4068 Planarity : 0.004 0.052 4689 Dihedral : 11.382 169.228 3780 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.47 % Allowed : 15.22 % Favored : 81.32 % 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: 0.60 (0.15), residues: 3303 helix: 0.68 (0.15), residues: 1260 sheet: 0.09 (0.22), residues: 567 loop : 0.49 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP O 356 HIS 0.004 0.001 HIS P 88 PHE 0.014 0.001 PHE O 31 TYR 0.010 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 408 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 310 time to evaluate : 3.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 44 MET cc_start: 0.2747 (mmm) cc_final: 0.2399 (mmm) REVERT: J 82 MET cc_start: 0.8280 (tpt) cc_final: 0.8016 (tpt) REVERT: J 227 MET cc_start: 0.8278 (mmm) cc_final: 0.7789 (tpp) REVERT: J 283 MET cc_start: 0.9090 (mmm) cc_final: 0.8874 (mmm) REVERT: J 326 LYS cc_start: 0.8280 (pttt) cc_final: 0.7839 (pttt) REVERT: J 330 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.7844 (mt) REVERT: K 72 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7865 (mt-10) REVERT: K 227 MET cc_start: 0.8735 (mmm) cc_final: 0.8452 (mmm) REVERT: L 17 VAL cc_start: 0.8643 (OUTLIER) cc_final: 0.8412 (p) REVERT: L 57 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8247 (mm-30) REVERT: L 119 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8455 (ttp) REVERT: M 61 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8305 (mttp) REVERT: M 95 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7934 (mtt-85) REVERT: M 118 LYS cc_start: 0.8606 (tptm) cc_final: 0.8378 (mtmt) REVERT: M 137 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8462 (mm110) REVERT: M 283 MET cc_start: 0.8685 (mmp) cc_final: 0.8423 (mmm) REVERT: M 326 LYS cc_start: 0.8170 (pptt) cc_final: 0.7054 (mmtm) REVERT: N 9 VAL cc_start: 0.9143 (OUTLIER) cc_final: 0.8776 (t) REVERT: N 137 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8728 (mt0) REVERT: N 225 ASN cc_start: 0.8193 (t0) cc_final: 0.7720 (m110) REVERT: N 253 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8328 (pm20) REVERT: N 336 LYS cc_start: 0.8649 (tptm) cc_final: 0.8405 (tttt) REVERT: N 372 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8239 (ptp90) REVERT: O 17 VAL cc_start: 0.8288 (OUTLIER) cc_final: 0.8073 (p) REVERT: O 41 GLN cc_start: 0.7410 (tt0) cc_final: 0.6960 (tp40) REVERT: O 225 ASN cc_start: 0.8495 (OUTLIER) cc_final: 0.8040 (m110) REVERT: O 227 MET cc_start: 0.8746 (mmm) cc_final: 0.8518 (mmm) REVERT: O 244 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7643 (p0) REVERT: O 283 MET cc_start: 0.8984 (mmt) cc_final: 0.8710 (mmm) REVERT: O 363 ASP cc_start: 0.7912 (p0) cc_final: 0.7660 (p0) REVERT: P 17 VAL cc_start: 0.8543 (OUTLIER) cc_final: 0.8211 (p) REVERT: P 47 MET cc_start: 0.6994 (mtp) cc_final: 0.5885 (ptt) REVERT: P 57 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8224 (mm-30) REVERT: P 211 ASP cc_start: 0.8800 (OUTLIER) cc_final: 0.8551 (t70) REVERT: P 225 ASN cc_start: 0.8167 (m-40) cc_final: 0.7761 (m110) REVERT: P 227 MET cc_start: 0.8663 (mmm) cc_final: 0.8298 (mmm) REVERT: P 244 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7966 (p0) REVERT: P 269 MET cc_start: 0.8822 (ptp) cc_final: 0.8599 (ptm) REVERT: P 360 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8211 (tm-30) REVERT: Q 54 VAL cc_start: 0.9043 (OUTLIER) cc_final: 0.8820 (t) REVERT: Q 72 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7873 (mt-10) REVERT: Q 149 THR cc_start: 0.8748 (t) cc_final: 0.8530 (m) REVERT: Q 241 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8560 (tt0) REVERT: R 227 MET cc_start: 0.8771 (mmm) cc_final: 0.8132 (mmt) REVERT: R 283 MET cc_start: 0.8363 (mmt) cc_final: 0.8066 (tpp) REVERT: R 286 ASP cc_start: 0.7599 (t0) cc_final: 0.7226 (m-30) REVERT: R 291 LYS cc_start: 0.6244 (mmtt) cc_final: 0.5704 (mptt) REVERT: R 325 MET cc_start: 0.6763 (ptm) cc_final: 0.6324 (ptm) outliers start: 98 outliers final: 40 residues processed: 377 average time/residue: 2.5227 time to fit residues: 1121.7930 Evaluate side-chains 359 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 296 time to evaluate : 3.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 17 VAL 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 330 ILE Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 57 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 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 137 GLN 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 9 VAL 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 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 149 THR Chi-restraints excluded: chain O residue 211 ASP Chi-restraints excluded: chain O residue 225 ASN Chi-restraints excluded: chain O residue 244 ASP Chi-restraints excluded: chain O residue 324 THR 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 244 ASP 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 P residue 360 GLN Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 52 SER Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 72 GLU Chi-restraints excluded: chain Q residue 83 GLU Chi-restraints excluded: chain Q residue 241 GLU 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 108 optimal weight: 2.9990 chunk 289 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 322 optimal weight: 0.9990 chunk 267 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 169 optimal weight: 0.5980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 12 ASN P 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3898 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= 0.209 Angle : 0.594 7.024 36657 Z= 0.288 Chirality : 0.043 0.141 4068 Planarity : 0.004 0.051 4689 Dihedral : 11.074 173.002 3778 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.04 % Allowed : 15.92 % Favored : 81.03 % 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: 0.76 (0.15), residues: 3303 helix: 0.90 (0.15), residues: 1260 sheet: 0.16 (0.22), residues: 567 loop : 0.50 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 79 HIS 0.004 0.001 HIS P 88 PHE 0.010 0.001 PHE O 31 TYR 0.009 0.001 TYR P 69 ARG 0.010 0.000 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 391 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 305 time to evaluate : 3.219 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: 0.2680 (mmm) cc_final: 0.2408 (mmm) REVERT: J 82 MET cc_start: 0.8124 (tpt) cc_final: 0.7814 (tpt) REVERT: J 283 MET cc_start: 0.9053 (mmm) cc_final: 0.8752 (mmm) REVERT: J 330 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.7788 (mt) REVERT: K 72 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7831 (mt-10) REVERT: K 227 MET cc_start: 0.8726 (mmm) cc_final: 0.8428 (mmm) REVERT: L 17 VAL cc_start: 0.8622 (OUTLIER) cc_final: 0.8419 (p) REVERT: L 57 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8311 (mm-30) REVERT: L 241 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8216 (mm-30) REVERT: L 328 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8216 (ttpt) REVERT: M 61 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8301 (mttt) REVERT: M 72 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7828 (tm-30) REVERT: M 95 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.8003 (mtt-85) REVERT: M 118 LYS cc_start: 0.8601 (tptm) cc_final: 0.8371 (mtmt) REVERT: M 137 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8467 (mm110) REVERT: M 283 MET cc_start: 0.8693 (mmp) cc_final: 0.8452 (mmm) REVERT: M 326 LYS cc_start: 0.8062 (pptt) cc_final: 0.6910 (mmtm) REVERT: N 9 VAL cc_start: 0.9338 (OUTLIER) cc_final: 0.8906 (t) REVERT: N 137 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8582 (mt0) REVERT: N 225 ASN cc_start: 0.8196 (t0) cc_final: 0.7734 (m110) REVERT: N 253 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8402 (pm20) REVERT: N 336 LYS cc_start: 0.8628 (tptm) cc_final: 0.8419 (tttt) REVERT: N 372 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8238 (ptp90) REVERT: O 17 VAL cc_start: 0.8264 (OUTLIER) cc_final: 0.8024 (p) REVERT: O 41 GLN cc_start: 0.7356 (tt0) cc_final: 0.6919 (tp40) REVERT: O 225 ASN cc_start: 0.8502 (OUTLIER) cc_final: 0.8061 (m110) REVERT: O 227 MET cc_start: 0.8732 (mmm) cc_final: 0.8510 (mmm) REVERT: O 244 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7628 (p0) REVERT: O 283 MET cc_start: 0.8957 (mmt) cc_final: 0.8698 (mmm) REVERT: O 363 ASP cc_start: 0.7843 (p0) cc_final: 0.7434 (p0) REVERT: P 17 VAL cc_start: 0.8525 (OUTLIER) cc_final: 0.8191 (p) REVERT: P 47 MET cc_start: 0.6967 (mtp) cc_final: 0.5882 (ptt) REVERT: P 57 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8230 (mm-30) REVERT: P 211 ASP cc_start: 0.8794 (OUTLIER) cc_final: 0.8542 (t70) REVERT: P 225 ASN cc_start: 0.8175 (m-40) cc_final: 0.7766 (m110) REVERT: P 227 MET cc_start: 0.8651 (mmm) cc_final: 0.8296 (mmm) REVERT: P 269 MET cc_start: 0.8816 (ptp) cc_final: 0.8606 (ptm) REVERT: Q 72 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7862 (mt-10) REVERT: Q 83 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7419 (tm-30) REVERT: Q 149 THR cc_start: 0.8738 (t) cc_final: 0.8527 (m) REVERT: Q 241 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8513 (tt0) REVERT: Q 355 MET cc_start: 0.9103 (mtp) cc_final: 0.8887 (mpp) REVERT: Q 360 GLN cc_start: 0.8373 (tm-30) cc_final: 0.8008 (tm-30) REVERT: R 227 MET cc_start: 0.8757 (mmm) cc_final: 0.8544 (mmt) REVERT: R 286 ASP cc_start: 0.7584 (t0) cc_final: 0.7228 (m-30) REVERT: R 291 LYS cc_start: 0.6153 (mmtt) cc_final: 0.5582 (mptt) outliers start: 86 outliers final: 40 residues processed: 365 average time/residue: 2.4860 time to fit residues: 1058.5438 Evaluate side-chains 354 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 291 time to evaluate : 3.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 17 VAL 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 299 MET Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 330 ILE 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 L residue 17 VAL Chi-restraints excluded: chain L residue 57 GLU 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 137 GLN 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 9 VAL 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 348 SER Chi-restraints excluded: chain N residue 363 ASP Chi-restraints excluded: chain N residue 372 ARG Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 149 THR Chi-restraints excluded: chain O residue 211 ASP Chi-restraints excluded: chain O residue 225 ASN Chi-restraints excluded: chain O residue 244 ASP Chi-restraints excluded: chain O residue 324 THR 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 72 GLU Chi-restraints excluded: chain Q residue 83 GLU Chi-restraints excluded: chain Q residue 234 SER Chi-restraints excluded: chain Q residue 241 GLU Chi-restraints excluded: chain Q residue 269 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 310 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 183 optimal weight: 0.7980 chunk 235 optimal weight: 2.9990 chunk 182 optimal weight: 0.6980 chunk 271 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 320 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 195 optimal weight: 0.5980 chunk 148 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 297 ASN N 12 ASN P 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27009 Z= 0.163 Angle : 0.573 6.752 36657 Z= 0.275 Chirality : 0.043 0.144 4068 Planarity : 0.004 0.051 4689 Dihedral : 10.506 165.467 3777 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.48 % Allowed : 16.74 % Favored : 80.79 % 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: 0.97 (0.15), residues: 3303 helix: 1.14 (0.15), residues: 1260 sheet: 0.22 (0.22), residues: 567 loop : 0.57 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 356 HIS 0.004 0.001 HIS N 161 PHE 0.010 0.001 PHE O 31 TYR 0.007 0.001 TYR N 294 ARG 0.008 0.000 ARG O 95 *********************** 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 385 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 315 time to evaluate : 3.188 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 82 MET cc_start: 0.8153 (tpt) cc_final: 0.7843 (tpt) REVERT: J 283 MET cc_start: 0.8987 (mmm) cc_final: 0.8703 (mmm) REVERT: K 227 MET cc_start: 0.8714 (mmm) cc_final: 0.8426 (mmm) REVERT: L 328 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8234 (tttm) REVERT: M 61 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8285 (mttp) REVERT: M 95 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7908 (mtt-85) REVERT: M 118 LYS cc_start: 0.8585 (tptm) cc_final: 0.8326 (mtmt) REVERT: M 137 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8476 (mm110) REVERT: M 283 MET cc_start: 0.8674 (mmp) cc_final: 0.8421 (mmm) REVERT: M 326 LYS cc_start: 0.7994 (pptt) cc_final: 0.6895 (mmtm) REVERT: N 9 VAL cc_start: 0.9274 (OUTLIER) cc_final: 0.8863 (t) REVERT: N 225 ASN cc_start: 0.8151 (t0) cc_final: 0.7784 (m110) REVERT: N 253 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8167 (pm20) REVERT: N 336 LYS cc_start: 0.8594 (tptm) cc_final: 0.8369 (ttmm) REVERT: N 344 SER cc_start: 0.8844 (OUTLIER) cc_final: 0.8546 (p) REVERT: N 372 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8271 (ptp90) REVERT: O 17 VAL cc_start: 0.8171 (OUTLIER) cc_final: 0.7903 (p) REVERT: O 41 GLN cc_start: 0.7340 (tt0) cc_final: 0.6917 (tp40) REVERT: O 225 ASN cc_start: 0.8495 (t0) cc_final: 0.8071 (m110) REVERT: O 227 MET cc_start: 0.8719 (mmm) cc_final: 0.8479 (mmm) REVERT: O 244 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7751 (p0) REVERT: O 283 MET cc_start: 0.8911 (mmt) cc_final: 0.8642 (mmm) REVERT: O 360 GLN cc_start: 0.7735 (tt0) cc_final: 0.7416 (pm20) REVERT: O 363 ASP cc_start: 0.7920 (p0) cc_final: 0.7488 (p0) REVERT: P 17 VAL cc_start: 0.8489 (OUTLIER) cc_final: 0.8148 (p) REVERT: P 57 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8214 (mm-30) REVERT: P 95 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7920 (mtt-85) REVERT: P 211 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8510 (t70) REVERT: P 227 MET cc_start: 0.8627 (mmm) cc_final: 0.8294 (mmm) REVERT: Q 83 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7419 (tm-30) REVERT: Q 149 THR cc_start: 0.8728 (t) cc_final: 0.8526 (m) REVERT: Q 241 GLU cc_start: 0.8697 (tt0) cc_final: 0.8447 (tt0) REVERT: Q 355 MET cc_start: 0.9094 (mtp) cc_final: 0.8848 (mpp) REVERT: Q 360 GLN cc_start: 0.8385 (tm-30) cc_final: 0.8008 (tm-30) REVERT: R 227 MET cc_start: 0.8749 (mmm) cc_final: 0.8538 (mmt) REVERT: R 269 MET cc_start: 0.8282 (ptp) cc_final: 0.7988 (ptp) REVERT: R 286 ASP cc_start: 0.7541 (t0) cc_final: 0.7205 (m-30) REVERT: R 291 LYS cc_start: 0.6093 (mmtt) cc_final: 0.5604 (mptt) outliers start: 70 outliers final: 32 residues processed: 366 average time/residue: 2.4370 time to fit residues: 1050.9446 Evaluate side-chains 348 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 301 time to evaluate : 3.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 330 ILE Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain L residue 95 ARG 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 61 LYS Chi-restraints excluded: chain M residue 95 ARG Chi-restraints excluded: chain M residue 137 GLN 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 9 VAL 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 344 SER Chi-restraints excluded: chain N residue 363 ASP 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 324 THR 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 198 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 63 optimal weight: 0.0370 chunk 62 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 218 optimal weight: 0.5980 chunk 158 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 252 optimal weight: 2.9990 overall best weight: 1.3262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 12 ASN P 246 GLN ** Q 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4110 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= 0.211 Angle : 0.585 6.795 36657 Z= 0.282 Chirality : 0.043 0.140 4068 Planarity : 0.004 0.055 4689 Dihedral : 10.252 161.524 3776 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.62 % Allowed : 17.16 % Favored : 80.22 % 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: 0.26 (0.22), residues: 567 loop : 0.56 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 79 HIS 0.003 0.001 HIS M 161 PHE 0.009 0.001 PHE L 31 TYR 0.009 0.001 TYR P 69 ARG 0.008 0.000 ARG N 95 *********************** 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 380 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 306 time to evaluate : 3.206 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 82 MET cc_start: 0.8143 (tpt) cc_final: 0.7874 (tpt) REVERT: J 283 MET cc_start: 0.8994 (mmm) cc_final: 0.8721 (mmm) REVERT: K 227 MET cc_start: 0.8726 (mmm) cc_final: 0.8414 (mmm) REVERT: M 61 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8300 (mttp) REVERT: M 95 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7911 (mtt-85) REVERT: M 137 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8475 (mm110) REVERT: M 283 MET cc_start: 0.8681 (mmp) cc_final: 0.8408 (mmm) REVERT: M 326 LYS cc_start: 0.8050 (pptt) cc_final: 0.6951 (mmtm) REVERT: N 9 VAL cc_start: 0.9290 (OUTLIER) cc_final: 0.8838 (t) REVERT: N 225 ASN cc_start: 0.8140 (t0) cc_final: 0.7791 (m110) REVERT: N 253 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8400 (pm20) REVERT: N 344 SER cc_start: 0.8848 (OUTLIER) cc_final: 0.8550 (p) REVERT: N 372 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8255 (ptp90) REVERT: O 17 VAL cc_start: 0.8187 (OUTLIER) cc_final: 0.7931 (p) REVERT: O 41 GLN cc_start: 0.7337 (tt0) cc_final: 0.6915 (tp40) REVERT: O 132 MET cc_start: 0.9368 (ppp) cc_final: 0.9077 (ppp) REVERT: O 225 ASN cc_start: 0.8526 (OUTLIER) cc_final: 0.8099 (m110) REVERT: O 227 MET cc_start: 0.8720 (mmm) cc_final: 0.8481 (mmm) REVERT: O 238 LYS cc_start: 0.8674 (mmmm) cc_final: 0.8455 (mmtp) REVERT: O 244 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7711 (p0) REVERT: O 283 MET cc_start: 0.8904 (mmt) cc_final: 0.8635 (mmm) REVERT: O 360 GLN cc_start: 0.7742 (tt0) cc_final: 0.7424 (pm20) REVERT: O 363 ASP cc_start: 0.7853 (p0) cc_final: 0.7429 (p0) REVERT: P 17 VAL cc_start: 0.8510 (OUTLIER) cc_final: 0.8171 (p) REVERT: P 57 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8259 (mm-30) REVERT: P 95 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7930 (mtt-85) REVERT: P 211 ASP cc_start: 0.8804 (OUTLIER) cc_final: 0.8559 (t70) REVERT: P 225 ASN cc_start: 0.8192 (OUTLIER) cc_final: 0.7780 (m110) REVERT: P 227 MET cc_start: 0.8646 (mmm) cc_final: 0.8289 (mmm) REVERT: P 336 LYS cc_start: 0.8542 (tptm) cc_final: 0.8187 (ttpt) REVERT: Q 83 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7397 (tm-30) REVERT: Q 355 MET cc_start: 0.9093 (mtp) cc_final: 0.8820 (mpp) REVERT: Q 360 GLN cc_start: 0.8390 (tm-30) cc_final: 0.8011 (tm-30) REVERT: R 227 MET cc_start: 0.8756 (mmm) cc_final: 0.8546 (mmt) REVERT: R 269 MET cc_start: 0.8342 (ptp) cc_final: 0.8134 (ptp) REVERT: R 283 MET cc_start: 0.8270 (mmt) cc_final: 0.7960 (tpp) REVERT: R 286 ASP cc_start: 0.7573 (t0) cc_final: 0.7212 (m-30) REVERT: R 291 LYS cc_start: 0.6168 (mmtt) cc_final: 0.5676 (mptt) REVERT: R 325 MET cc_start: 0.7000 (ptm) cc_final: 0.6786 (ptm) outliers start: 74 outliers final: 44 residues processed: 355 average time/residue: 2.4323 time to fit residues: 1009.5830 Evaluate side-chains 360 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 300 time to evaluate : 3.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 17 VAL 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 330 ILE Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 128 ASN Chi-restraints excluded: chain L residue 95 ARG 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 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 137 GLN Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 253 GLU Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain N residue 12 ASN Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 137 GLN 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 372 ARG Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 149 THR Chi-restraints excluded: chain O residue 211 ASP Chi-restraints excluded: chain O residue 225 ASN Chi-restraints excluded: chain O residue 244 ASP Chi-restraints excluded: chain O residue 324 THR 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 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 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 271 SER Chi-restraints excluded: chain R residue 338 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 291 optimal weight: 1.9990 chunk 307 optimal weight: 4.9990 chunk 280 optimal weight: 3.9990 chunk 299 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 234 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 270 optimal weight: 4.9990 chunk 282 optimal weight: 2.9990 chunk 298 optimal weight: 0.0980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 12 ASN N 360 GLN ** Q 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 27009 Z= 0.238 Angle : 0.704 59.198 36657 Z= 0.367 Chirality : 0.043 0.141 4068 Planarity : 0.004 0.050 4689 Dihedral : 10.243 161.334 3776 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.51 % Allowed : 17.52 % Favored : 79.97 % 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: 0.26 (0.22), residues: 567 loop : 0.56 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 79 HIS 0.003 0.001 HIS M 161 PHE 0.009 0.001 PHE L 31 TYR 0.009 0.001 TYR P 69 ARG 0.007 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 369 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 298 time to evaluate : 3.187 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: J 82 MET cc_start: 0.8141 (tpt) cc_final: 0.7877 (tpt) REVERT: J 283 MET cc_start: 0.8999 (mmm) cc_final: 0.8725 (mmm) REVERT: K 137 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8460 (mt0) REVERT: K 227 MET cc_start: 0.8728 (mmm) cc_final: 0.8411 (mmm) REVERT: M 61 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8303 (mttp) REVERT: M 95 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7913 (mtt-85) REVERT: M 137 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8475 (mm110) REVERT: M 283 MET cc_start: 0.8686 (mmp) cc_final: 0.8411 (mmm) REVERT: M 326 LYS cc_start: 0.8058 (pptt) cc_final: 0.6961 (mmtm) REVERT: N 9 VAL cc_start: 0.9284 (OUTLIER) cc_final: 0.8834 (t) REVERT: N 225 ASN cc_start: 0.8144 (t0) cc_final: 0.7792 (m110) REVERT: N 253 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8409 (pm20) REVERT: N 328 LYS cc_start: 0.8418 (ttmt) cc_final: 0.8022 (tttt) REVERT: N 344 SER cc_start: 0.8855 (OUTLIER) cc_final: 0.8558 (p) REVERT: N 372 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8255 (ptp90) REVERT: O 17 VAL cc_start: 0.8194 (OUTLIER) cc_final: 0.7937 (p) REVERT: O 41 GLN cc_start: 0.7338 (tt0) cc_final: 0.6915 (tp40) REVERT: O 132 MET cc_start: 0.9368 (ppp) cc_final: 0.9082 (ppp) REVERT: O 225 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.8101 (m110) REVERT: O 227 MET cc_start: 0.8721 (mmm) cc_final: 0.8483 (mmm) REVERT: O 238 LYS cc_start: 0.8675 (mmmm) cc_final: 0.8454 (mmtp) REVERT: O 244 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7717 (p0) REVERT: O 283 MET cc_start: 0.8908 (mmt) cc_final: 0.8642 (mmm) REVERT: O 360 GLN cc_start: 0.7747 (tt0) cc_final: 0.7426 (pm20) REVERT: O 363 ASP cc_start: 0.7859 (p0) cc_final: 0.7434 (p0) REVERT: P 17 VAL cc_start: 0.8513 (OUTLIER) cc_final: 0.8176 (p) REVERT: P 57 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8243 (mm-30) REVERT: P 95 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7933 (mtt-85) REVERT: P 211 ASP cc_start: 0.8803 (OUTLIER) cc_final: 0.8565 (t70) REVERT: P 225 ASN cc_start: 0.8194 (OUTLIER) cc_final: 0.7783 (m110) REVERT: P 227 MET cc_start: 0.8648 (mmm) cc_final: 0.8289 (mmm) REVERT: P 336 LYS cc_start: 0.8548 (tptm) cc_final: 0.8192 (ttpt) REVERT: Q 83 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7399 (tm-30) REVERT: Q 355 MET cc_start: 0.9093 (mtp) cc_final: 0.8819 (mpp) REVERT: Q 360 GLN cc_start: 0.8390 (tm-30) cc_final: 0.8012 (tm-30) REVERT: R 227 MET cc_start: 0.8753 (mmm) cc_final: 0.8547 (mmt) REVERT: R 269 MET cc_start: 0.8346 (ptp) cc_final: 0.8143 (ptp) REVERT: R 283 MET cc_start: 0.8271 (mmt) cc_final: 0.7965 (tpp) REVERT: R 286 ASP cc_start: 0.7575 (t0) cc_final: 0.7213 (m-30) REVERT: R 291 LYS cc_start: 0.6171 (mmtt) cc_final: 0.5684 (mptt) REVERT: R 325 MET cc_start: 0.7013 (ptm) cc_final: 0.6796 (ptm) outliers start: 71 outliers final: 44 residues processed: 347 average time/residue: 2.4731 time to fit residues: 1008.8456 Evaluate side-chains 359 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 298 time to evaluate : 3.199 ------------------------------------------------------------------------------- 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 330 ILE Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 128 ASN Chi-restraints excluded: chain K residue 137 GLN Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 95 ARG 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 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 137 GLN 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 9 VAL Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 137 GLN 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 372 ARG Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 149 THR Chi-restraints excluded: chain O residue 211 ASP Chi-restraints excluded: chain O residue 225 ASN Chi-restraints excluded: chain O residue 244 ASP Chi-restraints excluded: chain O residue 324 THR 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 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 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 271 SER 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 196 optimal weight: 3.9990 chunk 316 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 chunk 150 optimal weight: 0.2980 chunk 219 optimal weight: 1.9990 chunk 331 optimal weight: 6.9990 chunk 305 optimal weight: 0.9980 chunk 264 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 204 optimal weight: 2.9990 chunk 161 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: ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 12 ASN ** N 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 27009 Z= 0.238 Angle : 0.704 59.198 36657 Z= 0.367 Chirality : 0.043 0.141 4068 Planarity : 0.004 0.050 4689 Dihedral : 10.243 161.334 3776 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.19 % Allowed : 17.83 % Favored : 79.97 % 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: 0.26 (0.22), residues: 567 loop : 0.56 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 79 HIS 0.003 0.001 HIS M 161 PHE 0.009 0.001 PHE L 31 TYR 0.009 0.001 TYR P 69 ARG 0.007 0.000 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 360 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 298 time to evaluate : 3.170 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: J 82 MET cc_start: 0.8141 (tpt) cc_final: 0.7877 (tpt) REVERT: J 283 MET cc_start: 0.8999 (mmm) cc_final: 0.8725 (mmm) REVERT: K 137 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8460 (mt0) REVERT: K 227 MET cc_start: 0.8728 (mmm) cc_final: 0.8411 (mmm) REVERT: M 61 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8304 (mttp) REVERT: M 95 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7913 (mtt-85) REVERT: M 137 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8474 (mm110) REVERT: M 283 MET cc_start: 0.8686 (mmp) cc_final: 0.8411 (mmm) REVERT: M 326 LYS cc_start: 0.8058 (pptt) cc_final: 0.6961 (mmtm) REVERT: N 9 VAL cc_start: 0.9294 (OUTLIER) cc_final: 0.8834 (t) REVERT: N 225 ASN cc_start: 0.8144 (t0) cc_final: 0.7792 (m110) REVERT: N 253 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8408 (pm20) REVERT: N 328 LYS cc_start: 0.8418 (ttmt) cc_final: 0.8021 (tttt) REVERT: N 344 SER cc_start: 0.8855 (OUTLIER) cc_final: 0.8558 (p) REVERT: N 372 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8255 (ptp90) REVERT: O 17 VAL cc_start: 0.8193 (OUTLIER) cc_final: 0.7937 (p) REVERT: O 41 GLN cc_start: 0.7337 (tt0) cc_final: 0.6915 (tp40) REVERT: O 132 MET cc_start: 0.9369 (ppp) cc_final: 0.9082 (ppp) REVERT: O 225 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.8100 (m110) REVERT: O 227 MET cc_start: 0.8721 (mmm) cc_final: 0.8483 (mmm) REVERT: O 238 LYS cc_start: 0.8675 (mmmm) cc_final: 0.8454 (mmtp) REVERT: O 244 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7717 (p0) REVERT: O 283 MET cc_start: 0.8907 (mmt) cc_final: 0.8642 (mmm) REVERT: O 360 GLN cc_start: 0.7747 (tt0) cc_final: 0.7426 (pm20) REVERT: O 363 ASP cc_start: 0.7860 (p0) cc_final: 0.7435 (p0) REVERT: P 17 VAL cc_start: 0.8513 (OUTLIER) cc_final: 0.8176 (p) REVERT: P 57 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8243 (mm-30) REVERT: P 95 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7933 (mtt-85) REVERT: P 211 ASP cc_start: 0.8810 (OUTLIER) cc_final: 0.8565 (t70) REVERT: P 225 ASN cc_start: 0.8194 (OUTLIER) cc_final: 0.7783 (m110) REVERT: P 227 MET cc_start: 0.8649 (mmm) cc_final: 0.8289 (mmm) REVERT: P 336 LYS cc_start: 0.8550 (tptm) cc_final: 0.8192 (ttpt) REVERT: Q 83 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7399 (tm-30) REVERT: Q 355 MET cc_start: 0.9093 (mtp) cc_final: 0.8819 (mpp) REVERT: Q 360 GLN cc_start: 0.8391 (tm-30) cc_final: 0.8012 (tm-30) REVERT: R 227 MET cc_start: 0.8753 (mmm) cc_final: 0.8547 (mmt) REVERT: R 269 MET cc_start: 0.8346 (ptp) cc_final: 0.8143 (ptp) REVERT: R 283 MET cc_start: 0.8271 (mmt) cc_final: 0.7965 (tpp) REVERT: R 286 ASP cc_start: 0.7575 (t0) cc_final: 0.7213 (m-30) REVERT: R 291 LYS cc_start: 0.6171 (mmtt) cc_final: 0.5684 (mptt) REVERT: R 325 MET cc_start: 0.7013 (ptm) cc_final: 0.6796 (ptm) outliers start: 62 outliers final: 44 residues processed: 341 average time/residue: 2.4971 time to fit residues: 1000.3022 Evaluate side-chains 358 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 297 time to evaluate : 3.246 ------------------------------------------------------------------------------- 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 330 ILE Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 128 ASN Chi-restraints excluded: chain K residue 137 GLN Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 95 ARG 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 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 137 GLN 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 9 VAL Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 137 GLN 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 372 ARG Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 149 THR Chi-restraints excluded: chain O residue 211 ASP Chi-restraints excluded: chain O residue 225 ASN Chi-restraints excluded: chain O residue 244 ASP Chi-restraints excluded: chain O residue 324 THR 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 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 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 271 SER 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 209 optimal weight: 2.9990 chunk 281 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 243 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 264 optimal weight: 0.5980 chunk 110 optimal weight: 0.0970 chunk 271 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 12 ASN ** N 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.121857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.090114 restraints weight = 93756.169| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.62 r_work: 0.3004 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 27009 Z= 0.238 Angle : 0.704 59.198 36657 Z= 0.367 Chirality : 0.043 0.141 4068 Planarity : 0.004 0.050 4689 Dihedral : 10.243 161.334 3776 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.19 % Allowed : 17.83 % Favored : 79.97 % 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: 0.26 (0.22), residues: 567 loop : 0.56 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 79 HIS 0.003 0.001 HIS M 161 PHE 0.009 0.001 PHE L 31 TYR 0.009 0.001 TYR P 69 ARG 0.007 0.000 ARG J 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16678.57 seconds wall clock time: 282 minutes 55.60 seconds (16975.60 seconds total)