Starting phenix.real_space_refine on Sun Dec 29 09:01:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c4c_16424/12_2024/8c4c_16424_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c4c_16424/12_2024/8c4c_16424.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c4c_16424/12_2024/8c4c_16424.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c4c_16424/12_2024/8c4c_16424.map" model { file = "/net/cci-nas-00/data/ceres_data/8c4c_16424/12_2024/8c4c_16424_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c4c_16424/12_2024/8c4c_16424_trim.cif" } resolution = 2.7 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= 0.000 sd= 0.002 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 24 5.49 5 Mg 8 5.21 5 S 184 5.16 5 C 17852 2.51 5 N 4796 2.21 5 O 5436 1.98 5 H 27864 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 56164 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5760 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5760 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 349} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5760 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 349} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5760 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 349} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5760 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 349} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5760 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 349} 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: "G" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5760 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 349} 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: "H" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5760 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 349} 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: 2455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2455 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 9, 'TRANS': 146} Chain: "L" Number of atoms: 2455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2455 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 9, 'TRANS': 146} Chain: "M" Number of atoms: 2455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2455 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 9, 'TRANS': 146} Chain: "N" Number of atoms: 2455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2455 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 9, 'TRANS': 146} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 21.88, per 1000 atoms: 0.39 Number of scatterers: 56164 At special positions: 0 Unit cell: (99.12, 119.77, 271.754, 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 184 16.00 P 24 15.00 Mg 8 11.99 O 5436 8.00 N 4796 7.00 C 17852 6.00 H 27864 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: 12.00 Conformation dependent library (CDL) restraints added in 3.7 seconds 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6648 Finding SS restraints... Secondary structure from input PDB file: 208 helices and 47 sheets defined 54.7% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.98 Creating SS restraints... Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 78 through 93 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.918A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 171 through 175 Processing helix chain 'A' and resid 184 through 195 removed outlier: 4.214A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 217 removed outlier: 3.610A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 260 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 261 through 262 No H-bonds generated for 'chain 'A' and resid 261 through 262' Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 282 Processing helix chain 'A' and resid 286 through 295 removed outlier: 4.592A pdb=" N LYS A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.286A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 319 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.912A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 373 removed outlier: 3.579A pdb=" N LYS A 373 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.913A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.521A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 205 through 217 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 263 Proline residue: B 258 - end of helix removed outlier: 4.700A pdb=" N LEU B 261 " --> pdb=" O CYS B 257 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N PHE B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 285 Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 349 through 355 removed outlier: 4.219A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 3.910A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.815A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.690A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.629A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 263 removed outlier: 3.513A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Proline residue: C 258 - end of helix removed outlier: 4.599A pdb=" N LEU C 261 " --> pdb=" O CYS C 257 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 268 Processing helix chain 'C' and resid 273 through 285 Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 353 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 4.008A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 93 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.797A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.751A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.611A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 257 Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 285 Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 350 through 356 removed outlier: 4.503A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TRP D 356 " --> pdb=" O GLN D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 368 through 374 removed outlier: 3.902A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 93 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.667A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.562A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.564A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 260 Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 261 through 262 No H-bonds generated for 'chain 'E' and resid 261 through 262' Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 289 through 295 Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 337 through 349 Processing helix chain 'E' and resid 350 through 353 Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 368 through 374 removed outlier: 4.021A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 78 through 93 Processing helix chain 'F' and resid 97 through 101 Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.668A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 146 Processing helix chain 'F' and resid 172 through 175 Processing helix chain 'F' and resid 181 through 194 removed outlier: 3.628A pdb=" N THR F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 197 No H-bonds generated for 'chain 'F' and resid 195 through 197' Processing helix chain 'F' and resid 202 through 217 removed outlier: 3.605A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 233 Processing helix chain 'F' and resid 252 through 257 Processing helix chain 'F' and resid 258 through 262 Processing helix chain 'F' and resid 263 through 268 Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 289 through 295 removed outlier: 3.529A pdb=" N ALA F 295 " --> pdb=" O LYS F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 305 Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 337 through 348 Processing helix chain 'F' and resid 349 through 355 removed outlier: 4.201A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 368 through 374 removed outlier: 3.930A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 61 Processing helix chain 'G' and resid 78 through 92 Processing helix chain 'G' and resid 97 through 101 Processing helix chain 'G' and resid 112 through 126 removed outlier: 3.759A pdb=" N ARG G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 146 Processing helix chain 'G' and resid 172 through 175 Processing helix chain 'G' and resid 181 through 194 removed outlier: 3.724A pdb=" N THR G 194 " --> pdb=" O MET G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 202 through 217 removed outlier: 3.502A pdb=" N GLU G 207 " --> pdb=" O THR G 203 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE G 208 " --> pdb=" O ALA G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 233 Processing helix chain 'G' and resid 252 through 260 Proline residue: G 258 - end of helix Processing helix chain 'G' and resid 261 through 262 No H-bonds generated for 'chain 'G' and resid 261 through 262' Processing helix chain 'G' and resid 263 through 268 Processing helix chain 'G' and resid 273 through 285 Processing helix chain 'G' and resid 289 through 295 Processing helix chain 'G' and resid 301 through 305 Processing helix chain 'G' and resid 308 through 321 Processing helix chain 'G' and resid 337 through 348 Processing helix chain 'G' and resid 349 through 355 removed outlier: 4.177A pdb=" N GLN G 354 " --> pdb=" O THR G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 366 Processing helix chain 'G' and resid 369 through 374 Processing helix chain 'H' and resid 55 through 61 Processing helix chain 'H' and resid 78 through 92 Processing helix chain 'H' and resid 112 through 126 removed outlier: 3.772A pdb=" N ARG H 116 " --> pdb=" O PRO H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 146 Processing helix chain 'H' and resid 172 through 175 Processing helix chain 'H' and resid 181 through 194 removed outlier: 3.699A pdb=" N THR H 194 " --> pdb=" O MET H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 197 No H-bonds generated for 'chain 'H' and resid 195 through 197' Processing helix chain 'H' and resid 202 through 217 removed outlier: 3.536A pdb=" N ILE H 208 " --> pdb=" O ALA H 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 233 Processing helix chain 'H' and resid 252 through 260 Proline residue: H 258 - end of helix Processing helix chain 'H' and resid 261 through 262 No H-bonds generated for 'chain 'H' and resid 261 through 262' Processing helix chain 'H' and resid 263 through 268 Processing helix chain 'H' and resid 273 through 284 Processing helix chain 'H' and resid 286 through 295 removed outlier: 4.556A pdb=" N LYS H 291 " --> pdb=" O ILE H 287 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ASP H 292 " --> pdb=" O ASP H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 305 Processing helix chain 'H' and resid 308 through 321 Processing helix chain 'H' and resid 337 through 348 Processing helix chain 'H' and resid 350 through 355 removed outlier: 3.866A pdb=" N GLN H 354 " --> pdb=" O THR H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 366 Processing helix chain 'H' and resid 368 through 374 removed outlier: 4.002A pdb=" N ARG H 372 " --> pdb=" O SER H 368 " (cutoff:3.500A) Processing helix chain 'K' and resid 525 through 529 Processing helix chain 'K' and resid 531 through 536 Processing helix chain 'K' and resid 541 through 554 Processing helix chain 'K' and resid 561 through 576 Processing helix chain 'K' and resid 579 through 590 Processing helix chain 'K' and resid 592 through 595 Processing helix chain 'K' and resid 596 through 612 Processing helix chain 'K' and resid 615 through 631 Processing helix chain 'K' and resid 635 through 639 Processing helix chain 'K' and resid 640 through 651 Processing helix chain 'K' and resid 654 through 658 Processing helix chain 'L' and resid 523 through 529 removed outlier: 4.136A pdb=" N SER L 527 " --> pdb=" O SER L 524 " (cutoff:3.500A) Processing helix chain 'L' and resid 531 through 536 removed outlier: 3.585A pdb=" N HIS L 536 " --> pdb=" O VAL L 532 " (cutoff:3.500A) Processing helix chain 'L' and resid 541 through 554 Processing helix chain 'L' and resid 561 through 576 Processing helix chain 'L' and resid 579 through 591 Processing helix chain 'L' and resid 592 through 595 Processing helix chain 'L' and resid 596 through 612 Processing helix chain 'L' and resid 615 through 631 Processing helix chain 'L' and resid 635 through 639 Processing helix chain 'L' and resid 640 through 651 Processing helix chain 'L' and resid 654 through 658 Processing helix chain 'M' and resid 525 through 529 Processing helix chain 'M' and resid 531 through 536 removed outlier: 3.609A pdb=" N HIS M 536 " --> pdb=" O VAL M 532 " (cutoff:3.500A) Processing helix chain 'M' and resid 541 through 554 Processing helix chain 'M' and resid 561 through 576 Processing helix chain 'M' and resid 579 through 590 Processing helix chain 'M' and resid 592 through 595 Processing helix chain 'M' and resid 596 through 612 Processing helix chain 'M' and resid 615 through 631 Processing helix chain 'M' and resid 635 through 639 Processing helix chain 'M' and resid 640 through 651 Processing helix chain 'M' and resid 654 through 659 Processing helix chain 'N' and resid 525 through 529 Processing helix chain 'N' and resid 531 through 536 removed outlier: 3.552A pdb=" N HIS N 536 " --> pdb=" O VAL N 532 " (cutoff:3.500A) Processing helix chain 'N' and resid 541 through 554 Processing helix chain 'N' and resid 561 through 576 Processing helix chain 'N' and resid 579 through 592 removed outlier: 4.172A pdb=" N ASP N 592 " --> pdb=" O ALA N 588 " (cutoff:3.500A) Processing helix chain 'N' and resid 593 through 595 No H-bonds generated for 'chain 'N' and resid 593 through 595' Processing helix chain 'N' and resid 596 through 612 Processing helix chain 'N' and resid 615 through 631 Processing helix chain 'N' and resid 635 through 639 Processing helix chain 'N' and resid 640 through 651 Processing helix chain 'N' and resid 654 through 658 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA3, first strand: chain 'A' and resid 103 through 107 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 removed outlier: 3.513A pdb=" N VAL A 152 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.606A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA9, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.431A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB3, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.279A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB5, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB6, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.459A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB9, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.556A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC2, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC3, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.428A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC6, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.610A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC8, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AC9, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.378A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AD3, first strand: chain 'F' and resid 29 through 32 removed outlier: 6.642A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD5, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AD6, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AD7, first strand: chain 'F' and resid 169 through 170 removed outlier: 6.370A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AD9, first strand: chain 'G' and resid 29 through 32 removed outlier: 6.707A pdb=" N LEU G 8 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N THR G 106 " --> pdb=" O LEU G 8 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N CYS G 10 " --> pdb=" O THR G 106 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AE2, first strand: chain 'G' and resid 71 through 72 Processing sheet with id=AE3, first strand: chain 'G' and resid 169 through 170 Processing sheet with id=AE4, first strand: chain 'G' and resid 169 through 170 removed outlier: 6.351A pdb=" N ASN G 297 " --> pdb=" O ILE G 330 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 238 through 241 Processing sheet with id=AE6, first strand: chain 'H' and resid 29 through 32 removed outlier: 3.518A pdb=" N PHE H 31 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU H 8 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N THR H 106 " --> pdb=" O LEU H 8 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N CYS H 10 " --> pdb=" O THR H 106 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AE8, first strand: chain 'H' and resid 71 through 72 Processing sheet with id=AE9, first strand: chain 'H' and resid 169 through 170 Processing sheet with id=AF1, first strand: chain 'H' and resid 169 through 170 removed outlier: 6.399A pdb=" N ASN H 297 " --> pdb=" O ILE H 330 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 238 through 241 1478 hydrogen bonds defined for protein. 3825 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: 24.00 Time building geometry restraints manager: 14.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 27756 1.03 - 1.23: 111 1.23 - 1.42: 11861 1.42 - 1.62: 16724 1.62 - 1.81: 324 Bond restraints: 56776 Sorted by residual: bond pdb=" CE1 HIC G 73 " pdb=" HE1 HIC G 73 " ideal model delta sigma weight residual 0.930 1.096 -0.166 2.00e-02 2.50e+03 6.86e+01 bond pdb=" CE1 HIC B 73 " pdb=" HE1 HIC B 73 " ideal model delta sigma weight residual 0.930 1.096 -0.166 2.00e-02 2.50e+03 6.85e+01 bond pdb=" CE1 HIC H 73 " pdb=" HE1 HIC H 73 " ideal model delta sigma weight residual 0.930 1.095 -0.165 2.00e-02 2.50e+03 6.83e+01 bond pdb=" CE1 HIC A 73 " pdb=" HE1 HIC A 73 " ideal model delta sigma weight residual 0.930 1.095 -0.165 2.00e-02 2.50e+03 6.83e+01 bond pdb=" CE1 HIC F 73 " pdb=" HE1 HIC F 73 " ideal model delta sigma weight residual 0.930 1.095 -0.165 2.00e-02 2.50e+03 6.81e+01 ... (remaining 56771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 100745 1.51 - 3.01: 1600 3.01 - 4.52: 288 4.52 - 6.03: 61 6.03 - 7.53: 10 Bond angle restraints: 102704 Sorted by residual: angle pdb=" C LYS M 636 " pdb=" CA LYS M 636 " pdb=" CB LYS M 636 " ideal model delta sigma weight residual 117.23 111.04 6.19 1.36e+00 5.41e-01 2.07e+01 angle pdb=" C LYS N 636 " pdb=" CA LYS N 636 " pdb=" CB LYS N 636 " ideal model delta sigma weight residual 117.23 111.20 6.03 1.36e+00 5.41e-01 1.97e+01 angle pdb=" C GLY B 42 " pdb=" N VAL B 43 " pdb=" CA VAL B 43 " ideal model delta sigma weight residual 121.70 129.23 -7.53 1.80e+00 3.09e-01 1.75e+01 angle pdb=" C GLY C 42 " pdb=" N VAL C 43 " pdb=" CA VAL C 43 " ideal model delta sigma weight residual 121.70 129.21 -7.51 1.80e+00 3.09e-01 1.74e+01 angle pdb=" C GLY F 42 " pdb=" N VAL F 43 " pdb=" CA VAL F 43 " ideal model delta sigma weight residual 121.70 128.91 -7.21 1.80e+00 3.09e-01 1.60e+01 ... (remaining 102699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.08: 24538 21.08 - 42.17: 1586 42.17 - 63.25: 542 63.25 - 84.33: 64 84.33 - 105.42: 26 Dihedral angle restraints: 26756 sinusoidal: 14728 harmonic: 12028 Sorted by residual: dihedral pdb=" CA VAL A 9 " pdb=" C VAL A 9 " pdb=" N CYS A 10 " pdb=" CA CYS A 10 " ideal model delta harmonic sigma weight residual -180.00 -150.31 -29.69 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" C5' ADP E 802 " pdb=" O5' ADP E 802 " pdb=" PA ADP E 802 " pdb=" O2A ADP E 802 " ideal model delta sinusoidal sigma weight residual -60.00 45.42 -105.42 1 2.00e+01 2.50e-03 3.04e+01 dihedral pdb=" CA CYS A 10 " pdb=" C CYS A 10 " pdb=" N ASP A 11 " pdb=" CA ASP A 11 " ideal model delta harmonic sigma weight residual 180.00 152.50 27.50 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 26753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2718 0.030 - 0.061: 1109 0.061 - 0.091: 228 0.091 - 0.121: 269 0.121 - 0.151: 20 Chirality restraints: 4344 Sorted by residual: chirality pdb=" CA ILE A 165 " pdb=" N ILE A 165 " pdb=" C ILE A 165 " pdb=" CB ILE A 165 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.72e-01 chirality pdb=" CA ILE E 357 " pdb=" N ILE E 357 " pdb=" C ILE E 357 " pdb=" CB ILE E 357 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA ILE H 357 " pdb=" N ILE H 357 " pdb=" C ILE H 357 " pdb=" CB ILE H 357 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 4341 not shown) Planarity restraints: 8400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP K 592 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.31e+00 pdb=" CG ASP K 592 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASP K 592 " 0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP K 592 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 95 " 0.151 9.50e-02 1.11e+02 5.07e-02 3.19e+00 pdb=" NE ARG D 95 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG D 95 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG D 95 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 95 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG D 95 " -0.006 2.00e-02 2.50e+03 pdb="HH12 ARG D 95 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG D 95 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG D 95 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 566 " 0.148 9.50e-02 1.11e+02 4.97e-02 3.10e+00 pdb=" NE ARG L 566 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG L 566 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG L 566 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG L 566 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG L 566 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG L 566 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG L 566 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG L 566 " -0.001 2.00e-02 2.50e+03 ... (remaining 8397 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.08: 1093 2.08 - 2.71: 94425 2.71 - 3.34: 172898 3.34 - 3.97: 227316 3.97 - 4.60: 352995 Nonbonded interactions: 848727 Sorted by model distance: nonbonded pdb=" OE1 GLN H 49 " pdb=" H GLN H 49 " model vdw 1.456 2.450 nonbonded pdb=" O GLY A 168 " pdb=" H VAL C 43 " model vdw 1.541 2.450 nonbonded pdb=" OE1 GLU M 598 " pdb=" H GLU M 598 " model vdw 1.550 2.450 nonbonded pdb=" HZ2 LYS C 213 " pdb=" O2' ADP C 401 " model vdw 1.568 2.450 nonbonded pdb=" HZ1 LYS E 213 " pdb=" O2' ADP E 802 " model vdw 1.573 2.450 ... (remaining 848722 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 'A' and resid 6 through 375) selection = (chain 'B' and resid 6 through 375) selection = (chain 'C' and resid 6 through 375) selection = (chain 'D' and resid 6 through 375) selection = (chain 'E' and resid 6 through 375) selection = (chain 'F' and resid 6 through 375) selection = (chain 'G' and resid 6 through 375) selection = (chain 'H' and resid 6 through 375) } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 0.010 Normalize map: mean=0, sd=1: 5.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.720 Extract box with map and model: 1.640 Check model and map are aligned: 0.310 Set scattering table: 0.390 Process input model: 99.540 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.260 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:12.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 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 : 0.004 0.060 28912 Z= 0.226 Angle : 0.585 7.535 39208 Z= 0.296 Chirality : 0.041 0.151 4344 Planarity : 0.003 0.066 5016 Dihedral : 15.853 105.415 10780 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.32 % Favored : 97.60 % Rotamer: Outliers : 0.89 % Allowed : 11.69 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: 1.30 (0.15), residues: 3536 helix: 0.92 (0.14), residues: 1580 sheet: -0.31 (0.26), residues: 360 loop : 1.38 (0.17), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 340 HIS 0.006 0.001 HIS A 40 PHE 0.010 0.001 PHE A 255 TYR 0.009 0.001 TYR C 143 ARG 0.010 0.000 ARG L 566 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 497 time to evaluate : 3.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.1178 (tpt) cc_final: 0.0666 (tpt) REVERT: A 81 ASP cc_start: 0.7955 (m-30) cc_final: 0.7596 (m-30) REVERT: A 157 ASP cc_start: 0.7867 (t70) cc_final: 0.7054 (t0) REVERT: A 190 MET cc_start: 0.8114 (ptp) cc_final: 0.7823 (ptp) REVERT: A 191 LYS cc_start: 0.7683 (tttp) cc_final: 0.7371 (tttp) REVERT: A 205 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7257 (mt-10) REVERT: A 224 GLU cc_start: 0.7533 (mm-30) cc_final: 0.6595 (mp0) REVERT: A 227 MET cc_start: 0.8050 (mmt) cc_final: 0.7474 (mmm) REVERT: A 291 LYS cc_start: 0.8235 (ttpp) cc_final: 0.7864 (ttmm) REVERT: A 334 GLU cc_start: 0.6736 (pm20) cc_final: 0.6129 (pp20) REVERT: A 357 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7838 (mt) REVERT: B 95 ARG cc_start: 0.6926 (mtt-85) cc_final: 0.6710 (mtt-85) REVERT: B 187 ASP cc_start: 0.8132 (m-30) cc_final: 0.7732 (m-30) REVERT: B 191 LYS cc_start: 0.7881 (tmtt) cc_final: 0.7362 (tttm) REVERT: B 241 GLU cc_start: 0.7884 (tt0) cc_final: 0.7633 (tt0) REVERT: B 283 MET cc_start: 0.8577 (mmm) cc_final: 0.8285 (mmm) REVERT: B 297 ASN cc_start: 0.8959 (m110) cc_final: 0.8747 (m110) REVERT: B 328 LYS cc_start: 0.8033 (tttp) cc_final: 0.7710 (ttpp) REVERT: B 372 ARG cc_start: 0.6986 (mtm-85) cc_final: 0.6658 (mtm180) REVERT: C 24 ASP cc_start: 0.7898 (m-30) cc_final: 0.7660 (m-30) REVERT: C 25 ASP cc_start: 0.7508 (p0) cc_final: 0.7119 (p0) REVERT: C 68 LYS cc_start: 0.7919 (mttm) cc_final: 0.7718 (mtmt) REVERT: C 72 GLU cc_start: 0.7351 (tt0) cc_final: 0.7130 (mt-10) REVERT: C 83 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7564 (tt0) REVERT: C 190 MET cc_start: 0.7976 (ptm) cc_final: 0.7724 (mtp) REVERT: C 276 GLU cc_start: 0.7723 (tt0) cc_final: 0.7266 (mt-10) REVERT: C 284 LYS cc_start: 0.8079 (mttt) cc_final: 0.7736 (mttm) REVERT: C 334 GLU cc_start: 0.7053 (pm20) cc_final: 0.6703 (pm20) REVERT: C 359 LYS cc_start: 0.7689 (tptm) cc_final: 0.7379 (tptt) REVERT: C 360 GLN cc_start: 0.6620 (tm-30) cc_final: 0.6402 (tt0) REVERT: C 363 ASP cc_start: 0.7033 (m-30) cc_final: 0.6806 (m-30) REVERT: D 72 GLU cc_start: 0.7423 (pt0) cc_final: 0.7137 (mt-10) REVERT: D 95 ARG cc_start: 0.7289 (mtt-85) cc_final: 0.6766 (mmt90) REVERT: D 206 ARG cc_start: 0.7746 (ttm-80) cc_final: 0.7525 (ttm110) REVERT: D 225 ASN cc_start: 0.6984 (m-40) cc_final: 0.6728 (t0) REVERT: D 276 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7464 (mt-10) REVERT: D 298 VAL cc_start: 0.8056 (OUTLIER) cc_final: 0.7736 (t) REVERT: E 95 ARG cc_start: 0.7132 (mtm-85) cc_final: 0.6578 (mmt90) REVERT: E 128 ASN cc_start: 0.7339 (m110) cc_final: 0.6501 (t0) REVERT: E 178 LEU cc_start: 0.7574 (tp) cc_final: 0.7312 (tp) REVERT: E 191 LYS cc_start: 0.8039 (tttm) cc_final: 0.7198 (tttt) REVERT: E 299 MET cc_start: 0.8798 (mmm) cc_final: 0.8560 (mtp) REVERT: E 328 LYS cc_start: 0.7908 (tttt) cc_final: 0.7114 (mttp) REVERT: E 334 GLU cc_start: 0.7319 (pm20) cc_final: 0.7021 (pm20) REVERT: E 360 GLN cc_start: 0.7336 (tt0) cc_final: 0.6430 (pm20) REVERT: F 49 GLN cc_start: 0.6839 (mt0) cc_final: 0.6581 (mm110) REVERT: F 51 ASP cc_start: 0.7302 (p0) cc_final: 0.7073 (p0) REVERT: F 61 LYS cc_start: 0.7822 (mttm) cc_final: 0.7616 (mtmm) REVERT: F 72 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7169 (mm-30) REVERT: F 80 ASP cc_start: 0.7847 (m-30) cc_final: 0.7400 (m-30) REVERT: F 95 ARG cc_start: 0.7067 (mtp85) cc_final: 0.6654 (mtt-85) REVERT: F 125 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7242 (mm-30) REVERT: F 162 ASN cc_start: 0.8354 (m110) cc_final: 0.8009 (m110) REVERT: F 167 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8209 (mm-30) REVERT: F 206 ARG cc_start: 0.7589 (ttm110) cc_final: 0.7257 (ttm110) REVERT: F 226 GLU cc_start: 0.7864 (tp30) cc_final: 0.7581 (tp30) REVERT: F 326 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.6652 (ptmm) REVERT: F 328 LYS cc_start: 0.8205 (tttp) cc_final: 0.7747 (tptm) REVERT: F 334 GLU cc_start: 0.7042 (pm20) cc_final: 0.6700 (pm20) REVERT: F 354 GLN cc_start: 0.7645 (mm-40) cc_final: 0.7440 (mm110) REVERT: F 358 THR cc_start: 0.7786 (m) cc_final: 0.7103 (p) REVERT: G 25 ASP cc_start: 0.7131 (p0) cc_final: 0.6814 (m-30) REVERT: G 95 ARG cc_start: 0.7295 (mtt-85) cc_final: 0.6933 (mtm110) REVERT: G 118 LYS cc_start: 0.7834 (mmmt) cc_final: 0.7340 (mmmm) REVERT: G 190 MET cc_start: 0.8611 (mtp) cc_final: 0.8341 (ttm) REVERT: G 224 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7192 (mm-30) REVERT: G 227 MET cc_start: 0.7977 (mmm) cc_final: 0.7704 (mmm) REVERT: G 246 GLN cc_start: 0.7923 (mt0) cc_final: 0.7386 (mt0) REVERT: G 292 ASP cc_start: 0.8053 (m-30) cc_final: 0.7780 (m-30) REVERT: G 326 LYS cc_start: 0.7596 (mmtm) cc_final: 0.6929 (mmtp) REVERT: G 355 MET cc_start: 0.8307 (mmm) cc_final: 0.7806 (mtt) REVERT: H 24 ASP cc_start: 0.6798 (m-30) cc_final: 0.6458 (m-30) REVERT: H 25 ASP cc_start: 0.6633 (p0) cc_final: 0.6329 (p0) REVERT: H 68 LYS cc_start: 0.8268 (mmtm) cc_final: 0.7982 (mptt) REVERT: H 72 GLU cc_start: 0.7408 (tt0) cc_final: 0.7034 (mt-10) REVERT: H 93 GLU cc_start: 0.7391 (mm-30) cc_final: 0.7164 (mm-30) REVERT: H 113 LYS cc_start: 0.5103 (mptt) cc_final: 0.4154 (mmtm) REVERT: H 117 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7133 (mt-10) REVERT: H 167 GLU cc_start: 0.7653 (mp0) cc_final: 0.7439 (mm-30) REVERT: H 206 ARG cc_start: 0.7789 (ttm110) cc_final: 0.7355 (ttp-110) REVERT: H 226 GLU cc_start: 0.7911 (tp30) cc_final: 0.7670 (tp30) REVERT: H 286 ASP cc_start: 0.6402 (m-30) cc_final: 0.6010 (m-30) REVERT: H 292 ASP cc_start: 0.7820 (m-30) cc_final: 0.7574 (m-30) REVERT: H 299 MET cc_start: 0.8344 (mtp) cc_final: 0.8129 (mmm) REVERT: H 305 MET cc_start: 0.8212 (mmm) cc_final: 0.7974 (tpp) REVERT: H 314 GLN cc_start: 0.7624 (tp40) cc_final: 0.7190 (tp40) REVERT: H 326 LYS cc_start: 0.7009 (mmpt) cc_final: 0.6707 (pttm) REVERT: H 328 LYS cc_start: 0.7681 (ttmt) cc_final: 0.7080 (tmtt) REVERT: H 336 LYS cc_start: 0.8128 (ttmt) cc_final: 0.7768 (tttt) REVERT: H 355 MET cc_start: 0.7649 (mpt) cc_final: 0.7436 (mpt) REVERT: H 360 GLN cc_start: 0.6652 (tm130) cc_final: 0.5990 (tp-100) REVERT: K 538 MET cc_start: 0.7860 (ttm) cc_final: 0.7454 (ttm) REVERT: K 578 ASN cc_start: 0.6340 (t0) cc_final: 0.6017 (t0) REVERT: K 595 LYS cc_start: 0.5970 (mmtp) cc_final: 0.5673 (mmtp) REVERT: K 598 GLU cc_start: 0.5788 (pm20) cc_final: 0.5172 (pt0) REVERT: K 603 MET cc_start: 0.7304 (tpt) cc_final: 0.7078 (tpt) REVERT: K 617 GLU cc_start: 0.6685 (mp0) cc_final: 0.6466 (mt-10) REVERT: K 621 GLU cc_start: 0.7340 (tt0) cc_final: 0.6851 (mt-10) REVERT: K 629 GLU cc_start: 0.7384 (mm-30) cc_final: 0.6941 (mm-30) REVERT: K 664 SER cc_start: 0.6627 (t) cc_final: 0.6201 (p) REVERT: L 574 GLU cc_start: 0.7166 (tm-30) cc_final: 0.6962 (tm-30) REVERT: L 578 ASN cc_start: 0.7245 (p0) cc_final: 0.7044 (p0) REVERT: L 582 LYS cc_start: 0.6423 (mtpt) cc_final: 0.5931 (mmtp) REVERT: L 604 GLU cc_start: 0.6593 (mm-30) cc_final: 0.5893 (tp30) REVERT: L 608 GLU cc_start: 0.6889 (tp30) cc_final: 0.6679 (mm-30) REVERT: L 629 GLU cc_start: 0.7344 (mm-30) cc_final: 0.7121 (mp0) REVERT: M 527 SER cc_start: 0.8179 (m) cc_final: 0.7819 (p) REVERT: M 533 THR cc_start: 0.8034 (m) cc_final: 0.7657 (p) REVERT: M 541 ASP cc_start: 0.7512 (t0) cc_final: 0.6764 (t0) REVERT: M 557 ASP cc_start: 0.7118 (t0) cc_final: 0.6590 (t70) REVERT: M 604 GLU cc_start: 0.6541 (mm-30) cc_final: 0.6167 (tt0) REVERT: M 634 ARG cc_start: 0.6812 (ttp80) cc_final: 0.6436 (ttp-110) REVERT: M 644 SER cc_start: 0.7029 (p) cc_final: 0.6789 (m) REVERT: M 664 SER cc_start: 0.5236 (t) cc_final: 0.4871 (t) REVERT: M 665 TYR cc_start: 0.6146 (m-80) cc_final: 0.5758 (m-80) REVERT: N 521 LYS cc_start: 0.7030 (ttpp) cc_final: 0.6694 (tttp) REVERT: N 544 GLU cc_start: 0.6942 (mm-30) cc_final: 0.6582 (tp30) REVERT: N 557 ASP cc_start: 0.6732 (t0) cc_final: 0.6476 (t70) REVERT: N 574 GLU cc_start: 0.6888 (tt0) cc_final: 0.6605 (tt0) REVERT: N 603 MET cc_start: 0.6173 (tpt) cc_final: 0.5584 (tpt) REVERT: N 621 GLU cc_start: 0.6737 (mt-10) cc_final: 0.6421 (mt-10) REVERT: N 663 GLU cc_start: 0.5069 (tp30) cc_final: 0.4710 (tp30) outliers start: 27 outliers final: 22 residues processed: 519 average time/residue: 2.8806 time to fit residues: 1731.6238 Evaluate side-chains 389 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 364 time to evaluate : 3.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 326 LYS Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain K residue 642 VAL Chi-restraints excluded: chain N residue 666 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 2.9990 chunk 269 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 279 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 323 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN B 297 ASN D 246 GLN F 297 ASN G 49 GLN G 225 ASN G 360 GLN H 128 ASN K 645 ASN M 589 GLN M 625 GLN N 589 GLN N 612 HIS N 645 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 28912 Z= 0.402 Angle : 0.711 7.936 39208 Z= 0.368 Chirality : 0.048 0.182 4344 Planarity : 0.005 0.072 5016 Dihedral : 8.483 117.559 4036 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.05 % Favored : 96.89 % Rotamer: Outliers : 2.87 % Allowed : 12.15 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: 0.75 (0.14), residues: 3536 helix: 0.47 (0.13), residues: 1600 sheet: -0.59 (0.22), residues: 480 loop : 1.25 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP E 340 HIS 0.007 0.002 HIS G 161 PHE 0.022 0.002 PHE B 266 TYR 0.014 0.002 TYR L 665 ARG 0.009 0.001 ARG C 335 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 354 time to evaluate : 3.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8124 (m-30) cc_final: 0.7717 (m-30) REVERT: A 190 MET cc_start: 0.7885 (ptp) cc_final: 0.7633 (ptm) REVERT: A 191 LYS cc_start: 0.7645 (tttp) cc_final: 0.7333 (ttpp) REVERT: A 224 GLU cc_start: 0.7499 (mm-30) cc_final: 0.6688 (mm-30) REVERT: A 227 MET cc_start: 0.8102 (mmt) cc_final: 0.7506 (mmm) REVERT: A 291 LYS cc_start: 0.7992 (ttpp) cc_final: 0.7650 (ttmm) REVERT: A 299 MET cc_start: 0.8371 (mmt) cc_final: 0.7968 (mtp) REVERT: A 334 GLU cc_start: 0.6809 (pm20) cc_final: 0.6166 (pp20) REVERT: A 357 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7807 (mt) REVERT: B 47 MET cc_start: 0.1646 (OUTLIER) cc_final: 0.0471 (ptm) REVERT: B 95 ARG cc_start: 0.6952 (mtt-85) cc_final: 0.6661 (mtt-85) REVERT: B 187 ASP cc_start: 0.8093 (m-30) cc_final: 0.7715 (m-30) REVERT: B 283 MET cc_start: 0.8541 (mmm) cc_final: 0.8262 (mmm) REVERT: B 328 LYS cc_start: 0.8061 (tttp) cc_final: 0.7761 (ttpp) REVERT: B 372 ARG cc_start: 0.7112 (mtm-85) cc_final: 0.6803 (mtm180) REVERT: C 24 ASP cc_start: 0.7836 (m-30) cc_final: 0.7571 (m-30) REVERT: C 25 ASP cc_start: 0.7568 (p0) cc_final: 0.7133 (p0) REVERT: C 68 LYS cc_start: 0.8018 (mttm) cc_final: 0.7634 (mtmt) REVERT: C 83 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7536 (tt0) REVERT: C 99 GLU cc_start: 0.7408 (pm20) cc_final: 0.7114 (pm20) REVERT: C 276 GLU cc_start: 0.7809 (tt0) cc_final: 0.7316 (mt-10) REVERT: C 328 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7318 (ttmm) REVERT: C 334 GLU cc_start: 0.7221 (pm20) cc_final: 0.6939 (pm20) REVERT: C 355 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7425 (mmt) REVERT: C 359 LYS cc_start: 0.7666 (tptm) cc_final: 0.7358 (tptt) REVERT: C 363 ASP cc_start: 0.7014 (m-30) cc_final: 0.6811 (m-30) REVERT: D 72 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7062 (mt-10) REVERT: D 84 LYS cc_start: 0.8161 (ptpp) cc_final: 0.7957 (ptpp) REVERT: D 95 ARG cc_start: 0.7470 (mtt-85) cc_final: 0.6911 (mmt90) REVERT: D 107 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8118 (tt0) REVERT: D 206 ARG cc_start: 0.7706 (ttm-80) cc_final: 0.7485 (ttm110) REVERT: D 276 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7590 (tt0) REVERT: E 72 GLU cc_start: 0.7564 (mt-10) cc_final: 0.6985 (tt0) REVERT: E 95 ARG cc_start: 0.7117 (mtm-85) cc_final: 0.6575 (mmt90) REVERT: E 128 ASN cc_start: 0.7456 (m110) cc_final: 0.6546 (t0) REVERT: E 178 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7720 (tp) REVERT: E 241 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7790 (tt0) REVERT: E 328 LYS cc_start: 0.7933 (tttt) cc_final: 0.7147 (mttp) REVERT: E 334 GLU cc_start: 0.7568 (pm20) cc_final: 0.7208 (pm20) REVERT: E 360 GLN cc_start: 0.7191 (tt0) cc_final: 0.6556 (pm20) REVERT: F 49 GLN cc_start: 0.6790 (mt0) cc_final: 0.6512 (mm110) REVERT: F 51 ASP cc_start: 0.7307 (p0) cc_final: 0.7079 (p0) REVERT: F 72 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7148 (mm-30) REVERT: F 80 ASP cc_start: 0.7754 (m-30) cc_final: 0.7360 (m-30) REVERT: F 95 ARG cc_start: 0.7098 (mtp85) cc_final: 0.6630 (mtt-85) REVERT: F 125 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7223 (mm-30) REVERT: F 162 ASN cc_start: 0.8323 (m110) cc_final: 0.8065 (m110) REVERT: F 167 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8201 (mm-30) REVERT: F 206 ARG cc_start: 0.7656 (ttm110) cc_final: 0.7200 (ttm110) REVERT: F 226 GLU cc_start: 0.7800 (tp30) cc_final: 0.7472 (tp30) REVERT: F 326 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.6613 (ptmm) REVERT: F 328 LYS cc_start: 0.8136 (tttp) cc_final: 0.7705 (tptm) REVERT: F 334 GLU cc_start: 0.7353 (pm20) cc_final: 0.7079 (pm20) REVERT: F 354 GLN cc_start: 0.7629 (mm-40) cc_final: 0.7382 (mm110) REVERT: F 355 MET cc_start: 0.8151 (mtt) cc_final: 0.7767 (mtp) REVERT: F 358 THR cc_start: 0.7997 (m) cc_final: 0.7554 (p) REVERT: F 363 ASP cc_start: 0.7531 (m-30) cc_final: 0.7222 (m-30) REVERT: G 25 ASP cc_start: 0.6906 (p0) cc_final: 0.6702 (m-30) REVERT: G 95 ARG cc_start: 0.7361 (mtt-85) cc_final: 0.7006 (mtm110) REVERT: G 113 LYS cc_start: 0.8154 (mmtt) cc_final: 0.7713 (mmtp) REVERT: G 118 LYS cc_start: 0.7768 (mmmt) cc_final: 0.7308 (mmmm) REVERT: G 125 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7679 (mt-10) REVERT: G 283 MET cc_start: 0.8708 (mmm) cc_final: 0.8478 (mmm) REVERT: G 292 ASP cc_start: 0.8021 (m-30) cc_final: 0.7758 (m-30) REVERT: G 326 LYS cc_start: 0.7613 (mmtm) cc_final: 0.6974 (mmtp) REVERT: G 355 MET cc_start: 0.8025 (mmm) cc_final: 0.7805 (mtt) REVERT: H 24 ASP cc_start: 0.6683 (m-30) cc_final: 0.6345 (m-30) REVERT: H 25 ASP cc_start: 0.6741 (p0) cc_final: 0.6300 (p0) REVERT: H 68 LYS cc_start: 0.8272 (mmtm) cc_final: 0.7931 (mptt) REVERT: H 72 GLU cc_start: 0.7505 (tt0) cc_final: 0.7008 (mm-30) REVERT: H 93 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7231 (mm-30) REVERT: H 113 LYS cc_start: 0.5147 (OUTLIER) cc_final: 0.4697 (mppt) REVERT: H 167 GLU cc_start: 0.7781 (mp0) cc_final: 0.7549 (mm-30) REVERT: H 206 ARG cc_start: 0.7765 (ttm110) cc_final: 0.7290 (ttp-110) REVERT: H 276 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7388 (mt-10) REVERT: H 286 ASP cc_start: 0.5915 (m-30) cc_final: 0.5499 (m-30) REVERT: H 299 MET cc_start: 0.8487 (mtp) cc_final: 0.8240 (mmm) REVERT: H 314 GLN cc_start: 0.7749 (tp40) cc_final: 0.7192 (tp40) REVERT: H 326 LYS cc_start: 0.7138 (mmpt) cc_final: 0.6778 (pttm) REVERT: H 328 LYS cc_start: 0.7758 (ttmt) cc_final: 0.7148 (tmtt) REVERT: H 336 LYS cc_start: 0.8120 (ttmt) cc_final: 0.7741 (ttpt) REVERT: H 354 GLN cc_start: 0.7216 (OUTLIER) cc_final: 0.6957 (tp40) REVERT: K 578 ASN cc_start: 0.6554 (t0) cc_final: 0.6255 (t0) REVERT: K 595 LYS cc_start: 0.5985 (mmtp) cc_final: 0.5679 (mmtp) REVERT: K 598 GLU cc_start: 0.5974 (pm20) cc_final: 0.5312 (pt0) REVERT: K 603 MET cc_start: 0.7348 (tpt) cc_final: 0.7092 (tpt) REVERT: K 608 GLU cc_start: 0.6812 (mt-10) cc_final: 0.6196 (mm-30) REVERT: K 617 GLU cc_start: 0.6555 (mp0) cc_final: 0.6229 (mt-10) REVERT: K 621 GLU cc_start: 0.7357 (tt0) cc_final: 0.6892 (mt-10) REVERT: L 555 GLU cc_start: 0.7511 (tt0) cc_final: 0.7310 (tt0) REVERT: L 574 GLU cc_start: 0.7201 (tm-30) cc_final: 0.6580 (tp30) REVERT: L 582 LYS cc_start: 0.6385 (mtpt) cc_final: 0.5938 (mmtp) REVERT: L 595 LYS cc_start: 0.6528 (ptpt) cc_final: 0.6022 (mtmt) REVERT: L 604 GLU cc_start: 0.6592 (mm-30) cc_final: 0.6040 (tp30) REVERT: L 608 GLU cc_start: 0.6780 (tp30) cc_final: 0.6567 (mm-30) REVERT: L 629 GLU cc_start: 0.7279 (mm-30) cc_final: 0.7066 (mp0) REVERT: M 521 LYS cc_start: 0.6889 (tttp) cc_final: 0.6390 (tttm) REVERT: M 527 SER cc_start: 0.8024 (m) cc_final: 0.7754 (p) REVERT: M 533 THR cc_start: 0.8066 (OUTLIER) cc_final: 0.7676 (p) REVERT: M 541 ASP cc_start: 0.7298 (t0) cc_final: 0.6537 (t0) REVERT: M 604 GLU cc_start: 0.6505 (mm-30) cc_final: 0.6069 (tt0) REVERT: M 664 SER cc_start: 0.5099 (t) cc_final: 0.4828 (t) REVERT: M 665 TYR cc_start: 0.6230 (m-80) cc_final: 0.5974 (m-80) REVERT: N 528 THR cc_start: 0.8117 (OUTLIER) cc_final: 0.7767 (p) REVERT: N 543 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.6997 (ttt90) REVERT: N 544 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6469 (tp30) REVERT: N 557 ASP cc_start: 0.6973 (t0) cc_final: 0.6717 (t70) REVERT: N 566 ARG cc_start: 0.6442 (ttt180) cc_final: 0.6164 (mtt180) REVERT: N 616 LYS cc_start: 0.7087 (ttpt) cc_final: 0.6708 (tttm) REVERT: N 663 GLU cc_start: 0.4992 (tp30) cc_final: 0.4728 (tp30) outliers start: 87 outliers final: 40 residues processed: 416 average time/residue: 2.6809 time to fit residues: 1303.5163 Evaluate side-chains 383 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 327 time to evaluate : 3.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 354 GLN Chi-restraints excluded: chain K residue 527 SER Chi-restraints excluded: chain K residue 642 VAL Chi-restraints excluded: chain K residue 655 SER Chi-restraints excluded: chain L residue 544 GLU Chi-restraints excluded: chain L residue 663 GLU Chi-restraints excluded: chain M residue 533 THR Chi-restraints excluded: chain M residue 559 SER Chi-restraints excluded: chain M residue 580 THR Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain N residue 528 THR Chi-restraints excluded: chain N residue 543 ARG Chi-restraints excluded: chain N residue 544 GLU Chi-restraints excluded: chain N residue 590 CYS Chi-restraints excluded: chain N residue 611 THR Chi-restraints excluded: chain N residue 666 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 179 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 269 optimal weight: 0.0870 chunk 220 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 323 optimal weight: 4.9990 chunk 349 optimal weight: 1.9990 chunk 288 optimal weight: 0.9980 chunk 321 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 259 optimal weight: 3.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN F 49 GLN G 225 ASN L 534 ASN M 589 GLN N 589 GLN N 645 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28912 Z= 0.227 Angle : 0.611 7.295 39208 Z= 0.307 Chirality : 0.044 0.173 4344 Planarity : 0.004 0.041 5016 Dihedral : 7.996 109.971 4024 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.57 % Favored : 97.37 % Rotamer: Outliers : 2.28 % Allowed : 12.75 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: 0.77 (0.14), residues: 3536 helix: 0.58 (0.13), residues: 1592 sheet: -0.53 (0.24), residues: 408 loop : 1.03 (0.17), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 79 HIS 0.007 0.001 HIS A 40 PHE 0.014 0.001 PHE K 568 TYR 0.009 0.001 TYR C 337 ARG 0.004 0.000 ARG G 335 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 343 time to evaluate : 3.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7755 (ptpp) cc_final: 0.7039 (mttp) REVERT: A 81 ASP cc_start: 0.8128 (m-30) cc_final: 0.7713 (m-30) REVERT: A 190 MET cc_start: 0.7834 (ptp) cc_final: 0.7555 (ptm) REVERT: A 191 LYS cc_start: 0.7607 (tttp) cc_final: 0.7323 (tttp) REVERT: A 224 GLU cc_start: 0.7499 (mm-30) cc_final: 0.6724 (tp30) REVERT: A 227 MET cc_start: 0.8037 (mmt) cc_final: 0.7393 (mmm) REVERT: A 288 ASP cc_start: 0.8174 (m-30) cc_final: 0.7967 (m-30) REVERT: A 291 LYS cc_start: 0.7973 (ttpp) cc_final: 0.7652 (ttmm) REVERT: A 299 MET cc_start: 0.8347 (mmt) cc_final: 0.7954 (mtp) REVERT: A 334 GLU cc_start: 0.6751 (pm20) cc_final: 0.6209 (pp20) REVERT: A 357 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7814 (mt) REVERT: A 360 GLN cc_start: 0.7047 (tt0) cc_final: 0.6621 (tt0) REVERT: B 47 MET cc_start: 0.1368 (OUTLIER) cc_final: 0.0932 (mmm) REVERT: B 187 ASP cc_start: 0.8006 (m-30) cc_final: 0.7600 (m-30) REVERT: B 283 MET cc_start: 0.8552 (mmm) cc_final: 0.8272 (mmm) REVERT: B 328 LYS cc_start: 0.8071 (tttp) cc_final: 0.7547 (mttp) REVERT: B 372 ARG cc_start: 0.7050 (mtm-85) cc_final: 0.6800 (mtm180) REVERT: C 24 ASP cc_start: 0.7850 (m-30) cc_final: 0.7570 (m-30) REVERT: C 25 ASP cc_start: 0.7453 (p0) cc_final: 0.7048 (p0) REVERT: C 68 LYS cc_start: 0.8029 (mttm) cc_final: 0.7653 (mtmt) REVERT: C 83 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7458 (tt0) REVERT: C 99 GLU cc_start: 0.7363 (pm20) cc_final: 0.7076 (pm20) REVERT: C 105 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7644 (mp) REVERT: C 276 GLU cc_start: 0.7818 (tt0) cc_final: 0.7328 (mt-10) REVERT: C 328 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7299 (ttmm) REVERT: C 334 GLU cc_start: 0.7255 (pm20) cc_final: 0.7037 (pm20) REVERT: C 355 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7482 (mmt) REVERT: C 359 LYS cc_start: 0.7773 (tptm) cc_final: 0.7443 (tptt) REVERT: C 363 ASP cc_start: 0.7072 (m-30) cc_final: 0.6827 (m-30) REVERT: D 72 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7049 (mt-10) REVERT: D 95 ARG cc_start: 0.7363 (mtt-85) cc_final: 0.6863 (mmt90) REVERT: D 206 ARG cc_start: 0.7685 (ttm-80) cc_final: 0.7482 (ttm110) REVERT: D 276 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7573 (mt-10) REVERT: E 72 GLU cc_start: 0.7555 (mt-10) cc_final: 0.6868 (tt0) REVERT: E 95 ARG cc_start: 0.7124 (mtm-85) cc_final: 0.6592 (mmt90) REVERT: E 128 ASN cc_start: 0.7428 (m110) cc_final: 0.6533 (t0) REVERT: E 241 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7714 (tt0) REVERT: E 328 LYS cc_start: 0.7930 (tttt) cc_final: 0.7139 (mttp) REVERT: E 360 GLN cc_start: 0.7280 (tt0) cc_final: 0.6636 (pm20) REVERT: F 51 ASP cc_start: 0.7287 (p0) cc_final: 0.7074 (p0) REVERT: F 72 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7095 (mm-30) REVERT: F 80 ASP cc_start: 0.7732 (m-30) cc_final: 0.7359 (m-30) REVERT: F 95 ARG cc_start: 0.7090 (mtp85) cc_final: 0.6619 (mtt-85) REVERT: F 125 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7242 (mm-30) REVERT: F 167 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8222 (mm-30) REVERT: F 191 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7717 (tmtt) REVERT: F 206 ARG cc_start: 0.7630 (ttm110) cc_final: 0.7115 (ttm110) REVERT: F 226 GLU cc_start: 0.7763 (tp30) cc_final: 0.7424 (tp30) REVERT: F 326 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.6619 (ptmm) REVERT: F 328 LYS cc_start: 0.8144 (tttp) cc_final: 0.7718 (tptm) REVERT: F 354 GLN cc_start: 0.7666 (mm-40) cc_final: 0.7405 (mm110) REVERT: F 358 THR cc_start: 0.7967 (m) cc_final: 0.7552 (p) REVERT: F 363 ASP cc_start: 0.7460 (m-30) cc_final: 0.7210 (m-30) REVERT: G 95 ARG cc_start: 0.7353 (mtt-85) cc_final: 0.6997 (mtm110) REVERT: G 113 LYS cc_start: 0.8052 (mmtt) cc_final: 0.7690 (mmtp) REVERT: G 117 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7587 (mt-10) REVERT: G 118 LYS cc_start: 0.7810 (mmmt) cc_final: 0.7250 (mmmm) REVERT: G 125 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7626 (mt-10) REVERT: G 269 MET cc_start: 0.8508 (mtp) cc_final: 0.8302 (mtt) REVERT: G 292 ASP cc_start: 0.7924 (m-30) cc_final: 0.7712 (m-30) REVERT: G 326 LYS cc_start: 0.7595 (mmtm) cc_final: 0.6978 (mmtp) REVERT: H 24 ASP cc_start: 0.6692 (m-30) cc_final: 0.6364 (m-30) REVERT: H 25 ASP cc_start: 0.6801 (p0) cc_final: 0.6358 (p0) REVERT: H 68 LYS cc_start: 0.8268 (mmtm) cc_final: 0.7936 (mptt) REVERT: H 72 GLU cc_start: 0.7431 (tt0) cc_final: 0.6925 (mt-10) REVERT: H 93 GLU cc_start: 0.7381 (mm-30) cc_final: 0.7180 (mm-30) REVERT: H 113 LYS cc_start: 0.5117 (OUTLIER) cc_final: 0.4665 (mppt) REVERT: H 167 GLU cc_start: 0.7815 (mp0) cc_final: 0.7540 (mm-30) REVERT: H 206 ARG cc_start: 0.7818 (ttm110) cc_final: 0.7374 (ttp-110) REVERT: H 276 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7439 (mt-10) REVERT: H 299 MET cc_start: 0.8443 (mtp) cc_final: 0.7957 (mmm) REVERT: H 314 GLN cc_start: 0.7748 (tp40) cc_final: 0.7212 (tp40) REVERT: H 326 LYS cc_start: 0.7054 (mmpt) cc_final: 0.6788 (pttm) REVERT: H 328 LYS cc_start: 0.7744 (ttmt) cc_final: 0.7137 (tmtt) REVERT: H 334 GLU cc_start: 0.7755 (pm20) cc_final: 0.6694 (tp30) REVERT: H 336 LYS cc_start: 0.8134 (ttmt) cc_final: 0.7808 (tttm) REVERT: H 354 GLN cc_start: 0.7141 (OUTLIER) cc_final: 0.6874 (tp40) REVERT: K 578 ASN cc_start: 0.6630 (t0) cc_final: 0.6334 (t0) REVERT: K 608 GLU cc_start: 0.6809 (mt-10) cc_final: 0.6193 (mm-30) REVERT: K 617 GLU cc_start: 0.6587 (mp0) cc_final: 0.6167 (mt-10) REVERT: K 621 GLU cc_start: 0.7400 (tt0) cc_final: 0.6890 (mt-10) REVERT: L 538 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7623 (mtp) REVERT: L 555 GLU cc_start: 0.7452 (tt0) cc_final: 0.7232 (tt0) REVERT: L 574 GLU cc_start: 0.7282 (tm-30) cc_final: 0.6637 (tp30) REVERT: L 582 LYS cc_start: 0.6394 (mtpt) cc_final: 0.6040 (mttt) REVERT: L 595 LYS cc_start: 0.6608 (ptpt) cc_final: 0.6105 (mtmt) REVERT: L 629 GLU cc_start: 0.7278 (mm-30) cc_final: 0.7006 (mp0) REVERT: M 521 LYS cc_start: 0.6821 (tttp) cc_final: 0.6269 (tttm) REVERT: M 527 SER cc_start: 0.7985 (m) cc_final: 0.7741 (p) REVERT: M 533 THR cc_start: 0.7990 (m) cc_final: 0.7630 (p) REVERT: M 541 ASP cc_start: 0.7291 (t0) cc_final: 0.6505 (t70) REVERT: M 604 GLU cc_start: 0.6464 (mm-30) cc_final: 0.5966 (tt0) REVERT: M 644 SER cc_start: 0.7158 (p) cc_final: 0.6904 (m) REVERT: M 664 SER cc_start: 0.5311 (t) cc_final: 0.5048 (t) REVERT: M 665 TYR cc_start: 0.6196 (m-80) cc_final: 0.5945 (m-80) REVERT: N 528 THR cc_start: 0.8167 (OUTLIER) cc_final: 0.7861 (p) REVERT: N 543 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.6977 (ttt90) REVERT: N 544 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6486 (tp30) REVERT: N 566 ARG cc_start: 0.6375 (ttt180) cc_final: 0.6095 (mtt180) REVERT: N 616 LYS cc_start: 0.7081 (ttpt) cc_final: 0.6713 (tttm) REVERT: N 663 GLU cc_start: 0.5124 (tp30) cc_final: 0.4913 (tp30) outliers start: 69 outliers final: 31 residues processed: 386 average time/residue: 2.7878 time to fit residues: 1247.4084 Evaluate side-chains 372 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 326 time to evaluate : 3.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 191 LYS Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 354 GLN Chi-restraints excluded: chain K residue 642 VAL Chi-restraints excluded: chain K residue 655 SER Chi-restraints excluded: chain L residue 538 MET Chi-restraints excluded: chain L residue 544 GLU Chi-restraints excluded: chain L residue 663 GLU Chi-restraints excluded: chain M residue 580 THR Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain N residue 528 THR Chi-restraints excluded: chain N residue 543 ARG Chi-restraints excluded: chain N residue 544 GLU Chi-restraints excluded: chain N residue 590 CYS Chi-restraints excluded: chain N residue 611 THR Chi-restraints excluded: chain N residue 666 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 319 optimal weight: 1.9990 chunk 243 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 217 optimal weight: 0.5980 chunk 325 optimal weight: 0.9990 chunk 344 optimal weight: 2.9990 chunk 169 optimal weight: 0.2980 chunk 308 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN B 225 ASN D 12 ASN G 225 ASN K 645 ASN N 589 GLN N 645 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 28912 Z= 0.231 Angle : 0.606 7.084 39208 Z= 0.304 Chirality : 0.043 0.166 4344 Planarity : 0.004 0.042 5016 Dihedral : 7.921 110.601 4023 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.86 % Favored : 97.09 % Rotamer: Outliers : 2.34 % Allowed : 13.14 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: 0.77 (0.14), residues: 3536 helix: 0.58 (0.13), residues: 1608 sheet: -0.58 (0.24), residues: 408 loop : 1.06 (0.17), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 79 HIS 0.007 0.001 HIS A 40 PHE 0.013 0.001 PHE B 266 TYR 0.009 0.001 TYR A 362 ARG 0.006 0.001 ARG F 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 331 time to evaluate : 3.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7714 (ptpp) cc_final: 0.7053 (mttp) REVERT: A 81 ASP cc_start: 0.8106 (m-30) cc_final: 0.7706 (m-30) REVERT: A 190 MET cc_start: 0.7773 (ptp) cc_final: 0.7515 (ptm) REVERT: A 191 LYS cc_start: 0.7624 (tttp) cc_final: 0.7311 (tttp) REVERT: A 224 GLU cc_start: 0.7505 (mm-30) cc_final: 0.6688 (tp30) REVERT: A 227 MET cc_start: 0.8025 (mmt) cc_final: 0.7419 (mmm) REVERT: A 288 ASP cc_start: 0.8191 (m-30) cc_final: 0.7982 (m-30) REVERT: A 291 LYS cc_start: 0.7954 (ttpp) cc_final: 0.7649 (ttmm) REVERT: A 299 MET cc_start: 0.8358 (mmt) cc_final: 0.7987 (mtp) REVERT: A 334 GLU cc_start: 0.6716 (pm20) cc_final: 0.6117 (pp20) REVERT: A 357 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7760 (mt) REVERT: A 360 GLN cc_start: 0.7000 (tt0) cc_final: 0.6611 (tt0) REVERT: B 47 MET cc_start: 0.1362 (OUTLIER) cc_final: 0.0969 (mmm) REVERT: B 83 GLU cc_start: 0.7736 (tt0) cc_final: 0.7211 (mt-10) REVERT: B 187 ASP cc_start: 0.7991 (m-30) cc_final: 0.7602 (m-30) REVERT: B 283 MET cc_start: 0.8514 (mmm) cc_final: 0.8241 (mmm) REVERT: B 328 LYS cc_start: 0.8047 (tttp) cc_final: 0.7558 (mttp) REVERT: B 334 GLU cc_start: 0.7074 (pm20) cc_final: 0.6836 (pp20) REVERT: B 372 ARG cc_start: 0.7038 (mtm-85) cc_final: 0.6802 (mtm180) REVERT: C 24 ASP cc_start: 0.7869 (m-30) cc_final: 0.7597 (m-30) REVERT: C 25 ASP cc_start: 0.7404 (p0) cc_final: 0.7025 (p0) REVERT: C 68 LYS cc_start: 0.8048 (mttm) cc_final: 0.7665 (mtmt) REVERT: C 83 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7448 (tt0) REVERT: C 99 GLU cc_start: 0.7395 (pm20) cc_final: 0.7105 (pm20) REVERT: C 105 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7629 (mp) REVERT: C 276 GLU cc_start: 0.7817 (tt0) cc_final: 0.7301 (mt-10) REVERT: C 328 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7295 (ttmm) REVERT: C 334 GLU cc_start: 0.7277 (pm20) cc_final: 0.7076 (pm20) REVERT: C 355 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7495 (mmt) REVERT: C 359 LYS cc_start: 0.7764 (tptm) cc_final: 0.7394 (tptt) REVERT: C 363 ASP cc_start: 0.7008 (m-30) cc_final: 0.6734 (m-30) REVERT: D 47 MET cc_start: 0.2505 (OUTLIER) cc_final: 0.2266 (tmt) REVERT: D 72 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.7042 (mt-10) REVERT: D 95 ARG cc_start: 0.7332 (mtt-85) cc_final: 0.6829 (mmt90) REVERT: D 206 ARG cc_start: 0.7716 (ttm-80) cc_final: 0.7501 (ttm110) REVERT: D 276 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7593 (mt-10) REVERT: E 72 GLU cc_start: 0.7549 (mt-10) cc_final: 0.6860 (tt0) REVERT: E 95 ARG cc_start: 0.7088 (mtm-85) cc_final: 0.6564 (mmt90) REVERT: E 128 ASN cc_start: 0.7482 (m110) cc_final: 0.6608 (t0) REVERT: E 328 LYS cc_start: 0.7951 (tttt) cc_final: 0.7142 (mttp) REVERT: E 351 THR cc_start: 0.7514 (OUTLIER) cc_final: 0.7116 (m) REVERT: E 360 GLN cc_start: 0.7291 (tt0) cc_final: 0.6653 (pm20) REVERT: F 51 ASP cc_start: 0.7308 (p0) cc_final: 0.7102 (p0) REVERT: F 72 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7234 (mp0) REVERT: F 80 ASP cc_start: 0.7690 (m-30) cc_final: 0.7322 (m-30) REVERT: F 95 ARG cc_start: 0.7100 (mtp85) cc_final: 0.6624 (mtt-85) REVERT: F 125 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7208 (mm-30) REVERT: F 167 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8238 (mm-30) REVERT: F 178 LEU cc_start: 0.7926 (tp) cc_final: 0.7393 (mt) REVERT: F 191 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7719 (tmtt) REVERT: F 206 ARG cc_start: 0.7633 (ttm110) cc_final: 0.7219 (ttm110) REVERT: F 226 GLU cc_start: 0.7787 (tp30) cc_final: 0.7453 (tp30) REVERT: F 326 LYS cc_start: 0.7870 (tppp) cc_final: 0.6662 (ptmm) REVERT: F 328 LYS cc_start: 0.8177 (tttp) cc_final: 0.7746 (tptm) REVERT: F 354 GLN cc_start: 0.7661 (mm-40) cc_final: 0.7389 (mm110) REVERT: F 358 THR cc_start: 0.7971 (m) cc_final: 0.7563 (p) REVERT: F 363 ASP cc_start: 0.7435 (m-30) cc_final: 0.7169 (m-30) REVERT: G 95 ARG cc_start: 0.7374 (mtt-85) cc_final: 0.7020 (mtm110) REVERT: G 113 LYS cc_start: 0.8057 (mmtt) cc_final: 0.7696 (mmtp) REVERT: G 117 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7616 (mt-10) REVERT: G 118 LYS cc_start: 0.7820 (mmmt) cc_final: 0.7263 (mmmm) REVERT: G 125 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7635 (mt-10) REVERT: G 292 ASP cc_start: 0.7885 (m-30) cc_final: 0.7662 (m-30) REVERT: G 326 LYS cc_start: 0.7589 (mmtm) cc_final: 0.6980 (mmtp) REVERT: H 24 ASP cc_start: 0.6725 (m-30) cc_final: 0.6306 (m-30) REVERT: H 25 ASP cc_start: 0.6792 (p0) cc_final: 0.6337 (p0) REVERT: H 28 ARG cc_start: 0.7526 (ttm170) cc_final: 0.7272 (tpp-160) REVERT: H 68 LYS cc_start: 0.8275 (mmtm) cc_final: 0.7928 (mptt) REVERT: H 72 GLU cc_start: 0.7493 (tt0) cc_final: 0.7143 (mp0) REVERT: H 93 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7212 (mm-30) REVERT: H 113 LYS cc_start: 0.5132 (OUTLIER) cc_final: 0.4684 (mppt) REVERT: H 167 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7496 (mm-30) REVERT: H 206 ARG cc_start: 0.7829 (ttm110) cc_final: 0.7394 (ttp-110) REVERT: H 276 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7405 (mt-10) REVERT: H 299 MET cc_start: 0.8418 (mtp) cc_final: 0.7557 (mmt) REVERT: H 314 GLN cc_start: 0.7812 (tp40) cc_final: 0.7245 (tp40) REVERT: H 326 LYS cc_start: 0.7039 (mmpt) cc_final: 0.6794 (pttm) REVERT: H 328 LYS cc_start: 0.7780 (ttmt) cc_final: 0.7176 (tmtt) REVERT: H 334 GLU cc_start: 0.7756 (pm20) cc_final: 0.6678 (tp30) REVERT: H 336 LYS cc_start: 0.8145 (ttmt) cc_final: 0.7826 (tttm) REVERT: H 354 GLN cc_start: 0.7159 (OUTLIER) cc_final: 0.6906 (tp40) REVERT: K 578 ASN cc_start: 0.6629 (t0) cc_final: 0.6340 (t0) REVERT: K 608 GLU cc_start: 0.6784 (mt-10) cc_final: 0.6162 (mm-30) REVERT: K 617 GLU cc_start: 0.6588 (mp0) cc_final: 0.6172 (mt-10) REVERT: K 621 GLU cc_start: 0.7393 (tt0) cc_final: 0.6873 (mt-10) REVERT: L 555 GLU cc_start: 0.7475 (tt0) cc_final: 0.7227 (tt0) REVERT: L 574 GLU cc_start: 0.7228 (tm-30) cc_final: 0.6563 (tp30) REVERT: L 582 LYS cc_start: 0.6338 (mtpt) cc_final: 0.6002 (mttt) REVERT: L 595 LYS cc_start: 0.6512 (ptpt) cc_final: 0.6079 (mtmt) REVERT: L 616 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7392 (ttmt) REVERT: M 521 LYS cc_start: 0.6857 (tttp) cc_final: 0.6296 (tttm) REVERT: M 527 SER cc_start: 0.7956 (m) cc_final: 0.7751 (p) REVERT: M 533 THR cc_start: 0.8005 (OUTLIER) cc_final: 0.7656 (p) REVERT: M 541 ASP cc_start: 0.7298 (t0) cc_final: 0.6529 (t70) REVERT: M 604 GLU cc_start: 0.6477 (mm-30) cc_final: 0.5960 (tt0) REVERT: M 644 SER cc_start: 0.7126 (p) cc_final: 0.6890 (m) REVERT: M 664 SER cc_start: 0.5334 (t) cc_final: 0.5084 (t) REVERT: M 665 TYR cc_start: 0.6203 (m-80) cc_final: 0.5981 (m-80) REVERT: N 528 THR cc_start: 0.8161 (OUTLIER) cc_final: 0.7875 (p) REVERT: N 544 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6506 (tp30) REVERT: N 566 ARG cc_start: 0.6425 (ttt180) cc_final: 0.6114 (mtt180) REVERT: N 569 ASP cc_start: 0.6569 (OUTLIER) cc_final: 0.5884 (m-30) REVERT: N 616 LYS cc_start: 0.7031 (ttpt) cc_final: 0.6662 (tttm) outliers start: 71 outliers final: 37 residues processed: 377 average time/residue: 2.7502 time to fit residues: 1203.0405 Evaluate side-chains 381 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 327 time to evaluate : 3.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 191 LYS Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 373 LYS Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain H residue 354 GLN Chi-restraints excluded: chain K residue 642 VAL Chi-restraints excluded: chain K residue 655 SER Chi-restraints excluded: chain L residue 544 GLU Chi-restraints excluded: chain L residue 616 LYS Chi-restraints excluded: chain L residue 663 GLU Chi-restraints excluded: chain M residue 533 THR Chi-restraints excluded: chain M residue 580 THR Chi-restraints excluded: chain M residue 594 ASP Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain N residue 528 THR Chi-restraints excluded: chain N residue 544 GLU Chi-restraints excluded: chain N residue 569 ASP Chi-restraints excluded: chain N residue 580 THR Chi-restraints excluded: chain N residue 590 CYS Chi-restraints excluded: chain N residue 604 GLU Chi-restraints excluded: chain N residue 611 THR Chi-restraints excluded: chain N residue 666 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 286 optimal weight: 2.9990 chunk 195 optimal weight: 0.7980 chunk 4 optimal weight: 0.4980 chunk 256 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 293 optimal weight: 2.9990 chunk 237 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 chunk 308 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN E 137 GLN G 225 ASN H 246 GLN N 589 GLN N 645 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 28912 Z= 0.302 Angle : 0.647 7.539 39208 Z= 0.327 Chirality : 0.045 0.183 4344 Planarity : 0.005 0.045 5016 Dihedral : 8.158 120.181 4015 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.08 % Favored : 96.89 % Rotamer: Outliers : 2.84 % Allowed : 12.71 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: 0.63 (0.14), residues: 3536 helix: 0.47 (0.13), residues: 1600 sheet: -0.61 (0.25), residues: 368 loop : 0.90 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 340 HIS 0.007 0.001 HIS A 40 PHE 0.022 0.002 PHE B 266 TYR 0.012 0.002 TYR C 337 ARG 0.007 0.001 ARG G 335 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 330 time to evaluate : 3.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7726 (ptpp) cc_final: 0.7148 (mttp) REVERT: A 81 ASP cc_start: 0.8160 (m-30) cc_final: 0.7785 (m-30) REVERT: A 191 LYS cc_start: 0.7615 (tttp) cc_final: 0.7283 (tttp) REVERT: A 221 LEU cc_start: 0.8829 (tp) cc_final: 0.8564 (tm) REVERT: A 224 GLU cc_start: 0.7508 (mm-30) cc_final: 0.6627 (tp30) REVERT: A 227 MET cc_start: 0.7997 (mmt) cc_final: 0.7381 (mmm) REVERT: A 284 LYS cc_start: 0.8010 (mtpp) cc_final: 0.7641 (mttm) REVERT: A 291 LYS cc_start: 0.7961 (ttpp) cc_final: 0.7661 (ttmm) REVERT: A 299 MET cc_start: 0.8320 (mmt) cc_final: 0.7954 (mtp) REVERT: A 334 GLU cc_start: 0.6656 (pm20) cc_final: 0.6176 (pp20) REVERT: A 357 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7738 (mt) REVERT: A 360 GLN cc_start: 0.6981 (tt0) cc_final: 0.6609 (tt0) REVERT: B 47 MET cc_start: 0.1327 (OUTLIER) cc_final: 0.0978 (mmm) REVERT: B 95 ARG cc_start: 0.7233 (mtt-85) cc_final: 0.6921 (mtt-85) REVERT: B 176 MET cc_start: 0.8819 (mmm) cc_final: 0.8491 (mmm) REVERT: B 187 ASP cc_start: 0.8054 (m-30) cc_final: 0.7692 (m-30) REVERT: B 224 GLU cc_start: 0.7597 (tp30) cc_final: 0.6661 (mm-30) REVERT: B 283 MET cc_start: 0.8558 (mmm) cc_final: 0.8277 (mmm) REVERT: B 328 LYS cc_start: 0.8043 (tttp) cc_final: 0.7723 (ttpp) REVERT: B 372 ARG cc_start: 0.7077 (mtm-85) cc_final: 0.6855 (mtm180) REVERT: C 24 ASP cc_start: 0.7895 (m-30) cc_final: 0.7645 (m-30) REVERT: C 25 ASP cc_start: 0.7407 (p0) cc_final: 0.7042 (p0) REVERT: C 68 LYS cc_start: 0.8124 (mttm) cc_final: 0.7744 (mtmt) REVERT: C 99 GLU cc_start: 0.7412 (pm20) cc_final: 0.7099 (pm20) REVERT: C 105 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7649 (mp) REVERT: C 191 LYS cc_start: 0.8081 (ttmp) cc_final: 0.7669 (ttpp) REVERT: C 276 GLU cc_start: 0.7831 (tt0) cc_final: 0.7291 (mt-10) REVERT: C 299 MET cc_start: 0.8504 (mmm) cc_final: 0.8105 (mtt) REVERT: C 328 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7224 (mtmm) REVERT: C 355 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7570 (mmt) REVERT: C 363 ASP cc_start: 0.7042 (m-30) cc_final: 0.6814 (m-30) REVERT: D 72 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7082 (mt-10) REVERT: D 95 ARG cc_start: 0.7396 (mtt-85) cc_final: 0.6862 (mmt90) REVERT: D 206 ARG cc_start: 0.7717 (ttm-80) cc_final: 0.7481 (ttm110) REVERT: D 276 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7602 (mt-10) REVERT: E 72 GLU cc_start: 0.7539 (mt-10) cc_final: 0.6859 (tt0) REVERT: E 95 ARG cc_start: 0.7140 (mtm-85) cc_final: 0.6656 (mmt90) REVERT: E 128 ASN cc_start: 0.7486 (m110) cc_final: 0.6613 (t0) REVERT: E 241 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7745 (tt0) REVERT: E 328 LYS cc_start: 0.7936 (tttt) cc_final: 0.7149 (mttp) REVERT: E 351 THR cc_start: 0.7538 (OUTLIER) cc_final: 0.7217 (m) REVERT: E 360 GLN cc_start: 0.7373 (tt0) cc_final: 0.6714 (pm20) REVERT: F 51 ASP cc_start: 0.7291 (p0) cc_final: 0.7088 (p0) REVERT: F 72 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7244 (mp0) REVERT: F 80 ASP cc_start: 0.7694 (m-30) cc_final: 0.7316 (m-30) REVERT: F 95 ARG cc_start: 0.7090 (mtp85) cc_final: 0.6597 (mtt-85) REVERT: F 125 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7232 (mm-30) REVERT: F 167 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8261 (mm-30) REVERT: F 178 LEU cc_start: 0.7964 (tp) cc_final: 0.7394 (mt) REVERT: F 191 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7875 (tmmt) REVERT: F 206 ARG cc_start: 0.7643 (ttm110) cc_final: 0.7230 (ttm110) REVERT: F 226 GLU cc_start: 0.7835 (tp30) cc_final: 0.7456 (tp30) REVERT: F 326 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.6679 (ptmm) REVERT: F 328 LYS cc_start: 0.8116 (tttp) cc_final: 0.7674 (tptm) REVERT: F 354 GLN cc_start: 0.7690 (mm-40) cc_final: 0.7370 (mm110) REVERT: F 358 THR cc_start: 0.7972 (m) cc_final: 0.7583 (p) REVERT: G 117 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7648 (mt-10) REVERT: G 118 LYS cc_start: 0.7801 (mmmt) cc_final: 0.7278 (mmmm) REVERT: G 125 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7658 (mt-10) REVERT: G 292 ASP cc_start: 0.7950 (m-30) cc_final: 0.7746 (m-30) REVERT: G 326 LYS cc_start: 0.7583 (mmtm) cc_final: 0.6973 (mmtp) REVERT: H 24 ASP cc_start: 0.6730 (m-30) cc_final: 0.6289 (m-30) REVERT: H 25 ASP cc_start: 0.6896 (p0) cc_final: 0.6429 (p0) REVERT: H 28 ARG cc_start: 0.7547 (ttm170) cc_final: 0.7284 (tpp-160) REVERT: H 50 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7383 (mtmm) REVERT: H 68 LYS cc_start: 0.8257 (mmtm) cc_final: 0.7918 (mptt) REVERT: H 72 GLU cc_start: 0.7520 (tt0) cc_final: 0.7156 (mp0) REVERT: H 113 LYS cc_start: 0.5033 (OUTLIER) cc_final: 0.4527 (mppt) REVERT: H 167 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7550 (mm-30) REVERT: H 206 ARG cc_start: 0.7879 (ttm110) cc_final: 0.7439 (ttp-110) REVERT: H 276 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7417 (mt-10) REVERT: H 299 MET cc_start: 0.8408 (mtp) cc_final: 0.7534 (mmt) REVERT: H 314 GLN cc_start: 0.7778 (tp40) cc_final: 0.7261 (tp40) REVERT: H 326 LYS cc_start: 0.7052 (mmpt) cc_final: 0.6816 (pttm) REVERT: H 328 LYS cc_start: 0.7763 (ttmt) cc_final: 0.7128 (tmtt) REVERT: H 334 GLU cc_start: 0.7837 (pm20) cc_final: 0.6759 (tp30) REVERT: H 336 LYS cc_start: 0.8175 (ttmt) cc_final: 0.7867 (tttm) REVERT: H 354 GLN cc_start: 0.7193 (OUTLIER) cc_final: 0.6793 (tp-100) REVERT: K 578 ASN cc_start: 0.6639 (t0) cc_final: 0.6377 (t0) REVERT: K 617 GLU cc_start: 0.6573 (mp0) cc_final: 0.6159 (mt-10) REVERT: K 621 GLU cc_start: 0.7354 (tt0) cc_final: 0.6883 (mt-10) REVERT: L 555 GLU cc_start: 0.7464 (tt0) cc_final: 0.7201 (tt0) REVERT: L 574 GLU cc_start: 0.7237 (tm-30) cc_final: 0.6519 (tp30) REVERT: L 582 LYS cc_start: 0.6260 (mtpt) cc_final: 0.5911 (mttt) REVERT: L 595 LYS cc_start: 0.6418 (ptpt) cc_final: 0.6018 (mtmt) REVERT: L 616 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.7420 (ttmt) REVERT: M 521 LYS cc_start: 0.6892 (tttp) cc_final: 0.6383 (tttm) REVERT: M 527 SER cc_start: 0.7985 (m) cc_final: 0.7763 (p) REVERT: M 533 THR cc_start: 0.7961 (OUTLIER) cc_final: 0.7711 (t) REVERT: M 541 ASP cc_start: 0.7307 (t0) cc_final: 0.6539 (t70) REVERT: M 604 GLU cc_start: 0.6508 (mm-30) cc_final: 0.5981 (tt0) REVERT: M 644 SER cc_start: 0.7168 (p) cc_final: 0.6936 (m) REVERT: M 664 SER cc_start: 0.5201 (t) cc_final: 0.4999 (t) REVERT: N 528 THR cc_start: 0.8147 (OUTLIER) cc_final: 0.7883 (p) REVERT: N 543 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.6874 (ttt90) REVERT: N 544 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6490 (tp30) REVERT: N 566 ARG cc_start: 0.6409 (ttt180) cc_final: 0.6084 (mtt180) REVERT: N 569 ASP cc_start: 0.6555 (OUTLIER) cc_final: 0.5869 (m-30) REVERT: N 616 LYS cc_start: 0.7037 (ttpt) cc_final: 0.6695 (tttm) outliers start: 86 outliers final: 42 residues processed: 384 average time/residue: 2.7228 time to fit residues: 1215.3545 Evaluate side-chains 379 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 317 time to evaluate : 3.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 225 ASN Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 191 LYS Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 373 LYS Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 354 GLN Chi-restraints excluded: chain K residue 642 VAL Chi-restraints excluded: chain K residue 655 SER Chi-restraints excluded: chain L residue 544 GLU Chi-restraints excluded: chain L residue 616 LYS Chi-restraints excluded: chain L residue 663 GLU Chi-restraints excluded: chain M residue 533 THR Chi-restraints excluded: chain M residue 580 THR Chi-restraints excluded: chain M residue 594 ASP Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain N residue 528 THR Chi-restraints excluded: chain N residue 543 ARG Chi-restraints excluded: chain N residue 544 GLU Chi-restraints excluded: chain N residue 569 ASP Chi-restraints excluded: chain N residue 580 THR Chi-restraints excluded: chain N residue 590 CYS Chi-restraints excluded: chain N residue 604 GLU Chi-restraints excluded: chain N residue 611 THR Chi-restraints excluded: chain N residue 666 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 115 optimal weight: 3.9990 chunk 309 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 344 optimal weight: 1.9990 chunk 285 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 180 optimal weight: 0.0060 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 ASN N 645 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28912 Z= 0.216 Angle : 0.602 7.102 39208 Z= 0.301 Chirality : 0.043 0.171 4344 Planarity : 0.004 0.039 5016 Dihedral : 7.733 113.274 4012 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.97 % Favored : 97.00 % Rotamer: Outliers : 2.41 % Allowed : 12.91 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: 0.73 (0.14), residues: 3536 helix: 0.60 (0.13), residues: 1608 sheet: -0.65 (0.24), residues: 408 loop : 0.98 (0.17), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 79 HIS 0.007 0.001 HIS A 40 PHE 0.014 0.001 PHE K 568 TYR 0.009 0.001 TYR C 337 ARG 0.007 0.000 ARG F 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 333 time to evaluate : 3.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7650 (ptpp) cc_final: 0.7134 (mttp) REVERT: A 81 ASP cc_start: 0.8138 (m-30) cc_final: 0.7766 (m-30) REVERT: A 191 LYS cc_start: 0.7577 (tttp) cc_final: 0.7347 (tttt) REVERT: A 221 LEU cc_start: 0.8837 (tp) cc_final: 0.8578 (tm) REVERT: A 224 GLU cc_start: 0.7453 (mm-30) cc_final: 0.6602 (tp30) REVERT: A 227 MET cc_start: 0.7975 (mmt) cc_final: 0.7401 (mmm) REVERT: A 284 LYS cc_start: 0.7986 (mtpp) cc_final: 0.7602 (mttm) REVERT: A 291 LYS cc_start: 0.7899 (ttpp) cc_final: 0.7622 (ttmm) REVERT: A 299 MET cc_start: 0.8283 (mmt) cc_final: 0.7903 (mtp) REVERT: A 334 GLU cc_start: 0.6665 (pm20) cc_final: 0.6177 (pp20) REVERT: A 357 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7754 (mt) REVERT: B 47 MET cc_start: 0.1147 (OUTLIER) cc_final: 0.0932 (mmm) REVERT: B 83 GLU cc_start: 0.7790 (tt0) cc_final: 0.7242 (mt-10) REVERT: B 95 ARG cc_start: 0.7226 (mtt-85) cc_final: 0.6907 (mtt-85) REVERT: B 187 ASP cc_start: 0.7977 (m-30) cc_final: 0.7576 (m-30) REVERT: B 224 GLU cc_start: 0.7680 (tp30) cc_final: 0.6567 (mm-30) REVERT: B 283 MET cc_start: 0.8521 (mmm) cc_final: 0.8219 (mmm) REVERT: B 328 LYS cc_start: 0.8032 (tttp) cc_final: 0.7569 (mttp) REVERT: B 372 ARG cc_start: 0.7050 (mtm-85) cc_final: 0.6726 (mtm110) REVERT: C 24 ASP cc_start: 0.7902 (m-30) cc_final: 0.7646 (m-30) REVERT: C 25 ASP cc_start: 0.7392 (p0) cc_final: 0.6905 (p0) REVERT: C 68 LYS cc_start: 0.8118 (mttm) cc_final: 0.7745 (mtmt) REVERT: C 99 GLU cc_start: 0.7399 (pm20) cc_final: 0.7084 (pm20) REVERT: C 105 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7614 (mp) REVERT: C 191 LYS cc_start: 0.8075 (ttmp) cc_final: 0.7668 (ttpp) REVERT: C 276 GLU cc_start: 0.7832 (tt0) cc_final: 0.7308 (mt-10) REVERT: C 299 MET cc_start: 0.8494 (mmm) cc_final: 0.8150 (mtt) REVERT: C 328 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7257 (ttmm) REVERT: C 355 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7598 (mmt) REVERT: C 363 ASP cc_start: 0.7064 (m-30) cc_final: 0.6809 (m-30) REVERT: D 72 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.7078 (mt-10) REVERT: D 211 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7901 (t70) REVERT: D 276 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7586 (mt-10) REVERT: E 72 GLU cc_start: 0.7530 (mt-10) cc_final: 0.6867 (tt0) REVERT: E 95 ARG cc_start: 0.7107 (mtm-85) cc_final: 0.6619 (mmt90) REVERT: E 128 ASN cc_start: 0.7491 (m110) cc_final: 0.6631 (t0) REVERT: E 241 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7723 (tt0) REVERT: E 328 LYS cc_start: 0.7956 (tttt) cc_final: 0.7188 (mttp) REVERT: E 351 THR cc_start: 0.7531 (OUTLIER) cc_final: 0.7220 (m) REVERT: E 360 GLN cc_start: 0.7336 (tt0) cc_final: 0.6694 (pm20) REVERT: F 72 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7214 (mp0) REVERT: F 80 ASP cc_start: 0.7671 (m-30) cc_final: 0.7336 (m-30) REVERT: F 95 ARG cc_start: 0.7091 (mtp85) cc_final: 0.6605 (mtt-85) REVERT: F 125 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7213 (mm-30) REVERT: F 167 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8261 (mm-30) REVERT: F 178 LEU cc_start: 0.7917 (tp) cc_final: 0.7377 (mt) REVERT: F 206 ARG cc_start: 0.7617 (ttm110) cc_final: 0.7205 (ttm110) REVERT: F 226 GLU cc_start: 0.7823 (tp30) cc_final: 0.7434 (tp30) REVERT: F 326 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.6697 (ptmm) REVERT: F 328 LYS cc_start: 0.8148 (tttp) cc_final: 0.7713 (tptm) REVERT: F 354 GLN cc_start: 0.7669 (mm-40) cc_final: 0.7371 (mm110) REVERT: F 358 THR cc_start: 0.7975 (m) cc_final: 0.7601 (p) REVERT: G 117 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7646 (mt-10) REVERT: G 118 LYS cc_start: 0.7815 (mmmt) cc_final: 0.7264 (mmmm) REVERT: G 125 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7558 (mt-10) REVERT: G 292 ASP cc_start: 0.7943 (m-30) cc_final: 0.7733 (m-30) REVERT: G 326 LYS cc_start: 0.7537 (mmtm) cc_final: 0.6928 (mmtp) REVERT: H 24 ASP cc_start: 0.6727 (m-30) cc_final: 0.6302 (m-30) REVERT: H 25 ASP cc_start: 0.6878 (p0) cc_final: 0.6431 (p0) REVERT: H 28 ARG cc_start: 0.7551 (ttm170) cc_final: 0.7273 (tpp-160) REVERT: H 68 LYS cc_start: 0.8271 (mmtm) cc_final: 0.7937 (mptt) REVERT: H 72 GLU cc_start: 0.7512 (tt0) cc_final: 0.7149 (mp0) REVERT: H 113 LYS cc_start: 0.5080 (OUTLIER) cc_final: 0.4606 (mppt) REVERT: H 167 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7439 (mm-30) REVERT: H 176 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7572 (mtp) REVERT: H 276 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7449 (mt-10) REVERT: H 314 GLN cc_start: 0.7819 (tp40) cc_final: 0.7306 (tp40) REVERT: H 326 LYS cc_start: 0.7047 (mmpt) cc_final: 0.6831 (pttm) REVERT: H 328 LYS cc_start: 0.7753 (ttmt) cc_final: 0.7137 (tmtt) REVERT: H 334 GLU cc_start: 0.7814 (pm20) cc_final: 0.6685 (tp30) REVERT: H 336 LYS cc_start: 0.8182 (ttmt) cc_final: 0.7830 (tttm) REVERT: H 354 GLN cc_start: 0.7212 (OUTLIER) cc_final: 0.6812 (tp-100) REVERT: K 578 ASN cc_start: 0.6622 (t0) cc_final: 0.6360 (t0) REVERT: K 598 GLU cc_start: 0.5898 (pm20) cc_final: 0.5380 (pt0) REVERT: K 617 GLU cc_start: 0.6568 (mp0) cc_final: 0.6200 (mt-10) REVERT: K 621 GLU cc_start: 0.7334 (tt0) cc_final: 0.6877 (mt-10) REVERT: L 555 GLU cc_start: 0.7476 (tt0) cc_final: 0.7225 (tt0) REVERT: L 574 GLU cc_start: 0.7238 (tm-30) cc_final: 0.6554 (tp30) REVERT: L 582 LYS cc_start: 0.6225 (mtpt) cc_final: 0.5832 (mmtp) REVERT: L 595 LYS cc_start: 0.6386 (ptpt) cc_final: 0.6014 (mtmt) REVERT: L 616 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7397 (ttmt) REVERT: M 521 LYS cc_start: 0.6878 (tttp) cc_final: 0.6363 (tttm) REVERT: M 527 SER cc_start: 0.7926 (m) cc_final: 0.7705 (p) REVERT: M 533 THR cc_start: 0.7989 (OUTLIER) cc_final: 0.7773 (t) REVERT: M 541 ASP cc_start: 0.7295 (t0) cc_final: 0.6515 (t70) REVERT: M 604 GLU cc_start: 0.6506 (mm-30) cc_final: 0.5981 (tt0) REVERT: M 644 SER cc_start: 0.7124 (p) cc_final: 0.6903 (m) REVERT: N 528 THR cc_start: 0.8166 (OUTLIER) cc_final: 0.7909 (p) REVERT: N 544 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6571 (tp30) REVERT: N 566 ARG cc_start: 0.6348 (ttt180) cc_final: 0.6037 (mtt180) REVERT: N 569 ASP cc_start: 0.6638 (OUTLIER) cc_final: 0.5952 (m-30) REVERT: N 616 LYS cc_start: 0.7022 (ttpt) cc_final: 0.6681 (tttm) outliers start: 73 outliers final: 37 residues processed: 381 average time/residue: 2.6814 time to fit residues: 1193.6715 Evaluate side-chains 379 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 323 time to evaluate : 3.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 225 ASN Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 354 GLN Chi-restraints excluded: chain K residue 642 VAL Chi-restraints excluded: chain L residue 544 GLU Chi-restraints excluded: chain L residue 616 LYS Chi-restraints excluded: chain M residue 533 THR Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain N residue 528 THR Chi-restraints excluded: chain N residue 544 GLU Chi-restraints excluded: chain N residue 569 ASP Chi-restraints excluded: chain N residue 580 THR Chi-restraints excluded: chain N residue 590 CYS Chi-restraints excluded: chain N residue 611 THR Chi-restraints excluded: chain N residue 666 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 332 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 196 optimal weight: 0.7980 chunk 251 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 289 optimal weight: 2.9990 chunk 192 optimal weight: 0.6980 chunk 343 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN E 137 GLN G 225 ASN K 645 ASN N 645 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28912 Z= 0.278 Angle : 0.629 7.240 39208 Z= 0.317 Chirality : 0.044 0.173 4344 Planarity : 0.005 0.042 5016 Dihedral : 7.909 118.043 4012 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.97 % Favored : 97.00 % Rotamer: Outliers : 2.38 % Allowed : 13.47 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: 0.69 (0.14), residues: 3536 helix: 0.58 (0.13), residues: 1552 sheet: -0.61 (0.25), residues: 368 loop : 0.86 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 340 HIS 0.007 0.001 HIS A 40 PHE 0.020 0.002 PHE B 266 TYR 0.011 0.001 TYR C 337 ARG 0.009 0.001 ARG F 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 323 time to evaluate : 3.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.8184 (mmt-90) cc_final: 0.7926 (mtt90) REVERT: A 68 LYS cc_start: 0.7647 (ptpp) cc_final: 0.7167 (mttp) REVERT: A 81 ASP cc_start: 0.8118 (m-30) cc_final: 0.7749 (m-30) REVERT: A 191 LYS cc_start: 0.7620 (tttp) cc_final: 0.7193 (ttmt) REVERT: A 221 LEU cc_start: 0.8840 (tp) cc_final: 0.8594 (tm) REVERT: A 224 GLU cc_start: 0.7444 (mm-30) cc_final: 0.6578 (tp30) REVERT: A 227 MET cc_start: 0.7982 (mmt) cc_final: 0.7404 (mmm) REVERT: A 284 LYS cc_start: 0.8019 (mtpp) cc_final: 0.7633 (mttm) REVERT: A 291 LYS cc_start: 0.7907 (ttpp) cc_final: 0.7636 (ttmm) REVERT: A 299 MET cc_start: 0.8272 (mmt) cc_final: 0.8029 (mtt) REVERT: A 334 GLU cc_start: 0.6653 (pm20) cc_final: 0.6107 (pp20) REVERT: A 357 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7741 (mt) REVERT: B 83 GLU cc_start: 0.7797 (tt0) cc_final: 0.7244 (mt-10) REVERT: B 95 ARG cc_start: 0.7210 (mtt-85) cc_final: 0.6890 (mtt-85) REVERT: B 187 ASP cc_start: 0.8028 (m-30) cc_final: 0.7646 (m-30) REVERT: B 224 GLU cc_start: 0.7706 (tp30) cc_final: 0.6626 (mm-30) REVERT: B 283 MET cc_start: 0.8534 (mmm) cc_final: 0.8237 (mmm) REVERT: B 328 LYS cc_start: 0.8042 (tttp) cc_final: 0.7574 (mttp) REVERT: B 372 ARG cc_start: 0.7098 (mtm-85) cc_final: 0.6785 (mtm110) REVERT: C 24 ASP cc_start: 0.7936 (m-30) cc_final: 0.7679 (m-30) REVERT: C 25 ASP cc_start: 0.7279 (p0) cc_final: 0.6790 (p0) REVERT: C 68 LYS cc_start: 0.8121 (mttm) cc_final: 0.7742 (mtmt) REVERT: C 99 GLU cc_start: 0.7375 (pm20) cc_final: 0.7067 (pm20) REVERT: C 105 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7617 (mp) REVERT: C 191 LYS cc_start: 0.8012 (ttmp) cc_final: 0.7600 (ttpp) REVERT: C 276 GLU cc_start: 0.7740 (tt0) cc_final: 0.7231 (mt-10) REVERT: C 299 MET cc_start: 0.8519 (mmm) cc_final: 0.8163 (mtt) REVERT: C 328 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7222 (mtmm) REVERT: C 355 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7582 (mmt) REVERT: C 363 ASP cc_start: 0.7122 (m-30) cc_final: 0.6880 (m-30) REVERT: D 72 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7077 (mt-10) REVERT: D 122 ILE cc_start: 0.7953 (OUTLIER) cc_final: 0.7713 (mp) REVERT: D 211 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7924 (t70) REVERT: D 276 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7598 (mt-10) REVERT: E 72 GLU cc_start: 0.7545 (mt-10) cc_final: 0.6869 (tt0) REVERT: E 95 ARG cc_start: 0.7193 (mtm-85) cc_final: 0.6700 (mmt90) REVERT: E 128 ASN cc_start: 0.7486 (m110) cc_final: 0.6610 (t0) REVERT: E 178 LEU cc_start: 0.7953 (mt) cc_final: 0.7627 (mt) REVERT: E 241 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7723 (tt0) REVERT: E 328 LYS cc_start: 0.7934 (tttt) cc_final: 0.7154 (mttp) REVERT: E 351 THR cc_start: 0.7506 (OUTLIER) cc_final: 0.7226 (m) REVERT: E 360 GLN cc_start: 0.7351 (tt0) cc_final: 0.6714 (pm20) REVERT: F 72 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7170 (mp0) REVERT: F 80 ASP cc_start: 0.7738 (m-30) cc_final: 0.7401 (m-30) REVERT: F 95 ARG cc_start: 0.7091 (mtp85) cc_final: 0.6602 (mtt-85) REVERT: F 125 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7199 (mm-30) REVERT: F 167 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8261 (mm-30) REVERT: F 178 LEU cc_start: 0.7917 (tp) cc_final: 0.7376 (mt) REVERT: F 191 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7904 (tmtt) REVERT: F 206 ARG cc_start: 0.7614 (ttm110) cc_final: 0.7214 (ttm110) REVERT: F 226 GLU cc_start: 0.7840 (tp30) cc_final: 0.7434 (tp30) REVERT: F 326 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.6675 (ptmm) REVERT: F 328 LYS cc_start: 0.8116 (tttp) cc_final: 0.7677 (tptm) REVERT: F 354 GLN cc_start: 0.7671 (mm-40) cc_final: 0.7372 (mm110) REVERT: F 358 THR cc_start: 0.7982 (m) cc_final: 0.7625 (p) REVERT: G 117 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7658 (mt-10) REVERT: G 118 LYS cc_start: 0.7810 (mmmt) cc_final: 0.7243 (mmmm) REVERT: G 125 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7571 (mt-10) REVERT: G 326 LYS cc_start: 0.7585 (mmtm) cc_final: 0.6987 (mmtp) REVERT: H 24 ASP cc_start: 0.6760 (m-30) cc_final: 0.6328 (m-30) REVERT: H 25 ASP cc_start: 0.6897 (p0) cc_final: 0.6436 (p0) REVERT: H 28 ARG cc_start: 0.7536 (ttm170) cc_final: 0.7251 (tpp-160) REVERT: H 68 LYS cc_start: 0.8270 (mmtm) cc_final: 0.7933 (mptt) REVERT: H 72 GLU cc_start: 0.7485 (tt0) cc_final: 0.7115 (mp0) REVERT: H 113 LYS cc_start: 0.5063 (OUTLIER) cc_final: 0.3858 (mmtm) REVERT: H 167 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7537 (mm-30) REVERT: H 176 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.7653 (mtp) REVERT: H 276 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7429 (mt-10) REVERT: H 299 MET cc_start: 0.8398 (mtp) cc_final: 0.7833 (mmm) REVERT: H 314 GLN cc_start: 0.7803 (tp40) cc_final: 0.7285 (tp40) REVERT: H 326 LYS cc_start: 0.7057 (mmpt) cc_final: 0.6841 (pttm) REVERT: H 328 LYS cc_start: 0.7740 (ttmt) cc_final: 0.7131 (tmtt) REVERT: H 336 LYS cc_start: 0.8167 (ttmt) cc_final: 0.7801 (tttm) REVERT: H 354 GLN cc_start: 0.7212 (OUTLIER) cc_final: 0.6826 (tp-100) REVERT: K 578 ASN cc_start: 0.6619 (t0) cc_final: 0.6359 (t0) REVERT: K 598 GLU cc_start: 0.5937 (pm20) cc_final: 0.5412 (pt0) REVERT: K 617 GLU cc_start: 0.6596 (mp0) cc_final: 0.6199 (mt-10) REVERT: K 621 GLU cc_start: 0.7358 (tt0) cc_final: 0.6889 (mt-10) REVERT: L 574 GLU cc_start: 0.7190 (tm-30) cc_final: 0.6930 (tm-30) REVERT: L 582 LYS cc_start: 0.6206 (mtpt) cc_final: 0.5873 (mttt) REVERT: L 595 LYS cc_start: 0.6338 (ptpt) cc_final: 0.5998 (mtmt) REVERT: L 616 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7414 (ttmt) REVERT: M 521 LYS cc_start: 0.6878 (tttp) cc_final: 0.6361 (tttm) REVERT: M 527 SER cc_start: 0.7944 (m) cc_final: 0.7724 (p) REVERT: M 533 THR cc_start: 0.7961 (OUTLIER) cc_final: 0.7736 (t) REVERT: M 541 ASP cc_start: 0.7271 (t0) cc_final: 0.6477 (t70) REVERT: M 604 GLU cc_start: 0.6496 (mm-30) cc_final: 0.5968 (tt0) REVERT: M 644 SER cc_start: 0.7119 (p) cc_final: 0.6895 (m) REVERT: N 528 THR cc_start: 0.8135 (OUTLIER) cc_final: 0.7878 (p) REVERT: N 543 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.6882 (ttt90) REVERT: N 544 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6501 (tp30) REVERT: N 566 ARG cc_start: 0.6380 (ttt180) cc_final: 0.6035 (mtt180) REVERT: N 569 ASP cc_start: 0.6594 (OUTLIER) cc_final: 0.5897 (m-30) REVERT: N 616 LYS cc_start: 0.7019 (ttpt) cc_final: 0.6681 (tttm) outliers start: 72 outliers final: 42 residues processed: 370 average time/residue: 2.6663 time to fit residues: 1148.4315 Evaluate side-chains 378 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 315 time to evaluate : 3.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 225 ASN Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 191 LYS Chi-restraints excluded: chain F residue 225 ASN Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 364 GLU Chi-restraints excluded: chain G residue 373 LYS Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 354 GLN Chi-restraints excluded: chain K residue 642 VAL Chi-restraints excluded: chain L residue 544 GLU Chi-restraints excluded: chain L residue 616 LYS Chi-restraints excluded: chain M residue 533 THR Chi-restraints excluded: chain M residue 559 SER Chi-restraints excluded: chain M residue 594 ASP Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain N residue 528 THR Chi-restraints excluded: chain N residue 543 ARG Chi-restraints excluded: chain N residue 544 GLU Chi-restraints excluded: chain N residue 569 ASP Chi-restraints excluded: chain N residue 580 THR Chi-restraints excluded: chain N residue 590 CYS Chi-restraints excluded: chain N residue 611 THR Chi-restraints excluded: chain N residue 666 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 212 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 chunk 233 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 269 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN E 137 GLN G 225 ASN K 645 ASN N 645 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 28912 Z= 0.310 Angle : 0.651 7.644 39208 Z= 0.329 Chirality : 0.045 0.180 4344 Planarity : 0.005 0.042 5016 Dihedral : 8.083 119.811 4012 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.22 % Favored : 96.75 % Rotamer: Outliers : 2.31 % Allowed : 13.47 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.58 (0.14), residues: 3536 helix: 0.50 (0.13), residues: 1552 sheet: -0.66 (0.25), residues: 368 loop : 0.79 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 340 HIS 0.007 0.001 HIS G 161 PHE 0.024 0.002 PHE B 266 TYR 0.012 0.002 TYR C 337 ARG 0.010 0.001 ARG F 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 320 time to evaluate : 3.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.8157 (mmt-90) cc_final: 0.7872 (mtt90) REVERT: A 68 LYS cc_start: 0.7803 (ptpp) cc_final: 0.7175 (mttp) REVERT: A 81 ASP cc_start: 0.8083 (m-30) cc_final: 0.7710 (m-30) REVERT: A 221 LEU cc_start: 0.8865 (tp) cc_final: 0.8618 (tm) REVERT: A 224 GLU cc_start: 0.7355 (mm-30) cc_final: 0.6575 (tp30) REVERT: A 227 MET cc_start: 0.7975 (mmt) cc_final: 0.7397 (mmm) REVERT: A 284 LYS cc_start: 0.7977 (mtpp) cc_final: 0.7598 (mttm) REVERT: A 291 LYS cc_start: 0.7908 (ttpp) cc_final: 0.7641 (ttmm) REVERT: A 299 MET cc_start: 0.8279 (mmt) cc_final: 0.8040 (mtt) REVERT: A 334 GLU cc_start: 0.6749 (pm20) cc_final: 0.6216 (pp20) REVERT: A 357 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7730 (mt) REVERT: B 83 GLU cc_start: 0.7794 (tt0) cc_final: 0.7235 (mt-10) REVERT: B 187 ASP cc_start: 0.8057 (m-30) cc_final: 0.7688 (m-30) REVERT: B 224 GLU cc_start: 0.7697 (tp30) cc_final: 0.6609 (mm-30) REVERT: B 283 MET cc_start: 0.8553 (mmm) cc_final: 0.8294 (mmm) REVERT: B 328 LYS cc_start: 0.8045 (tttp) cc_final: 0.7579 (mttp) REVERT: B 372 ARG cc_start: 0.7091 (mtm-85) cc_final: 0.6787 (mtm110) REVERT: C 24 ASP cc_start: 0.7921 (m-30) cc_final: 0.7663 (m-30) REVERT: C 25 ASP cc_start: 0.7294 (p0) cc_final: 0.6781 (p0) REVERT: C 68 LYS cc_start: 0.8111 (mttm) cc_final: 0.7743 (mtmt) REVERT: C 99 GLU cc_start: 0.7403 (pm20) cc_final: 0.7095 (pm20) REVERT: C 105 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7632 (mp) REVERT: C 191 LYS cc_start: 0.8034 (ttmp) cc_final: 0.7629 (ttpp) REVERT: C 276 GLU cc_start: 0.7853 (tt0) cc_final: 0.7319 (mt-10) REVERT: C 299 MET cc_start: 0.8523 (mmm) cc_final: 0.8176 (mtt) REVERT: C 328 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7225 (ttmm) REVERT: C 355 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7607 (mmt) REVERT: C 363 ASP cc_start: 0.7135 (m-30) cc_final: 0.6884 (m-30) REVERT: D 72 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7087 (mt-10) REVERT: D 122 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7732 (mp) REVERT: D 276 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7604 (mt-10) REVERT: E 95 ARG cc_start: 0.7189 (mtm-85) cc_final: 0.6788 (mmt180) REVERT: E 128 ASN cc_start: 0.7481 (m110) cc_final: 0.6608 (t0) REVERT: E 178 LEU cc_start: 0.7978 (mt) cc_final: 0.7710 (mt) REVERT: E 241 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7752 (tt0) REVERT: E 328 LYS cc_start: 0.7952 (tttt) cc_final: 0.7164 (mttp) REVERT: E 360 GLN cc_start: 0.7365 (tt0) cc_final: 0.6720 (pm20) REVERT: F 72 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7166 (mp0) REVERT: F 80 ASP cc_start: 0.7709 (m-30) cc_final: 0.7434 (m-30) REVERT: F 95 ARG cc_start: 0.7076 (mtp85) cc_final: 0.6583 (mtt-85) REVERT: F 125 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7169 (mm-30) REVERT: F 167 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8270 (mm-30) REVERT: F 178 LEU cc_start: 0.7903 (tp) cc_final: 0.7366 (mt) REVERT: F 191 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7901 (tmtt) REVERT: F 206 ARG cc_start: 0.7631 (ttm110) cc_final: 0.7273 (ttm110) REVERT: F 226 GLU cc_start: 0.7901 (tp30) cc_final: 0.7500 (tp30) REVERT: F 326 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.6683 (ptmm) REVERT: F 328 LYS cc_start: 0.8099 (tttp) cc_final: 0.7666 (tptm) REVERT: F 354 GLN cc_start: 0.7667 (mm-40) cc_final: 0.7314 (mm110) REVERT: F 358 THR cc_start: 0.7968 (m) cc_final: 0.7646 (p) REVERT: G 118 LYS cc_start: 0.7812 (mmmt) cc_final: 0.7245 (mmmm) REVERT: G 283 MET cc_start: 0.8626 (mmm) cc_final: 0.8310 (mmm) REVERT: G 326 LYS cc_start: 0.7583 (mmtm) cc_final: 0.6987 (mmtp) REVERT: H 24 ASP cc_start: 0.6764 (m-30) cc_final: 0.6439 (m-30) REVERT: H 25 ASP cc_start: 0.6901 (p0) cc_final: 0.6453 (p0) REVERT: H 68 LYS cc_start: 0.8259 (mmtm) cc_final: 0.7930 (mptt) REVERT: H 72 GLU cc_start: 0.7498 (tt0) cc_final: 0.7130 (mp0) REVERT: H 113 LYS cc_start: 0.5048 (OUTLIER) cc_final: 0.4574 (mppt) REVERT: H 167 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7526 (mm-30) REVERT: H 176 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7680 (mtp) REVERT: H 276 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7438 (mt-10) REVERT: H 299 MET cc_start: 0.8377 (mtp) cc_final: 0.7770 (mmm) REVERT: H 314 GLN cc_start: 0.7791 (tp40) cc_final: 0.7272 (tp40) REVERT: H 326 LYS cc_start: 0.7060 (mmpt) cc_final: 0.6844 (pttm) REVERT: H 328 LYS cc_start: 0.7753 (ttmt) cc_final: 0.7140 (tmtt) REVERT: H 336 LYS cc_start: 0.8170 (ttmt) cc_final: 0.7801 (tttm) REVERT: H 354 GLN cc_start: 0.7184 (OUTLIER) cc_final: 0.6800 (tp-100) REVERT: K 578 ASN cc_start: 0.6610 (t0) cc_final: 0.6375 (t0) REVERT: K 598 GLU cc_start: 0.5949 (pm20) cc_final: 0.5415 (pt0) REVERT: K 617 GLU cc_start: 0.6570 (mp0) cc_final: 0.6178 (mt-10) REVERT: K 621 GLU cc_start: 0.7360 (tt0) cc_final: 0.6891 (mt-10) REVERT: L 574 GLU cc_start: 0.7207 (tm-30) cc_final: 0.6940 (tm-30) REVERT: L 582 LYS cc_start: 0.6262 (mtpt) cc_final: 0.5851 (mmtp) REVERT: L 595 LYS cc_start: 0.6333 (ptpt) cc_final: 0.6000 (mtmt) REVERT: L 616 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7422 (ttmt) REVERT: M 521 LYS cc_start: 0.6869 (tttp) cc_final: 0.6356 (tttm) REVERT: M 527 SER cc_start: 0.7946 (m) cc_final: 0.7723 (p) REVERT: M 533 THR cc_start: 0.7912 (OUTLIER) cc_final: 0.7678 (t) REVERT: M 541 ASP cc_start: 0.7286 (t0) cc_final: 0.6497 (t70) REVERT: M 604 GLU cc_start: 0.6490 (mm-30) cc_final: 0.5976 (tt0) REVERT: M 644 SER cc_start: 0.7172 (p) cc_final: 0.6944 (m) REVERT: N 528 THR cc_start: 0.8138 (OUTLIER) cc_final: 0.7893 (p) REVERT: N 544 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6563 (tp30) REVERT: N 566 ARG cc_start: 0.6407 (ttt180) cc_final: 0.6065 (mtt180) REVERT: N 569 ASP cc_start: 0.6631 (OUTLIER) cc_final: 0.5943 (m-30) REVERT: N 616 LYS cc_start: 0.7016 (ttpt) cc_final: 0.6681 (tttm) outliers start: 70 outliers final: 45 residues processed: 365 average time/residue: 2.7763 time to fit residues: 1182.7020 Evaluate side-chains 377 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 314 time to evaluate : 3.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 191 LYS Chi-restraints excluded: chain F residue 225 ASN Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 364 GLU Chi-restraints excluded: chain G residue 373 LYS Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 354 GLN Chi-restraints excluded: chain H residue 360 GLN Chi-restraints excluded: chain K residue 642 VAL Chi-restraints excluded: chain L residue 544 GLU Chi-restraints excluded: chain L residue 616 LYS Chi-restraints excluded: chain M residue 533 THR Chi-restraints excluded: chain M residue 559 SER Chi-restraints excluded: chain M residue 594 ASP Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 664 SER Chi-restraints excluded: chain N residue 528 THR Chi-restraints excluded: chain N residue 544 GLU Chi-restraints excluded: chain N residue 569 ASP Chi-restraints excluded: chain N residue 580 THR Chi-restraints excluded: chain N residue 590 CYS Chi-restraints excluded: chain N residue 611 THR Chi-restraints excluded: chain N residue 666 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 312 optimal weight: 1.9990 chunk 328 optimal weight: 3.9990 chunk 299 optimal weight: 0.9980 chunk 319 optimal weight: 0.8980 chunk 192 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 251 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 288 optimal weight: 4.9990 chunk 302 optimal weight: 0.8980 chunk 318 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN C 161 HIS E 137 GLN G 225 ASN K 645 ASN N 645 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28912 Z= 0.279 Angle : 0.636 7.453 39208 Z= 0.321 Chirality : 0.044 0.173 4344 Planarity : 0.005 0.053 5016 Dihedral : 8.008 118.643 4011 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.00 % Favored : 96.95 % Rotamer: Outliers : 2.34 % Allowed : 13.71 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.58 (0.14), residues: 3536 helix: 0.55 (0.13), residues: 1544 sheet: -0.73 (0.23), residues: 408 loop : 0.80 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 340 HIS 0.007 0.001 HIS A 40 PHE 0.018 0.002 PHE B 266 TYR 0.011 0.001 TYR C 337 ARG 0.010 0.001 ARG F 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 317 time to evaluate : 3.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.8193 (mmt-90) cc_final: 0.7891 (mtt90) REVERT: A 68 LYS cc_start: 0.7775 (ptpp) cc_final: 0.7161 (mttp) REVERT: A 81 ASP cc_start: 0.8104 (m-30) cc_final: 0.7732 (m-30) REVERT: A 221 LEU cc_start: 0.8864 (tp) cc_final: 0.8622 (tm) REVERT: A 224 GLU cc_start: 0.7329 (mm-30) cc_final: 0.6568 (tp30) REVERT: A 227 MET cc_start: 0.7963 (mmt) cc_final: 0.7390 (mmm) REVERT: A 284 LYS cc_start: 0.7980 (mtpp) cc_final: 0.7626 (mttm) REVERT: A 291 LYS cc_start: 0.7898 (ttpp) cc_final: 0.7642 (ttmm) REVERT: A 299 MET cc_start: 0.8272 (mmt) cc_final: 0.8019 (mtt) REVERT: A 334 GLU cc_start: 0.6737 (pm20) cc_final: 0.6250 (pp20) REVERT: A 357 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7721 (mt) REVERT: B 83 GLU cc_start: 0.7800 (tt0) cc_final: 0.7249 (mt-10) REVERT: B 187 ASP cc_start: 0.8016 (m-30) cc_final: 0.7631 (m-30) REVERT: B 224 GLU cc_start: 0.7695 (tp30) cc_final: 0.6604 (mm-30) REVERT: B 283 MET cc_start: 0.8542 (mmm) cc_final: 0.8287 (mmm) REVERT: B 328 LYS cc_start: 0.8034 (tttp) cc_final: 0.7591 (mttp) REVERT: B 372 ARG cc_start: 0.7100 (mtm-85) cc_final: 0.6792 (mtm180) REVERT: C 24 ASP cc_start: 0.7918 (m-30) cc_final: 0.7659 (m-30) REVERT: C 25 ASP cc_start: 0.7233 (p0) cc_final: 0.6701 (p0) REVERT: C 68 LYS cc_start: 0.8107 (mttm) cc_final: 0.7738 (mtmt) REVERT: C 99 GLU cc_start: 0.7400 (pm20) cc_final: 0.7091 (pm20) REVERT: C 105 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7628 (mp) REVERT: C 191 LYS cc_start: 0.8042 (ttmp) cc_final: 0.7621 (ttpp) REVERT: C 225 ASN cc_start: 0.7619 (t0) cc_final: 0.7265 (t0) REVERT: C 276 GLU cc_start: 0.7842 (tt0) cc_final: 0.7316 (mt-10) REVERT: C 299 MET cc_start: 0.8518 (mmm) cc_final: 0.8182 (mtt) REVERT: C 328 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7205 (ttmm) REVERT: C 355 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7604 (mmt) REVERT: C 363 ASP cc_start: 0.7141 (m-30) cc_final: 0.6896 (m-30) REVERT: D 72 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7091 (mt-10) REVERT: D 122 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7723 (mp) REVERT: D 276 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7607 (mt-10) REVERT: E 95 ARG cc_start: 0.7164 (mtm-85) cc_final: 0.6806 (mmt180) REVERT: E 128 ASN cc_start: 0.7484 (m110) cc_final: 0.6626 (t0) REVERT: E 241 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7747 (tt0) REVERT: E 328 LYS cc_start: 0.7941 (tttt) cc_final: 0.7162 (mttp) REVERT: E 360 GLN cc_start: 0.7371 (tt0) cc_final: 0.6728 (pm20) REVERT: F 72 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7157 (mp0) REVERT: F 80 ASP cc_start: 0.7701 (m-30) cc_final: 0.7425 (m-30) REVERT: F 95 ARG cc_start: 0.7089 (mtp85) cc_final: 0.6597 (mtt-85) REVERT: F 125 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7198 (mm-30) REVERT: F 167 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8272 (mm-30) REVERT: F 178 LEU cc_start: 0.7875 (tp) cc_final: 0.7345 (mt) REVERT: F 191 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7908 (tmtt) REVERT: F 206 ARG cc_start: 0.7623 (ttm110) cc_final: 0.7265 (ttm110) REVERT: F 226 GLU cc_start: 0.7909 (tp30) cc_final: 0.7506 (tp30) REVERT: F 326 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.6683 (ptmm) REVERT: F 328 LYS cc_start: 0.8096 (tttp) cc_final: 0.7667 (tptm) REVERT: F 354 GLN cc_start: 0.7635 (mm-40) cc_final: 0.7303 (mm110) REVERT: F 358 THR cc_start: 0.7962 (m) cc_final: 0.7638 (p) REVERT: G 117 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7671 (mt-10) REVERT: G 118 LYS cc_start: 0.7814 (mmmt) cc_final: 0.7241 (mmmm) REVERT: G 283 MET cc_start: 0.8615 (mmm) cc_final: 0.8302 (mmm) REVERT: G 326 LYS cc_start: 0.7557 (mmtm) cc_final: 0.6961 (mmtp) REVERT: H 24 ASP cc_start: 0.6700 (m-30) cc_final: 0.6384 (m-30) REVERT: H 25 ASP cc_start: 0.6905 (p0) cc_final: 0.6469 (p0) REVERT: H 68 LYS cc_start: 0.8258 (mmtm) cc_final: 0.7932 (mptt) REVERT: H 72 GLU cc_start: 0.7467 (tt0) cc_final: 0.7084 (mp0) REVERT: H 113 LYS cc_start: 0.5033 (OUTLIER) cc_final: 0.4549 (mppt) REVERT: H 167 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7487 (mm-30) REVERT: H 176 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7702 (mtp) REVERT: H 276 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7436 (mt-10) REVERT: H 299 MET cc_start: 0.8402 (mtp) cc_final: 0.7775 (mmm) REVERT: H 314 GLN cc_start: 0.7800 (tp40) cc_final: 0.7276 (tp40) REVERT: H 326 LYS cc_start: 0.7047 (mmpt) cc_final: 0.6817 (pttm) REVERT: H 328 LYS cc_start: 0.7749 (ttmt) cc_final: 0.7137 (tmtt) REVERT: H 336 LYS cc_start: 0.8167 (ttmt) cc_final: 0.7796 (tttm) REVERT: H 354 GLN cc_start: 0.7177 (OUTLIER) cc_final: 0.6796 (tp-100) REVERT: K 578 ASN cc_start: 0.6539 (t0) cc_final: 0.6286 (t0) REVERT: K 598 GLU cc_start: 0.5942 (pm20) cc_final: 0.5393 (pt0) REVERT: K 621 GLU cc_start: 0.7356 (tt0) cc_final: 0.6908 (mt-10) REVERT: L 582 LYS cc_start: 0.6290 (mtpt) cc_final: 0.5902 (mmtp) REVERT: L 595 LYS cc_start: 0.6309 (ptpt) cc_final: 0.5958 (mtmt) REVERT: L 616 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.7413 (ttmt) REVERT: M 521 LYS cc_start: 0.6877 (tttp) cc_final: 0.6366 (tttm) REVERT: M 527 SER cc_start: 0.7935 (m) cc_final: 0.7714 (p) REVERT: M 533 THR cc_start: 0.7908 (OUTLIER) cc_final: 0.7678 (t) REVERT: M 541 ASP cc_start: 0.7316 (t0) cc_final: 0.6537 (t70) REVERT: M 604 GLU cc_start: 0.6504 (mm-30) cc_final: 0.5966 (tt0) REVERT: M 644 SER cc_start: 0.7134 (p) cc_final: 0.6908 (m) REVERT: N 528 THR cc_start: 0.8143 (OUTLIER) cc_final: 0.7905 (p) REVERT: N 544 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6551 (tp30) REVERT: N 566 ARG cc_start: 0.6429 (ttt180) cc_final: 0.6095 (mtt180) REVERT: N 569 ASP cc_start: 0.6635 (OUTLIER) cc_final: 0.5942 (m-30) REVERT: N 616 LYS cc_start: 0.7018 (ttpt) cc_final: 0.6684 (tttm) outliers start: 71 outliers final: 49 residues processed: 361 average time/residue: 2.7926 time to fit residues: 1190.9131 Evaluate side-chains 380 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 313 time to evaluate : 3.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 191 LYS Chi-restraints excluded: chain F residue 225 ASN Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 364 GLU Chi-restraints excluded: chain G residue 373 LYS Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 271 SER Chi-restraints excluded: chain H residue 354 GLN Chi-restraints excluded: chain H residue 360 GLN Chi-restraints excluded: chain K residue 642 VAL Chi-restraints excluded: chain L residue 544 GLU Chi-restraints excluded: chain L residue 616 LYS Chi-restraints excluded: chain M residue 533 THR Chi-restraints excluded: chain M residue 559 SER Chi-restraints excluded: chain M residue 580 THR Chi-restraints excluded: chain M residue 594 ASP Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 664 SER Chi-restraints excluded: chain N residue 528 THR Chi-restraints excluded: chain N residue 544 GLU Chi-restraints excluded: chain N residue 569 ASP Chi-restraints excluded: chain N residue 580 THR Chi-restraints excluded: chain N residue 590 CYS Chi-restraints excluded: chain N residue 611 THR Chi-restraints excluded: chain N residue 666 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 209 optimal weight: 0.8980 chunk 338 optimal weight: 3.9990 chunk 206 optimal weight: 0.5980 chunk 160 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 chunk 354 optimal weight: 2.9990 chunk 326 optimal weight: 0.4980 chunk 282 optimal weight: 0.0970 chunk 29 optimal weight: 2.9990 chunk 218 optimal weight: 1.9990 chunk 173 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN G 225 ASN N 645 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28912 Z= 0.180 Angle : 0.585 7.009 39208 Z= 0.290 Chirality : 0.042 0.173 4344 Planarity : 0.004 0.046 5016 Dihedral : 7.468 106.411 4011 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.77 % Favored : 97.20 % Rotamer: Outliers : 1.65 % Allowed : 14.46 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.14), residues: 3536 helix: 0.76 (0.13), residues: 1560 sheet: -0.66 (0.24), residues: 408 loop : 0.91 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 79 HIS 0.007 0.001 HIS A 40 PHE 0.013 0.001 PHE A 255 TYR 0.009 0.001 TYR E 143 ARG 0.009 0.000 ARG F 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 322 time to evaluate : 3.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.8202 (mmt-90) cc_final: 0.7872 (mtt90) REVERT: A 68 LYS cc_start: 0.7750 (ptpp) cc_final: 0.7171 (mttp) REVERT: A 81 ASP cc_start: 0.8140 (m-30) cc_final: 0.7776 (m-30) REVERT: A 221 LEU cc_start: 0.8845 (tp) cc_final: 0.8626 (tm) REVERT: A 224 GLU cc_start: 0.7380 (mm-30) cc_final: 0.6545 (tp30) REVERT: A 227 MET cc_start: 0.7907 (mmt) cc_final: 0.7359 (mmm) REVERT: A 284 LYS cc_start: 0.7939 (mtpp) cc_final: 0.7557 (mttm) REVERT: A 291 LYS cc_start: 0.7895 (ttpp) cc_final: 0.7648 (ttmm) REVERT: A 299 MET cc_start: 0.8254 (mmt) cc_final: 0.8009 (mtt) REVERT: A 334 GLU cc_start: 0.6688 (pm20) cc_final: 0.6143 (pp20) REVERT: A 357 ILE cc_start: 0.8007 (OUTLIER) cc_final: 0.7689 (mt) REVERT: B 83 GLU cc_start: 0.7813 (tt0) cc_final: 0.7245 (mt-10) REVERT: B 95 ARG cc_start: 0.7215 (mtt-85) cc_final: 0.6886 (mtt-85) REVERT: B 187 ASP cc_start: 0.7978 (m-30) cc_final: 0.7591 (m-30) REVERT: B 224 GLU cc_start: 0.7691 (tp30) cc_final: 0.6592 (mm-30) REVERT: B 283 MET cc_start: 0.8512 (mmm) cc_final: 0.8240 (mmm) REVERT: B 328 LYS cc_start: 0.8017 (tttp) cc_final: 0.7600 (mttp) REVERT: B 334 GLU cc_start: 0.7003 (pm20) cc_final: 0.6736 (pp20) REVERT: B 372 ARG cc_start: 0.7101 (mtm-85) cc_final: 0.6766 (mtm180) REVERT: C 24 ASP cc_start: 0.7935 (m-30) cc_final: 0.7679 (m-30) REVERT: C 25 ASP cc_start: 0.7257 (p0) cc_final: 0.6790 (p0) REVERT: C 68 LYS cc_start: 0.8083 (mttm) cc_final: 0.7716 (mtmt) REVERT: C 99 GLU cc_start: 0.7392 (pm20) cc_final: 0.7123 (pm20) REVERT: C 105 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7604 (mp) REVERT: C 191 LYS cc_start: 0.8024 (ttmp) cc_final: 0.7618 (ttpp) REVERT: C 225 ASN cc_start: 0.7615 (t0) cc_final: 0.7251 (t0) REVERT: C 276 GLU cc_start: 0.7769 (tt0) cc_final: 0.7285 (mt-10) REVERT: C 299 MET cc_start: 0.8499 (mmm) cc_final: 0.8186 (mtt) REVERT: C 328 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7200 (mtmm) REVERT: C 363 ASP cc_start: 0.7162 (m-30) cc_final: 0.6903 (m-30) REVERT: D 72 GLU cc_start: 0.7362 (pt0) cc_final: 0.7078 (mt-10) REVERT: D 95 ARG cc_start: 0.7355 (mtt-85) cc_final: 0.6825 (mmt90) REVERT: D 276 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7628 (mt-10) REVERT: E 72 GLU cc_start: 0.7503 (mt-10) cc_final: 0.6854 (tt0) REVERT: E 95 ARG cc_start: 0.7058 (mtm-85) cc_final: 0.6751 (mmt180) REVERT: E 128 ASN cc_start: 0.7489 (m110) cc_final: 0.6654 (t0) REVERT: E 178 LEU cc_start: 0.7988 (mt) cc_final: 0.7708 (mt) REVERT: E 241 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7703 (tt0) REVERT: E 328 LYS cc_start: 0.7943 (tttt) cc_final: 0.7188 (mttp) REVERT: E 351 THR cc_start: 0.7458 (OUTLIER) cc_final: 0.7247 (m) REVERT: E 360 GLN cc_start: 0.7380 (tt0) cc_final: 0.6735 (pm20) REVERT: F 72 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7143 (mp0) REVERT: F 80 ASP cc_start: 0.7640 (m-30) cc_final: 0.7353 (m-30) REVERT: F 95 ARG cc_start: 0.7071 (mtp85) cc_final: 0.6593 (mtt-85) REVERT: F 125 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7179 (mm-30) REVERT: F 167 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8253 (mm-30) REVERT: F 178 LEU cc_start: 0.7848 (tp) cc_final: 0.7382 (mt) REVERT: F 206 ARG cc_start: 0.7609 (ttm110) cc_final: 0.7215 (ttm110) REVERT: F 226 GLU cc_start: 0.7892 (tp30) cc_final: 0.7489 (tp30) REVERT: F 326 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.6686 (ptmm) REVERT: F 328 LYS cc_start: 0.8131 (tttp) cc_final: 0.7709 (tptm) REVERT: F 354 GLN cc_start: 0.7568 (mm-40) cc_final: 0.7272 (mm110) REVERT: F 358 THR cc_start: 0.7960 (m) cc_final: 0.7655 (p) REVERT: G 117 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7629 (mt-10) REVERT: G 118 LYS cc_start: 0.7827 (mmmt) cc_final: 0.7246 (mmmm) REVERT: G 283 MET cc_start: 0.8596 (mmm) cc_final: 0.8302 (mmm) REVERT: G 326 LYS cc_start: 0.7527 (mmtm) cc_final: 0.7004 (mmtp) REVERT: H 24 ASP cc_start: 0.6627 (m-30) cc_final: 0.6307 (m-30) REVERT: H 25 ASP cc_start: 0.6761 (p0) cc_final: 0.6325 (p0) REVERT: H 68 LYS cc_start: 0.8275 (mmtm) cc_final: 0.7936 (mptt) REVERT: H 72 GLU cc_start: 0.7456 (tt0) cc_final: 0.7093 (mp0) REVERT: H 113 LYS cc_start: 0.5064 (OUTLIER) cc_final: 0.4613 (mppt) REVERT: H 167 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7497 (mm-30) REVERT: H 176 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7703 (mtp) REVERT: H 276 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7474 (mt-10) REVERT: H 314 GLN cc_start: 0.7821 (tp40) cc_final: 0.7315 (tp40) REVERT: H 328 LYS cc_start: 0.7706 (ttmt) cc_final: 0.7112 (tmtt) REVERT: H 336 LYS cc_start: 0.8184 (ttmt) cc_final: 0.7815 (tttm) REVERT: H 354 GLN cc_start: 0.7198 (OUTLIER) cc_final: 0.6818 (tp-100) REVERT: K 578 ASN cc_start: 0.6503 (t0) cc_final: 0.6254 (t0) REVERT: K 598 GLU cc_start: 0.6029 (pm20) cc_final: 0.5488 (pt0) REVERT: K 621 GLU cc_start: 0.7351 (tt0) cc_final: 0.6932 (mt-10) REVERT: L 574 GLU cc_start: 0.7289 (tm-30) cc_final: 0.6935 (tm-30) REVERT: L 582 LYS cc_start: 0.6287 (mtpt) cc_final: 0.5921 (mmtp) REVERT: L 595 LYS cc_start: 0.6275 (ptpt) cc_final: 0.5914 (mtmt) REVERT: L 616 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7370 (ttmt) REVERT: M 521 LYS cc_start: 0.6871 (tttp) cc_final: 0.6363 (tttm) REVERT: M 533 THR cc_start: 0.7957 (m) cc_final: 0.7757 (t) REVERT: M 541 ASP cc_start: 0.7262 (t0) cc_final: 0.6497 (t70) REVERT: M 604 GLU cc_start: 0.6447 (mm-30) cc_final: 0.5927 (tt0) REVERT: M 644 SER cc_start: 0.7096 (p) cc_final: 0.6892 (m) REVERT: N 528 THR cc_start: 0.8164 (OUTLIER) cc_final: 0.7940 (p) REVERT: N 566 ARG cc_start: 0.6344 (ttt180) cc_final: 0.6039 (mtt180) REVERT: N 616 LYS cc_start: 0.7025 (ttpt) cc_final: 0.6689 (tttm) outliers start: 50 outliers final: 33 residues processed: 355 average time/residue: 2.7394 time to fit residues: 1131.5625 Evaluate side-chains 360 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 315 time to evaluate : 3.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 225 ASN Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 364 GLU Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 354 GLN Chi-restraints excluded: chain K residue 642 VAL Chi-restraints excluded: chain L residue 544 GLU Chi-restraints excluded: chain L residue 616 LYS Chi-restraints excluded: chain M residue 559 SER Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 664 SER Chi-restraints excluded: chain N residue 528 THR Chi-restraints excluded: chain N residue 580 THR Chi-restraints excluded: chain N residue 611 THR Chi-restraints excluded: chain N residue 666 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 224 optimal weight: 0.5980 chunk 300 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 260 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 78 optimal weight: 0.4980 chunk 282 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 290 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN G 225 ASN N 645 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.096422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.084748 restraints weight = 113770.294| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.07 r_work: 0.2899 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28912 Z= 0.261 Angle : 0.620 6.955 39208 Z= 0.311 Chirality : 0.044 0.195 4344 Planarity : 0.005 0.046 5016 Dihedral : 7.742 115.056 4010 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.00 % Favored : 96.95 % Rotamer: Outliers : 1.85 % Allowed : 14.37 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.75 (0.14), residues: 3536 helix: 0.73 (0.13), residues: 1544 sheet: -0.67 (0.24), residues: 408 loop : 0.84 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 340 HIS 0.007 0.001 HIS A 40 PHE 0.018 0.002 PHE B 266 TYR 0.011 0.001 TYR E 91 ARG 0.009 0.001 ARG F 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17733.55 seconds wall clock time: 304 minutes 7.70 seconds (18247.70 seconds total)