Starting phenix.real_space_refine on Mon Mar 18 20:53:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8q_28933/03_2024/8f8q_28933_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8q_28933/03_2024/8f8q_28933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8q_28933/03_2024/8f8q_28933.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8q_28933/03_2024/8f8q_28933.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8q_28933/03_2024/8f8q_28933_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8q_28933/03_2024/8f8q_28933_updated.pdb" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 143 5.16 5 C 13862 2.51 5 N 3737 2.21 5 O 4246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "B PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22006 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2893 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: "G" Number of atoms: 2262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2262 Classifications: {'peptide': 278} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 267} Chain: "H" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2138 Classifications: {'peptide': 270} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 259} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.75, per 1000 atoms: 0.49 Number of scatterers: 22006 At special positions: 0 Unit cell: (81, 112.32, 258.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 143 16.00 P 12 15.00 Mg 6 11.99 O 4246 8.00 N 3737 7.00 C 13862 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 8.42 Conformation dependent library (CDL) restraints added in 4.1 seconds 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5158 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 130 helices and 32 sheets defined 39.3% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.74 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 196 removed outlier: 4.015A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 removed outlier: 3.692A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.941A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 338 through 348 removed outlier: 4.233A pdb=" N SER A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 370 through 373 No H-bonds generated for 'chain 'A' and resid 370 through 373' Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 194 removed outlier: 4.119A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.987A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.981A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 338 through 348 removed outlier: 4.036A pdb=" N SER B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 removed outlier: 4.241A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.846A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 252 through 256 removed outlier: 4.027A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 261 Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 290 through 294 Processing helix chain 'C' and resid 303 through 305 No H-bonds generated for 'chain 'C' and resid 303 through 305' Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 338 through 348 removed outlier: 4.062A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 369 through 373 Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 137 through 144 Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 195 removed outlier: 4.049A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 removed outlier: 3.985A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.927A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N CYS D 257 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 287 through 294 removed outlier: 5.208A pdb=" N LYS D 291 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 338 through 348 removed outlier: 4.003A pdb=" N SER D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 369 through 373 Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 79 through 91 Processing helix chain 'E' and resid 113 through 125 Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 182 through 194 removed outlier: 4.196A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 removed outlier: 3.815A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 253 through 256 No H-bonds generated for 'chain 'E' and resid 253 through 256' Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 274 through 283 Processing helix chain 'E' and resid 290 through 294 Processing helix chain 'E' and resid 302 through 304 No H-bonds generated for 'chain 'E' and resid 302 through 304' Processing helix chain 'E' and resid 309 through 320 Processing helix chain 'E' and resid 335 through 337 No H-bonds generated for 'chain 'E' and resid 335 through 337' Processing helix chain 'E' and resid 339 through 347 Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 369 through 373 removed outlier: 4.262A pdb=" N LYS E 373 " --> pdb=" O VAL E 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 64 removed outlier: 3.717A pdb=" N SER F 60 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG F 62 " --> pdb=" O GLN F 59 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY F 63 " --> pdb=" O SER F 60 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE F 64 " --> pdb=" O LYS F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 91 Processing helix chain 'F' and resid 113 through 125 Processing helix chain 'F' and resid 137 through 144 Processing helix chain 'F' and resid 172 through 174 No H-bonds generated for 'chain 'F' and resid 172 through 174' Processing helix chain 'F' and resid 182 through 194 removed outlier: 4.069A pdb=" N THR F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 216 removed outlier: 3.775A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 230 Processing helix chain 'F' and resid 253 through 256 No H-bonds generated for 'chain 'F' and resid 253 through 256' Processing helix chain 'F' and resid 258 through 261 Processing helix chain 'F' and resid 264 through 266 No H-bonds generated for 'chain 'F' and resid 264 through 266' Processing helix chain 'F' and resid 274 through 283 Processing helix chain 'F' and resid 287 through 295 removed outlier: 4.317A pdb=" N LYS F 291 " --> pdb=" O ILE F 287 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ASP F 292 " --> pdb=" O ASP F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 304 No H-bonds generated for 'chain 'F' and resid 302 through 304' Processing helix chain 'F' and resid 309 through 320 Processing helix chain 'F' and resid 339 through 347 Processing helix chain 'F' and resid 351 through 354 removed outlier: 3.671A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 351 through 354' Processing helix chain 'F' and resid 359 through 365 Processing helix chain 'F' and resid 369 through 371 No H-bonds generated for 'chain 'F' and resid 369 through 371' Processing helix chain 'G' and resid 10 through 22 Processing helix chain 'G' and resid 30 through 39 Processing helix chain 'G' and resid 43 through 47 Processing helix chain 'G' and resid 52 through 61 Processing helix chain 'G' and resid 119 through 135 removed outlier: 4.274A pdb=" N SER G 123 " --> pdb=" O SER G 119 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N CYS G 124 " --> pdb=" O TRP G 120 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA G 127 " --> pdb=" O SER G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 248 removed outlier: 4.136A pdb=" N GLU G 238 " --> pdb=" O ASN G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 253 No H-bonds generated for 'chain 'G' and resid 250 through 253' Processing helix chain 'G' and resid 274 through 281 removed outlier: 4.330A pdb=" N GLY G 280 " --> pdb=" O SER G 276 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS G 281 " --> pdb=" O TYR G 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 14 Processing helix chain 'H' and resid 21 through 26 Processing helix chain 'H' and resid 36 through 41 removed outlier: 3.578A pdb=" N LEU H 40 " --> pdb=" O CYS H 36 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER H 41 " --> pdb=" O GLU H 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 36 through 41' Processing helix chain 'H' and resid 91 through 111 removed outlier: 3.680A pdb=" N GLU H 99 " --> pdb=" O LYS H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 230 Processing helix chain 'H' and resid 232 through 243 Processing helix chain 'H' and resid 252 through 255 removed outlier: 4.046A pdb=" N PHE H 255 " --> pdb=" O ASN H 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 252 through 255' Processing helix chain 'H' and resid 258 through 270 Processing sheet with id= A, first strand: chain 'A' and resid 8 through 12 Processing sheet with id= B, first strand: chain 'A' and resid 35 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 103 through 107 Processing sheet with id= D, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.507A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= F, first strand: chain 'B' and resid 8 through 12 Processing sheet with id= G, first strand: chain 'B' and resid 35 through 38 Processing sheet with id= H, first strand: chain 'B' and resid 103 through 107 Processing sheet with id= I, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.275A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= K, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.550A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= M, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.394A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= O, first strand: chain 'D' and resid 132 through 136 removed outlier: 6.644A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 35 through 38 Processing sheet with id= Q, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.390A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 238 through 241 Processing sheet with id= S, first strand: chain 'E' and resid 132 through 136 removed outlier: 6.610A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 35 through 38 Processing sheet with id= U, first strand: chain 'E' and resid 297 through 300 removed outlier: 6.256A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 238 through 241 Processing sheet with id= W, first strand: chain 'F' and resid 8 through 12 Processing sheet with id= X, first strand: chain 'F' and resid 35 through 38 Processing sheet with id= Y, first strand: chain 'F' and resid 103 through 107 Processing sheet with id= Z, first strand: chain 'F' and resid 297 through 300 removed outlier: 6.388A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 238 through 241 Processing sheet with id= AB, first strand: chain 'G' and resid 63 through 65 removed outlier: 3.890A pdb=" N THR G 63 " --> pdb=" O ILE G 76 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'G' and resid 86 through 89 removed outlier: 3.597A pdb=" N ILE G 94 " --> pdb=" O ASP G 89 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 139 through 147 removed outlier: 4.445A pdb=" N THR G 180 " --> pdb=" O GLN G 187 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N GLN G 187 " --> pdb=" O THR G 180 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'H' and resid 48 through 52 removed outlier: 4.032A pdb=" N LYS H 48 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS H 57 " --> pdb=" O ASP H 52 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 116 through 123 removed outlier: 4.067A pdb=" N LYS H 145 " --> pdb=" O GLN H 178 " (cutoff:3.500A) 828 hydrogen bonds defined for protein. 2292 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: 6.79 Time building geometry restraints manager: 9.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7146 1.34 - 1.46: 4159 1.46 - 1.58: 10905 1.58 - 1.69: 18 1.69 - 1.81: 248 Bond restraints: 22476 Sorted by residual: bond pdb=" CE1 HIC F 73 " pdb=" NE2 HIC F 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.60e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.50e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.29e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.23e+00 bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.18e+00 ... (remaining 22471 not shown) Histogram of bond angle deviations from ideal: 99.86 - 107.17: 881 107.17 - 114.49: 12980 114.49 - 121.81: 11572 121.81 - 129.12: 4897 129.12 - 136.44: 148 Bond angle restraints: 30478 Sorted by residual: angle pdb=" C ASP H 247 " pdb=" N ALA H 248 " pdb=" CA ALA H 248 " ideal model delta sigma weight residual 121.31 128.47 -7.16 1.49e+00 4.50e-01 2.31e+01 angle pdb=" C GLY A 46 " pdb=" N MET A 47 " pdb=" CA MET A 47 " ideal model delta sigma weight residual 121.54 129.48 -7.94 1.91e+00 2.74e-01 1.73e+01 angle pdb=" C GLY D 46 " pdb=" N MET D 47 " pdb=" CA MET D 47 " ideal model delta sigma weight residual 121.54 129.30 -7.76 1.91e+00 2.74e-01 1.65e+01 angle pdb=" N ALA H 248 " pdb=" CA ALA H 248 " pdb=" C ALA H 248 " ideal model delta sigma weight residual 110.35 115.46 -5.11 1.40e+00 5.10e-01 1.33e+01 angle pdb=" C GLY B 46 " pdb=" N MET B 47 " pdb=" CA MET B 47 " ideal model delta sigma weight residual 122.61 128.25 -5.64 1.56e+00 4.11e-01 1.31e+01 ... (remaining 30473 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.20: 12707 23.20 - 46.41: 705 46.41 - 69.61: 117 69.61 - 92.82: 14 92.82 - 116.02: 6 Dihedral angle restraints: 13549 sinusoidal: 5506 harmonic: 8043 Sorted by residual: dihedral pdb=" CA PHE E 127 " pdb=" C PHE E 127 " pdb=" N ASN E 128 " pdb=" CA ASN E 128 " ideal model delta harmonic sigma weight residual -180.00 -150.42 -29.58 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 -176.02 116.02 1 2.00e+01 2.50e-03 3.45e+01 dihedral pdb=" O1B ADP F 401 " pdb=" O3A ADP F 401 " pdb=" PB ADP F 401 " pdb=" PA ADP F 401 " ideal model delta sinusoidal sigma weight residual -60.00 -175.12 115.12 1 2.00e+01 2.50e-03 3.42e+01 ... (remaining 13546 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1956 0.034 - 0.068: 902 0.068 - 0.102: 337 0.102 - 0.137: 144 0.137 - 0.171: 28 Chirality restraints: 3367 Sorted by residual: chirality pdb=" CA CYS B 257 " pdb=" N CYS B 257 " pdb=" C CYS B 257 " pdb=" CB CYS B 257 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.30e-01 chirality pdb=" CA CYS C 257 " pdb=" N CYS C 257 " pdb=" C CYS C 257 " pdb=" CB CYS C 257 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CA CYS E 257 " pdb=" N CYS E 257 " pdb=" C CYS E 257 " pdb=" CB CYS E 257 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.90e-01 ... (remaining 3364 not shown) Planarity restraints: 3918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 242 " 0.051 5.00e-02 4.00e+02 7.73e-02 9.56e+00 pdb=" N PRO E 243 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO E 243 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 243 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 163 " 0.037 5.00e-02 4.00e+02 5.68e-02 5.15e+00 pdb=" N PRO E 164 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO E 164 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 164 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 242 " -0.035 5.00e-02 4.00e+02 5.33e-02 4.54e+00 pdb=" N PRO A 243 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " -0.030 5.00e-02 4.00e+02 ... (remaining 3915 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 228 2.64 - 3.20: 17835 3.20 - 3.77: 34120 3.77 - 4.33: 48939 4.33 - 4.90: 80286 Nonbonded interactions: 181408 Sorted by model distance: nonbonded pdb=" O3B ADP E 401 " pdb="MG MG E 402 " model vdw 2.072 2.170 nonbonded pdb=" O3B ADP A 401 " pdb="MG MG A 402 " model vdw 2.077 2.170 nonbonded pdb=" O3B ADP D 401 " pdb="MG MG D 402 " model vdw 2.196 2.170 nonbonded pdb=" OH TYR G 198 " pdb=" OE1 GLU G 200 " model vdw 2.287 2.440 nonbonded pdb=" O GLN D 314 " pdb=" OG1 THR D 318 " model vdw 2.292 2.440 ... (remaining 181403 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 375 or resid 401 through 402)) selection = (chain 'B' and (resid 6 through 375 or resid 401 through 402)) selection = (chain 'C' and (resid 6 through 375 or resid 401 through 402)) selection = (chain 'D' and (resid 6 through 375 or resid 401 through 402)) selection = (chain 'E' and (resid 6 through 375 or resid 401 through 402)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.020 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: 0.010 Extract box with map and model: 13.880 Check model and map are aligned: 0.300 Set scattering table: 0.200 Process input model: 57.230 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 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 0.062 22476 Z= 0.255 Angle : 0.686 9.700 30478 Z= 0.364 Chirality : 0.049 0.171 3367 Planarity : 0.006 0.077 3918 Dihedral : 14.383 116.021 8391 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.93 % Allowed : 9.29 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.15), residues: 2744 helix: -1.31 (0.14), residues: 1094 sheet: 0.91 (0.21), residues: 589 loop : -0.58 (0.19), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 173 HIS 0.005 0.001 HIS G 209 PHE 0.018 0.002 PHE E 31 TYR 0.013 0.001 TYR H 59 ARG 0.004 0.001 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 704 time to evaluate : 2.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8727 (pt) cc_final: 0.8407 (mt) REVERT: A 44 MET cc_start: 0.7786 (mmm) cc_final: 0.7515 (mmm) REVERT: A 99 GLU cc_start: 0.7793 (pm20) cc_final: 0.7563 (mp0) REVERT: A 107 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7695 (tt0) REVERT: A 263 GLN cc_start: 0.8595 (mt0) cc_final: 0.8355 (mt0) REVERT: A 359 LYS cc_start: 0.8044 (tmtm) cc_final: 0.7499 (tmtm) REVERT: A 363 ASP cc_start: 0.7261 (m-30) cc_final: 0.6890 (m-30) REVERT: A 372 ARG cc_start: 0.7272 (mtm-85) cc_final: 0.7021 (mtm-85) REVERT: B 59 GLN cc_start: 0.8658 (tp-100) cc_final: 0.8443 (mm110) REVERT: B 99 GLU cc_start: 0.7887 (mp0) cc_final: 0.7429 (mp0) REVERT: B 299 MET cc_start: 0.8847 (mtm) cc_final: 0.8539 (mtm) REVERT: B 361 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7477 (mt-10) REVERT: C 91 TYR cc_start: 0.8851 (m-80) cc_final: 0.8529 (m-80) REVERT: C 128 ASN cc_start: 0.8202 (p0) cc_final: 0.7929 (p0) REVERT: C 143 TYR cc_start: 0.8691 (m-80) cc_final: 0.8450 (m-80) REVERT: C 222 ASP cc_start: 0.8195 (t0) cc_final: 0.7948 (t0) REVERT: C 263 GLN cc_start: 0.8812 (mt0) cc_final: 0.8585 (mt0) REVERT: C 286 ASP cc_start: 0.7808 (m-30) cc_final: 0.7603 (m-30) REVERT: C 297 ASN cc_start: 0.8565 (m110) cc_final: 0.8306 (m-40) REVERT: C 373 LYS cc_start: 0.8628 (mmmt) cc_final: 0.8143 (mmmm) REVERT: D 53 TYR cc_start: 0.8844 (m-80) cc_final: 0.8536 (m-80) REVERT: D 211 ASP cc_start: 0.8167 (t0) cc_final: 0.7965 (m-30) REVERT: D 242 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7984 (mp) REVERT: D 276 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7811 (mt-10) REVERT: D 334 GLU cc_start: 0.7617 (pm20) cc_final: 0.7406 (pm20) REVERT: D 359 LYS cc_start: 0.8262 (tptp) cc_final: 0.8048 (tmtm) REVERT: D 364 GLU cc_start: 0.7507 (tm-30) cc_final: 0.7112 (tm-30) REVERT: E 113 LYS cc_start: 0.8199 (mmmm) cc_final: 0.7986 (mtmm) REVERT: E 176 MET cc_start: 0.8578 (mtp) cc_final: 0.8334 (mtp) REVERT: E 224 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7713 (mm-30) REVERT: E 236 LEU cc_start: 0.8525 (mt) cc_final: 0.8271 (mp) REVERT: E 286 ASP cc_start: 0.7702 (t0) cc_final: 0.7414 (t0) REVERT: E 363 ASP cc_start: 0.7778 (m-30) cc_final: 0.7525 (m-30) REVERT: F 25 ASP cc_start: 0.7572 (p0) cc_final: 0.7305 (p0) REVERT: F 44 MET cc_start: 0.8279 (mmm) cc_final: 0.7945 (mtt) REVERT: F 84 LYS cc_start: 0.8699 (ttmm) cc_final: 0.8486 (ttmt) REVERT: F 229 THR cc_start: 0.8751 (p) cc_final: 0.8511 (t) REVERT: F 244 ASP cc_start: 0.8296 (p0) cc_final: 0.8085 (p0) REVERT: F 270 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7393 (mm-30) REVERT: F 325 MET cc_start: 0.8594 (tpp) cc_final: 0.8291 (tpp) REVERT: F 354 GLN cc_start: 0.7746 (pt0) cc_final: 0.7523 (pt0) REVERT: G 31 GLU cc_start: 0.5928 (OUTLIER) cc_final: 0.5597 (mm-30) REVERT: G 34 ASN cc_start: 0.6855 (t0) cc_final: 0.6469 (t0) REVERT: G 36 VAL cc_start: 0.8332 (m) cc_final: 0.8032 (p) REVERT: G 38 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8186 (tt) REVERT: G 58 ASN cc_start: 0.8171 (m-40) cc_final: 0.7943 (m110) REVERT: G 60 ASP cc_start: 0.7072 (m-30) cc_final: 0.6813 (m-30) REVERT: G 72 ASP cc_start: 0.7216 (t0) cc_final: 0.7009 (t0) REVERT: G 99 ASP cc_start: 0.7035 (t0) cc_final: 0.6540 (t0) REVERT: G 134 ASP cc_start: 0.7538 (t70) cc_final: 0.7187 (t0) REVERT: G 189 VAL cc_start: 0.7347 (OUTLIER) cc_final: 0.7070 (t) REVERT: G 200 GLU cc_start: 0.7785 (tt0) cc_final: 0.7355 (tt0) REVERT: G 206 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8347 (tp) REVERT: G 233 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6849 (mt-10) REVERT: G 266 ARG cc_start: 0.8407 (mpt-90) cc_final: 0.8069 (mmt-90) REVERT: G 270 ASP cc_start: 0.8367 (t0) cc_final: 0.7909 (t70) REVERT: G 281 LYS cc_start: 0.7938 (mtpp) cc_final: 0.7711 (mtpp) REVERT: H 11 ASP cc_start: 0.7598 (t0) cc_final: 0.7074 (t0) REVERT: H 23 LYS cc_start: 0.8253 (tmmt) cc_final: 0.7804 (tmmt) REVERT: H 168 LYS cc_start: 0.8265 (tttm) cc_final: 0.8023 (tttp) REVERT: H 222 ASN cc_start: 0.8786 (m-40) cc_final: 0.8274 (m110) REVERT: H 270 GLN cc_start: 0.7597 (mt0) cc_final: 0.7396 (mt0) outliers start: 93 outliers final: 30 residues processed: 767 average time/residue: 1.4141 time to fit residues: 1217.8506 Evaluate side-chains 684 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 648 time to evaluate : 2.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 252 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 4.9990 chunk 209 optimal weight: 1.9990 chunk 116 optimal weight: 0.2980 chunk 71 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 216 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 250 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 162 ASN A 225 ASN A 280 ASN B 111 ASN B 162 ASN C 121 GLN C 137 GLN C 246 GLN C 353 GLN C 371 HIS D 12 ASN D 115 ASN D 162 ASN E 78 ASN E 297 ASN E 353 GLN F 12 ASN F 246 GLN G 162 GLN G 164 GLN G 203 ASN G 205 GLN G 240 GLN G 261 GLN H 20 GLN H 241 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 22476 Z= 0.402 Angle : 0.637 10.121 30478 Z= 0.314 Chirality : 0.048 0.193 3367 Planarity : 0.006 0.126 3918 Dihedral : 8.579 112.764 3159 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.69 % Allowed : 16.93 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.43 (0.16), residues: 2744 helix: -0.41 (0.15), residues: 1123 sheet: 0.82 (0.21), residues: 566 loop : -0.58 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP H 148 HIS 0.010 0.002 HIS B 161 PHE 0.017 0.002 PHE E 31 TYR 0.016 0.002 TYR H 59 ARG 0.009 0.001 ARG E 210 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 663 time to evaluate : 2.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8711 (pt) cc_final: 0.8370 (mt) REVERT: A 99 GLU cc_start: 0.7861 (pm20) cc_final: 0.7584 (mp0) REVERT: A 263 GLN cc_start: 0.8640 (mt0) cc_final: 0.8381 (mt0) REVERT: A 338 SER cc_start: 0.8416 (m) cc_final: 0.8195 (m) REVERT: A 363 ASP cc_start: 0.7258 (m-30) cc_final: 0.6977 (m-30) REVERT: B 99 GLU cc_start: 0.7948 (mp0) cc_final: 0.7658 (mp0) REVERT: B 299 MET cc_start: 0.8902 (mtm) cc_final: 0.8692 (mtm) REVERT: B 361 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7509 (mt-10) REVERT: C 68 LYS cc_start: 0.8677 (mmtp) cc_final: 0.8403 (mttm) REVERT: C 91 TYR cc_start: 0.8892 (m-80) cc_final: 0.8553 (m-80) REVERT: C 128 ASN cc_start: 0.8234 (p0) cc_final: 0.7904 (p0) REVERT: C 143 TYR cc_start: 0.8732 (m-80) cc_final: 0.8524 (m-80) REVERT: C 222 ASP cc_start: 0.8227 (t0) cc_final: 0.7981 (t0) REVERT: C 263 GLN cc_start: 0.8845 (mt0) cc_final: 0.8641 (mt0) REVERT: C 286 ASP cc_start: 0.7933 (m-30) cc_final: 0.7701 (m-30) REVERT: C 297 ASN cc_start: 0.8617 (m110) cc_final: 0.8320 (m-40) REVERT: C 373 LYS cc_start: 0.8652 (mmmt) cc_final: 0.8424 (mmmt) REVERT: D 364 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7208 (tm-30) REVERT: E 50 LYS cc_start: 0.8043 (ptpp) cc_final: 0.7748 (mtpt) REVERT: E 61 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8007 (ptmt) REVERT: E 224 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7829 (mm-30) REVERT: E 236 LEU cc_start: 0.8513 (mt) cc_final: 0.8273 (mp) REVERT: E 286 ASP cc_start: 0.7773 (t0) cc_final: 0.7447 (t0) REVERT: E 363 ASP cc_start: 0.7840 (m-30) cc_final: 0.7587 (m-30) REVERT: F 25 ASP cc_start: 0.7713 (p0) cc_final: 0.7484 (p0) REVERT: F 44 MET cc_start: 0.8330 (mmm) cc_final: 0.7901 (mtt) REVERT: F 206 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7853 (ttt180) REVERT: F 325 MET cc_start: 0.8562 (tpp) cc_final: 0.8175 (tpp) REVERT: F 354 GLN cc_start: 0.7855 (pt0) cc_final: 0.7536 (pt0) REVERT: G 19 LYS cc_start: 0.7786 (tttp) cc_final: 0.7483 (tttp) REVERT: G 31 GLU cc_start: 0.6322 (OUTLIER) cc_final: 0.6105 (mm-30) REVERT: G 34 ASN cc_start: 0.7022 (t0) cc_final: 0.6653 (t0) REVERT: G 36 VAL cc_start: 0.8325 (m) cc_final: 0.8070 (p) REVERT: G 58 ASN cc_start: 0.8217 (m-40) cc_final: 0.7947 (m110) REVERT: G 60 ASP cc_start: 0.7200 (m-30) cc_final: 0.6937 (m-30) REVERT: G 72 ASP cc_start: 0.7419 (t0) cc_final: 0.7199 (t0) REVERT: G 99 ASP cc_start: 0.7019 (t0) cc_final: 0.6495 (t0) REVERT: G 134 ASP cc_start: 0.7591 (t70) cc_final: 0.7223 (t0) REVERT: G 176 GLU cc_start: 0.6849 (tm-30) cc_final: 0.6607 (tm-30) REVERT: G 189 VAL cc_start: 0.7449 (OUTLIER) cc_final: 0.7209 (t) REVERT: G 233 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6852 (mt-10) REVERT: G 268 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.7964 (mmmm) REVERT: G 270 ASP cc_start: 0.8413 (t0) cc_final: 0.8015 (t70) REVERT: G 281 LYS cc_start: 0.8041 (mtpp) cc_final: 0.7827 (mtpp) REVERT: H 11 ASP cc_start: 0.7575 (t0) cc_final: 0.7206 (t70) REVERT: H 23 LYS cc_start: 0.8270 (ttmt) cc_final: 0.7729 (tmmt) REVERT: H 168 LYS cc_start: 0.8304 (tttm) cc_final: 0.8052 (tttp) REVERT: H 222 ASN cc_start: 0.8836 (m-40) cc_final: 0.8370 (m110) REVERT: H 230 GLU cc_start: 0.7915 (mp0) cc_final: 0.7562 (mp0) REVERT: H 269 ARG cc_start: 0.7784 (tpp80) cc_final: 0.7289 (ttp80) outliers start: 111 outliers final: 60 residues processed: 711 average time/residue: 1.4760 time to fit residues: 1174.3942 Evaluate side-chains 709 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 644 time to evaluate : 2.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 206 ARG Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 166 LYS Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 207 VAL Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain G residue 268 LYS Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 245 SER Chi-restraints excluded: chain H residue 267 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 139 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 208 optimal weight: 0.6980 chunk 170 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 251 optimal weight: 1.9990 chunk 271 optimal weight: 0.7980 chunk 223 optimal weight: 0.2980 chunk 248 optimal weight: 0.0870 chunk 85 optimal weight: 0.9990 chunk 201 optimal weight: 0.4980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 162 ASN A 225 ASN A 280 ASN B 92 ASN C 115 ASN C 121 GLN C 137 GLN C 246 GLN C 353 GLN D 12 ASN D 92 ASN D 115 ASN D 162 ASN E 78 ASN E 297 ASN E 353 GLN F 12 ASN F 246 GLN G 162 GLN G 164 GLN G 205 GLN ** G 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 240 GLN G 261 GLN H 19 GLN H 20 GLN H 178 GLN H 241 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22476 Z= 0.194 Angle : 0.553 7.855 30478 Z= 0.267 Chirality : 0.044 0.150 3367 Planarity : 0.004 0.065 3918 Dihedral : 7.809 104.737 3136 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.35 % Allowed : 18.83 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.16), residues: 2744 helix: 0.16 (0.16), residues: 1119 sheet: 0.88 (0.22), residues: 566 loop : -0.46 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 173 HIS 0.005 0.001 HIS B 161 PHE 0.013 0.001 PHE C 255 TYR 0.019 0.001 TYR E 143 ARG 0.011 0.001 ARG G 121 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 666 time to evaluate : 2.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8708 (pt) cc_final: 0.8330 (mt) REVERT: A 99 GLU cc_start: 0.7853 (pm20) cc_final: 0.7575 (mp0) REVERT: A 263 GLN cc_start: 0.8650 (mt0) cc_final: 0.8367 (mt0) REVERT: A 363 ASP cc_start: 0.7198 (m-30) cc_final: 0.6962 (m-30) REVERT: B 99 GLU cc_start: 0.7939 (mp0) cc_final: 0.7689 (mp0) REVERT: B 153 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8632 (tp) REVERT: B 355 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8062 (mtm) REVERT: B 369 ILE cc_start: 0.8639 (tt) cc_final: 0.8426 (tp) REVERT: C 68 LYS cc_start: 0.8693 (mmtp) cc_final: 0.8419 (mttm) REVERT: C 91 TYR cc_start: 0.8841 (m-80) cc_final: 0.8426 (m-80) REVERT: C 123 MET cc_start: 0.8731 (tpp) cc_final: 0.8393 (mmp) REVERT: C 128 ASN cc_start: 0.8192 (p0) cc_final: 0.7867 (p0) REVERT: C 143 TYR cc_start: 0.8659 (m-80) cc_final: 0.8443 (m-80) REVERT: C 222 ASP cc_start: 0.8205 (t0) cc_final: 0.7971 (t0) REVERT: C 263 GLN cc_start: 0.8799 (mt0) cc_final: 0.8576 (mt0) REVERT: C 286 ASP cc_start: 0.7948 (m-30) cc_final: 0.7729 (m-30) REVERT: C 297 ASN cc_start: 0.8622 (m110) cc_final: 0.8312 (m-40) REVERT: C 373 LYS cc_start: 0.8644 (mmmt) cc_final: 0.8436 (mmmt) REVERT: D 53 TYR cc_start: 0.8818 (m-80) cc_final: 0.8541 (m-80) REVERT: D 276 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7907 (mt-10) REVERT: D 364 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7206 (tm-30) REVERT: E 50 LYS cc_start: 0.8018 (ptpp) cc_final: 0.7746 (mtpt) REVERT: E 61 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8021 (ptmt) REVERT: E 286 ASP cc_start: 0.7756 (t0) cc_final: 0.7425 (t0) REVERT: E 363 ASP cc_start: 0.7844 (m-30) cc_final: 0.7622 (m-30) REVERT: F 44 MET cc_start: 0.8331 (mmm) cc_final: 0.8051 (mtt) REVERT: F 68 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8298 (mptt) REVERT: F 84 LYS cc_start: 0.8716 (ttmm) cc_final: 0.8502 (ttmt) REVERT: G 19 LYS cc_start: 0.7763 (tttp) cc_final: 0.7460 (tttp) REVERT: G 34 ASN cc_start: 0.7008 (t0) cc_final: 0.6623 (t0) REVERT: G 36 VAL cc_start: 0.8336 (m) cc_final: 0.8083 (p) REVERT: G 58 ASN cc_start: 0.8157 (m-40) cc_final: 0.7884 (m110) REVERT: G 72 ASP cc_start: 0.7310 (t0) cc_final: 0.7081 (t0) REVERT: G 99 ASP cc_start: 0.6991 (t0) cc_final: 0.6465 (t0) REVERT: G 134 ASP cc_start: 0.7641 (t70) cc_final: 0.7284 (t0) REVERT: G 189 VAL cc_start: 0.7383 (OUTLIER) cc_final: 0.7138 (t) REVERT: G 266 ARG cc_start: 0.8428 (mpt-90) cc_final: 0.8151 (mmt-90) REVERT: G 270 ASP cc_start: 0.8402 (t0) cc_final: 0.7927 (t70) REVERT: G 281 LYS cc_start: 0.7985 (mtpp) cc_final: 0.7736 (mtpp) REVERT: H 11 ASP cc_start: 0.7596 (t0) cc_final: 0.7245 (t70) REVERT: H 13 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7780 (ttp) REVERT: H 23 LYS cc_start: 0.8190 (ttmt) cc_final: 0.7694 (tmmt) REVERT: H 47 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8253 (mm) REVERT: H 139 ASP cc_start: 0.6924 (t0) cc_final: 0.6634 (t0) REVERT: H 222 ASN cc_start: 0.8815 (m-40) cc_final: 0.8316 (m110) REVERT: H 230 GLU cc_start: 0.7907 (mp0) cc_final: 0.7563 (mp0) REVERT: H 269 ARG cc_start: 0.7754 (tpp80) cc_final: 0.7255 (ttp80) outliers start: 103 outliers final: 52 residues processed: 708 average time/residue: 1.5049 time to fit residues: 1190.0575 Evaluate side-chains 712 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 653 time to evaluate : 2.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 166 LYS Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain H residue 13 MET Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 216 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 248 optimal weight: 0.5980 chunk 188 optimal weight: 0.0040 chunk 130 optimal weight: 0.1980 chunk 27 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 251 optimal weight: 1.9990 chunk 266 optimal weight: 1.9990 chunk 131 optimal weight: 0.5980 chunk 238 optimal weight: 0.9990 chunk 71 optimal weight: 0.0980 overall best weight: 0.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN A 280 ASN B 225 ASN C 121 GLN C 137 GLN C 246 GLN C 353 GLN D 12 ASN D 92 ASN D 115 ASN D 162 ASN E 297 ASN E 353 GLN F 12 ASN F 246 GLN G 162 GLN G 164 GLN G 195 GLN G 205 GLN G 240 GLN H 19 GLN H 20 GLN H 241 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22476 Z= 0.159 Angle : 0.541 7.469 30478 Z= 0.258 Chirality : 0.043 0.147 3367 Planarity : 0.004 0.054 3918 Dihedral : 7.380 98.740 3130 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.18 % Allowed : 19.21 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.16), residues: 2744 helix: 0.47 (0.16), residues: 1128 sheet: 0.91 (0.21), residues: 567 loop : -0.34 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 173 HIS 0.004 0.001 HIS B 161 PHE 0.038 0.001 PHE G 163 TYR 0.022 0.001 TYR E 143 ARG 0.012 0.001 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 665 time to evaluate : 2.430 Fit side-chains revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8705 (pt) cc_final: 0.8349 (mt) REVERT: A 99 GLU cc_start: 0.7848 (pm20) cc_final: 0.7571 (mp0) REVERT: A 263 GLN cc_start: 0.8653 (mt0) cc_final: 0.8363 (mt0) REVERT: A 363 ASP cc_start: 0.7197 (m-30) cc_final: 0.6960 (m-30) REVERT: A 372 ARG cc_start: 0.7238 (mtm-85) cc_final: 0.6979 (mtm-85) REVERT: B 99 GLU cc_start: 0.7940 (mp0) cc_final: 0.7687 (mp0) REVERT: B 153 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8636 (tp) REVERT: C 68 LYS cc_start: 0.8699 (mmtp) cc_final: 0.8438 (mttm) REVERT: C 91 TYR cc_start: 0.8825 (m-80) cc_final: 0.8480 (m-80) REVERT: C 143 TYR cc_start: 0.8644 (m-80) cc_final: 0.8398 (m-80) REVERT: C 222 ASP cc_start: 0.8194 (t0) cc_final: 0.7955 (t0) REVERT: C 269 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8359 (mtm) REVERT: C 297 ASN cc_start: 0.8605 (m110) cc_final: 0.8103 (m-40) REVERT: D 83 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: D 364 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7203 (tm-30) REVERT: E 50 LYS cc_start: 0.8026 (ptpp) cc_final: 0.7737 (mtmt) REVERT: E 286 ASP cc_start: 0.7764 (t0) cc_final: 0.7442 (t0) REVERT: E 363 ASP cc_start: 0.7814 (m-30) cc_final: 0.7572 (m-30) REVERT: F 12 ASN cc_start: 0.8531 (m110) cc_final: 0.8189 (m-40) REVERT: F 44 MET cc_start: 0.8354 (mmm) cc_final: 0.7927 (mtt) REVERT: F 68 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8301 (mptt) REVERT: F 84 LYS cc_start: 0.8698 (ttmm) cc_final: 0.8478 (ttmt) REVERT: G 19 LYS cc_start: 0.7773 (tttp) cc_final: 0.7508 (tttp) REVERT: G 34 ASN cc_start: 0.6987 (t0) cc_final: 0.6607 (t0) REVERT: G 36 VAL cc_start: 0.8336 (m) cc_final: 0.8079 (p) REVERT: G 72 ASP cc_start: 0.7288 (t0) cc_final: 0.7054 (t0) REVERT: G 99 ASP cc_start: 0.6983 (t0) cc_final: 0.6470 (t0) REVERT: G 134 ASP cc_start: 0.7682 (t70) cc_final: 0.7329 (t0) REVERT: G 189 VAL cc_start: 0.7364 (OUTLIER) cc_final: 0.7128 (t) REVERT: G 266 ARG cc_start: 0.8490 (mpt-90) cc_final: 0.8177 (mmt-90) REVERT: G 270 ASP cc_start: 0.8407 (t0) cc_final: 0.7931 (t70) REVERT: G 281 LYS cc_start: 0.7985 (mtpp) cc_final: 0.7744 (mtpp) REVERT: H 11 ASP cc_start: 0.7594 (t0) cc_final: 0.7046 (t70) REVERT: H 13 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7798 (ttp) REVERT: H 15 ARG cc_start: 0.7860 (ptp90) cc_final: 0.7172 (ptp90) REVERT: H 23 LYS cc_start: 0.8107 (ttmt) cc_final: 0.7676 (tmmt) REVERT: H 47 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8284 (mm) REVERT: H 139 ASP cc_start: 0.6915 (t0) cc_final: 0.6584 (t0) REVERT: H 222 ASN cc_start: 0.8819 (m-40) cc_final: 0.8354 (m110) REVERT: H 230 GLU cc_start: 0.7915 (mp0) cc_final: 0.7556 (mp0) REVERT: H 269 ARG cc_start: 0.7701 (tpp80) cc_final: 0.7189 (ttp80) REVERT: H 270 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7530 (mt0) outliers start: 99 outliers final: 52 residues processed: 718 average time/residue: 1.4637 time to fit residues: 1176.1881 Evaluate side-chains 709 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 649 time to evaluate : 2.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 128 ASN Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 278 THR Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 166 LYS Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain H residue 13 MET Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 270 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 222 optimal weight: 5.9990 chunk 151 optimal weight: 0.1980 chunk 3 optimal weight: 3.9990 chunk 198 optimal weight: 0.9980 chunk 110 optimal weight: 0.0770 chunk 227 optimal weight: 0.0980 chunk 184 optimal weight: 0.0970 chunk 0 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 239 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.2136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN A 280 ASN B 92 ASN B 111 ASN B 225 ASN C 121 GLN C 137 GLN C 263 GLN C 353 GLN D 12 ASN D 92 ASN D 115 ASN D 162 ASN E 297 ASN E 353 GLN F 162 ASN F 246 GLN G 58 ASN G 162 GLN G 164 GLN G 195 GLN G 205 GLN G 240 GLN H 19 GLN H 20 GLN H 229 ASN H 241 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22476 Z= 0.140 Angle : 0.533 8.082 30478 Z= 0.252 Chirality : 0.042 0.148 3367 Planarity : 0.004 0.059 3918 Dihedral : 7.053 93.758 3128 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.84 % Allowed : 19.97 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.16), residues: 2744 helix: 0.64 (0.16), residues: 1140 sheet: 1.02 (0.22), residues: 563 loop : -0.18 (0.20), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 120 HIS 0.004 0.001 HIS B 161 PHE 0.035 0.001 PHE G 163 TYR 0.024 0.001 TYR E 143 ARG 0.015 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 695 time to evaluate : 2.276 Fit side-chains revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8704 (pt) cc_final: 0.8325 (mt) REVERT: A 195 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7434 (tp30) REVERT: A 263 GLN cc_start: 0.8626 (mt0) cc_final: 0.8311 (mt0) REVERT: A 316 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8131 (mm-30) REVERT: A 363 ASP cc_start: 0.7191 (m-30) cc_final: 0.6975 (m-30) REVERT: A 372 ARG cc_start: 0.7241 (mtm-85) cc_final: 0.6999 (mtm-85) REVERT: B 99 GLU cc_start: 0.7944 (mp0) cc_final: 0.7727 (mp0) REVERT: B 153 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8650 (tp) REVERT: B 355 MET cc_start: 0.8350 (mtm) cc_final: 0.8122 (mmm) REVERT: B 372 ARG cc_start: 0.7416 (mtm-85) cc_final: 0.7197 (mtm-85) REVERT: C 91 TYR cc_start: 0.8802 (m-80) cc_final: 0.8451 (m-80) REVERT: C 123 MET cc_start: 0.8695 (tpp) cc_final: 0.8353 (mmp) REVERT: C 143 TYR cc_start: 0.8604 (m-80) cc_final: 0.8302 (m-80) REVERT: C 221 LEU cc_start: 0.8788 (tp) cc_final: 0.8552 (tt) REVERT: C 222 ASP cc_start: 0.8192 (t0) cc_final: 0.7945 (t0) REVERT: C 297 ASN cc_start: 0.8575 (m110) cc_final: 0.8067 (m-40) REVERT: D 83 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: D 364 GLU cc_start: 0.7614 (tm-30) cc_final: 0.7315 (tm-30) REVERT: E 50 LYS cc_start: 0.8011 (ptpp) cc_final: 0.7742 (mtmt) REVERT: E 61 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.7990 (ptmt) REVERT: E 166 TYR cc_start: 0.8679 (t80) cc_final: 0.8172 (t80) REVERT: E 167 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7325 (mt-10) REVERT: E 286 ASP cc_start: 0.7765 (t0) cc_final: 0.7428 (t0) REVERT: E 363 ASP cc_start: 0.7779 (m-30) cc_final: 0.7539 (m-30) REVERT: F 25 ASP cc_start: 0.7625 (p0) cc_final: 0.7390 (p0) REVERT: F 44 MET cc_start: 0.8362 (mmm) cc_final: 0.7910 (mtt) REVERT: F 68 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8308 (mptt) REVERT: F 84 LYS cc_start: 0.8692 (ttmm) cc_final: 0.8469 (ttmm) REVERT: F 269 MET cc_start: 0.8385 (mtt) cc_final: 0.8121 (ttt) REVERT: G 19 LYS cc_start: 0.7780 (tttp) cc_final: 0.7542 (tttp) REVERT: G 34 ASN cc_start: 0.6909 (t0) cc_final: 0.6508 (t0) REVERT: G 59 MET cc_start: 0.7626 (mtt) cc_final: 0.7219 (mpp) REVERT: G 72 ASP cc_start: 0.7245 (t0) cc_final: 0.6995 (t0) REVERT: G 99 ASP cc_start: 0.6969 (t0) cc_final: 0.6457 (t0) REVERT: G 134 ASP cc_start: 0.7617 (t70) cc_final: 0.7296 (t0) REVERT: G 189 VAL cc_start: 0.7314 (OUTLIER) cc_final: 0.7070 (t) REVERT: G 266 ARG cc_start: 0.8469 (mpt-90) cc_final: 0.8165 (mmt-90) REVERT: G 270 ASP cc_start: 0.8392 (t0) cc_final: 0.7903 (t70) REVERT: G 281 LYS cc_start: 0.7865 (mtpp) cc_final: 0.7628 (mtpp) REVERT: H 11 ASP cc_start: 0.7600 (t0) cc_final: 0.7021 (t70) REVERT: H 13 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7829 (ttp) REVERT: H 15 ARG cc_start: 0.7929 (ptp90) cc_final: 0.7245 (ptp90) REVERT: H 23 LYS cc_start: 0.8080 (ttmt) cc_final: 0.7656 (tmmt) REVERT: H 31 LEU cc_start: 0.7253 (mm) cc_final: 0.6940 (mp) REVERT: H 133 LEU cc_start: 0.8726 (mt) cc_final: 0.8523 (mp) REVERT: H 139 ASP cc_start: 0.6895 (t0) cc_final: 0.6604 (t0) REVERT: H 222 ASN cc_start: 0.8825 (m-40) cc_final: 0.8356 (m110) REVERT: H 229 ASN cc_start: 0.8542 (t0) cc_final: 0.8315 (t0) REVERT: H 230 GLU cc_start: 0.7903 (mp0) cc_final: 0.7556 (mp0) REVERT: H 270 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7523 (mt0) outliers start: 91 outliers final: 51 residues processed: 734 average time/residue: 1.4733 time to fit residues: 1208.9340 Evaluate side-chains 731 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 673 time to evaluate : 2.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 336 LYS Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 128 ASN Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 166 LYS Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain H residue 13 MET Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 270 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 89 optimal weight: 3.9990 chunk 240 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 156 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 267 optimal weight: 0.9980 chunk 221 optimal weight: 0.0670 chunk 123 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 140 optimal weight: 0.9980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 ASN A 225 ASN A 280 ASN B 162 ASN C 12 ASN C 121 GLN C 137 GLN C 353 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN D 115 ASN D 162 ASN E 297 ASN E 353 GLN F 246 GLN G 58 ASN G 162 GLN G 164 GLN G 195 GLN G 205 GLN G 240 GLN H 19 GLN ** H 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22476 Z= 0.282 Angle : 0.590 10.525 30478 Z= 0.284 Chirality : 0.046 0.196 3367 Planarity : 0.004 0.055 3918 Dihedral : 7.235 99.112 3121 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.52 % Allowed : 20.14 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.16), residues: 2744 helix: 0.56 (0.16), residues: 1136 sheet: 0.98 (0.22), residues: 567 loop : -0.26 (0.20), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 148 HIS 0.007 0.001 HIS B 161 PHE 0.036 0.002 PHE G 163 TYR 0.030 0.001 TYR E 143 ARG 0.011 0.001 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 677 time to evaluate : 2.476 Fit side-chains revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8716 (pt) cc_final: 0.8326 (mt) REVERT: A 195 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7306 (tp30) REVERT: A 263 GLN cc_start: 0.8644 (mt0) cc_final: 0.8341 (mt0) REVERT: A 316 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8155 (mm-30) REVERT: A 363 ASP cc_start: 0.7234 (m-30) cc_final: 0.6997 (m-30) REVERT: A 372 ARG cc_start: 0.7244 (mtm-85) cc_final: 0.7023 (mtm-85) REVERT: B 99 GLU cc_start: 0.7962 (mp0) cc_final: 0.7749 (mp0) REVERT: B 153 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8647 (tp) REVERT: B 169 TYR cc_start: 0.8759 (m-80) cc_final: 0.8115 (m-80) REVERT: B 355 MET cc_start: 0.8400 (mtm) cc_final: 0.8145 (mmm) REVERT: B 372 ARG cc_start: 0.7416 (mtm-85) cc_final: 0.7131 (mtm-85) REVERT: C 68 LYS cc_start: 0.8690 (mmtp) cc_final: 0.8439 (mttm) REVERT: C 91 TYR cc_start: 0.8833 (m-80) cc_final: 0.8503 (m-80) REVERT: C 128 ASN cc_start: 0.8208 (p0) cc_final: 0.7889 (p0) REVERT: C 143 TYR cc_start: 0.8631 (m-80) cc_final: 0.8394 (m-80) REVERT: C 222 ASP cc_start: 0.8210 (t0) cc_final: 0.7978 (t0) REVERT: C 297 ASN cc_start: 0.8658 (m110) cc_final: 0.8334 (m-40) REVERT: D 83 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7392 (mp0) REVERT: D 178 LEU cc_start: 0.8697 (tp) cc_final: 0.8485 (tt) REVERT: D 286 ASP cc_start: 0.7969 (m-30) cc_final: 0.7742 (m-30) REVERT: D 364 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7338 (tm-30) REVERT: E 44 MET cc_start: 0.8418 (mtp) cc_final: 0.8212 (mtm) REVERT: E 50 LYS cc_start: 0.8065 (ptpp) cc_final: 0.7775 (mtmt) REVERT: E 61 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8006 (ptmt) REVERT: E 286 ASP cc_start: 0.7807 (t0) cc_final: 0.7445 (t0) REVERT: E 363 ASP cc_start: 0.7799 (m-30) cc_final: 0.7560 (m-30) REVERT: F 44 MET cc_start: 0.8333 (mmm) cc_final: 0.7973 (mtt) REVERT: F 68 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8278 (mptt) REVERT: F 84 LYS cc_start: 0.8705 (ttmm) cc_final: 0.8494 (ttmt) REVERT: F 269 MET cc_start: 0.8455 (mtt) cc_final: 0.8195 (ttt) REVERT: G 19 LYS cc_start: 0.7817 (tttp) cc_final: 0.7569 (tttp) REVERT: G 33 PHE cc_start: 0.7510 (t80) cc_final: 0.7283 (t80) REVERT: G 34 ASN cc_start: 0.6990 (t0) cc_final: 0.6586 (t0) REVERT: G 72 ASP cc_start: 0.7271 (t0) cc_final: 0.7043 (t0) REVERT: G 89 ASP cc_start: 0.6990 (m-30) cc_final: 0.6620 (m-30) REVERT: G 99 ASP cc_start: 0.6970 (t0) cc_final: 0.6459 (t0) REVERT: G 134 ASP cc_start: 0.7700 (t70) cc_final: 0.7435 (t0) REVERT: G 155 ILE cc_start: 0.7448 (mt) cc_final: 0.7176 (mt) REVERT: G 189 VAL cc_start: 0.7436 (OUTLIER) cc_final: 0.7204 (t) REVERT: G 266 ARG cc_start: 0.8521 (mpt-90) cc_final: 0.8199 (mmt-90) REVERT: G 270 ASP cc_start: 0.8417 (t0) cc_final: 0.7933 (t70) REVERT: G 281 LYS cc_start: 0.7933 (mtpp) cc_final: 0.7717 (mtpp) REVERT: H 11 ASP cc_start: 0.7668 (t0) cc_final: 0.7244 (t70) REVERT: H 13 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7814 (ttp) REVERT: H 23 LYS cc_start: 0.8099 (ttmt) cc_final: 0.7735 (tmmt) REVERT: H 31 LEU cc_start: 0.7271 (mm) cc_final: 0.6951 (mp) REVERT: H 139 ASP cc_start: 0.6894 (t0) cc_final: 0.6599 (t0) REVERT: H 222 ASN cc_start: 0.8846 (m-40) cc_final: 0.8354 (m110) REVERT: H 230 GLU cc_start: 0.7926 (mp0) cc_final: 0.7626 (mp0) REVERT: H 269 ARG cc_start: 0.7725 (tpp80) cc_final: 0.7228 (ttp80) REVERT: H 270 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7460 (mt0) outliers start: 107 outliers final: 72 residues processed: 726 average time/residue: 1.4666 time to fit residues: 1190.8417 Evaluate side-chains 755 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 676 time to evaluate : 2.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 278 THR Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 166 LYS Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 207 VAL Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain H residue 13 MET Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 270 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 257 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 152 optimal weight: 0.0970 chunk 195 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 224 optimal weight: 0.8980 chunk 149 optimal weight: 0.7980 chunk 266 optimal weight: 0.6980 chunk 166 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 92 ASN A 225 ASN A 280 ASN B 162 ASN C 121 GLN C 137 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 ASN D 162 ASN E 78 ASN E 297 ASN E 353 GLN ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 GLN G 58 ASN G 162 GLN G 164 GLN G 195 GLN G 205 GLN G 240 GLN H 19 GLN H 20 GLN H 241 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22476 Z= 0.277 Angle : 0.588 8.328 30478 Z= 0.284 Chirality : 0.046 0.219 3367 Planarity : 0.004 0.080 3918 Dihedral : 7.282 103.541 3119 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 5.02 % Allowed : 20.01 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.16), residues: 2744 helix: 0.53 (0.16), residues: 1136 sheet: 0.95 (0.22), residues: 565 loop : -0.32 (0.20), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 148 HIS 0.007 0.001 HIS B 161 PHE 0.033 0.002 PHE G 163 TYR 0.031 0.001 TYR E 143 ARG 0.016 0.001 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 678 time to evaluate : 2.467 Fit side-chains revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8708 (pt) cc_final: 0.8328 (mt) REVERT: A 178 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8475 (tp) REVERT: A 195 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7526 (tp30) REVERT: A 207 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7866 (mp0) REVERT: A 215 LYS cc_start: 0.8549 (mttm) cc_final: 0.8206 (mttm) REVERT: A 222 ASP cc_start: 0.8012 (t0) cc_final: 0.7786 (t0) REVERT: A 263 GLN cc_start: 0.8628 (mt0) cc_final: 0.8302 (mt0) REVERT: A 316 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8117 (mm-30) REVERT: A 363 ASP cc_start: 0.7217 (m-30) cc_final: 0.7000 (m-30) REVERT: A 364 GLU cc_start: 0.7219 (tm-30) cc_final: 0.6996 (tm-30) REVERT: B 99 GLU cc_start: 0.7966 (mp0) cc_final: 0.7756 (mp0) REVERT: B 153 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8628 (tp) REVERT: B 355 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8122 (mmm) REVERT: C 68 LYS cc_start: 0.8701 (mmtp) cc_final: 0.8451 (mttm) REVERT: C 91 TYR cc_start: 0.8833 (m-80) cc_final: 0.8499 (m-80) REVERT: C 123 MET cc_start: 0.8690 (tpp) cc_final: 0.8341 (mmp) REVERT: C 128 ASN cc_start: 0.8224 (p0) cc_final: 0.7906 (p0) REVERT: C 143 TYR cc_start: 0.8638 (m-80) cc_final: 0.8401 (m-80) REVERT: C 222 ASP cc_start: 0.8210 (t0) cc_final: 0.7961 (t0) REVERT: C 225 ASN cc_start: 0.8282 (m-40) cc_final: 0.7870 (m110) REVERT: C 284 LYS cc_start: 0.8649 (mtpm) cc_final: 0.8388 (mtpp) REVERT: C 297 ASN cc_start: 0.8668 (m110) cc_final: 0.8389 (m-40) REVERT: D 83 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: D 364 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7345 (tm-30) REVERT: E 44 MET cc_start: 0.8419 (mtp) cc_final: 0.8215 (mtm) REVERT: E 50 LYS cc_start: 0.8049 (ptpp) cc_final: 0.7768 (mtmt) REVERT: E 61 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8004 (ptmt) REVERT: E 167 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7464 (mm-30) REVERT: E 286 ASP cc_start: 0.7821 (t0) cc_final: 0.7489 (t0) REVERT: E 363 ASP cc_start: 0.7793 (m-30) cc_final: 0.7551 (m-30) REVERT: F 44 MET cc_start: 0.8332 (mmm) cc_final: 0.8105 (mtt) REVERT: F 68 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8281 (mptt) REVERT: F 84 LYS cc_start: 0.8715 (ttmm) cc_final: 0.8506 (ttmt) REVERT: F 215 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8037 (mppt) REVERT: F 269 MET cc_start: 0.8451 (mtt) cc_final: 0.8191 (ttt) REVERT: G 19 LYS cc_start: 0.7809 (tttp) cc_final: 0.7560 (tttp) REVERT: G 33 PHE cc_start: 0.7524 (t80) cc_final: 0.7306 (t80) REVERT: G 34 ASN cc_start: 0.7059 (t0) cc_final: 0.6666 (t0) REVERT: G 59 MET cc_start: 0.7656 (mtt) cc_final: 0.7243 (mpp) REVERT: G 72 ASP cc_start: 0.7268 (t0) cc_final: 0.7041 (t0) REVERT: G 99 ASP cc_start: 0.6958 (t0) cc_final: 0.6443 (t0) REVERT: G 134 ASP cc_start: 0.7708 (t70) cc_final: 0.7469 (t70) REVERT: G 155 ILE cc_start: 0.7464 (mt) cc_final: 0.7186 (mt) REVERT: G 189 VAL cc_start: 0.7420 (OUTLIER) cc_final: 0.7187 (t) REVERT: G 266 ARG cc_start: 0.8507 (mpt-90) cc_final: 0.8177 (mmt-90) REVERT: G 270 ASP cc_start: 0.8416 (t0) cc_final: 0.7938 (t70) REVERT: G 281 LYS cc_start: 0.7915 (mtpp) cc_final: 0.7698 (mtpp) REVERT: H 11 ASP cc_start: 0.7678 (t0) cc_final: 0.7268 (t70) REVERT: H 13 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7841 (ttp) REVERT: H 22 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6931 (mm-30) REVERT: H 23 LYS cc_start: 0.8116 (ttmt) cc_final: 0.7738 (tmmt) REVERT: H 31 LEU cc_start: 0.7325 (mm) cc_final: 0.6998 (mp) REVERT: H 139 ASP cc_start: 0.6897 (t0) cc_final: 0.6585 (t0) REVERT: H 222 ASN cc_start: 0.8832 (m-40) cc_final: 0.8355 (m110) REVERT: H 230 GLU cc_start: 0.7934 (mp0) cc_final: 0.7622 (mp0) REVERT: H 269 ARG cc_start: 0.7738 (tpp80) cc_final: 0.7215 (ttp80) outliers start: 119 outliers final: 75 residues processed: 729 average time/residue: 1.4502 time to fit residues: 1184.1438 Evaluate side-chains 764 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 679 time to evaluate : 2.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 278 THR Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 369 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 166 LYS Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 207 VAL Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain H residue 13 MET Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 267 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 164 optimal weight: 0.0170 chunk 106 optimal weight: 1.9990 chunk 158 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 169 optimal weight: 0.4980 chunk 181 optimal weight: 0.0570 chunk 131 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 209 optimal weight: 0.3980 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 280 ASN B 162 ASN C 121 GLN C 137 GLN C 353 GLN D 92 ASN D 115 ASN D 162 ASN E 78 ASN E 297 ASN E 353 GLN F 162 ASN F 246 GLN G 58 ASN G 162 GLN G 164 GLN G 195 GLN G 205 GLN G 240 GLN H 19 GLN H 229 ASN H 241 ASN ** H 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22476 Z= 0.159 Angle : 0.554 8.716 30478 Z= 0.264 Chirality : 0.043 0.195 3367 Planarity : 0.004 0.057 3918 Dihedral : 7.023 97.344 3119 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.88 % Allowed : 21.44 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.16), residues: 2744 helix: 0.89 (0.16), residues: 1110 sheet: 0.98 (0.22), residues: 565 loop : -0.25 (0.19), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 173 HIS 0.004 0.001 HIS B 161 PHE 0.027 0.001 PHE G 163 TYR 0.027 0.001 TYR E 143 ARG 0.008 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 684 time to evaluate : 2.357 Fit side-chains revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8689 (pt) cc_final: 0.8312 (mt) REVERT: A 195 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7490 (tp30) REVERT: A 207 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7818 (mp0) REVERT: A 215 LYS cc_start: 0.8524 (mttm) cc_final: 0.8189 (mttm) REVERT: A 263 GLN cc_start: 0.8612 (mt0) cc_final: 0.8309 (mt0) REVERT: A 316 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8126 (mm-30) REVERT: A 363 ASP cc_start: 0.7201 (m-30) cc_final: 0.6995 (m-30) REVERT: A 364 GLU cc_start: 0.7198 (tm-30) cc_final: 0.6972 (tm-30) REVERT: B 99 GLU cc_start: 0.7953 (mp0) cc_final: 0.7740 (mp0) REVERT: B 149 THR cc_start: 0.8870 (t) cc_final: 0.8652 (m) REVERT: B 153 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8636 (tp) REVERT: B 355 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8109 (mmm) REVERT: C 68 LYS cc_start: 0.8691 (mmtp) cc_final: 0.8444 (mmtm) REVERT: C 91 TYR cc_start: 0.8803 (m-80) cc_final: 0.8447 (m-80) REVERT: C 143 TYR cc_start: 0.8595 (m-80) cc_final: 0.8312 (m-80) REVERT: C 222 ASP cc_start: 0.8197 (t0) cc_final: 0.7948 (t0) REVERT: C 297 ASN cc_start: 0.8625 (m110) cc_final: 0.8120 (m-40) REVERT: D 83 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: D 286 ASP cc_start: 0.7947 (m-30) cc_final: 0.7724 (m-30) REVERT: D 364 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7334 (tm-30) REVERT: E 50 LYS cc_start: 0.8026 (ptpp) cc_final: 0.7761 (mtmt) REVERT: E 167 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7336 (mt-10) REVERT: E 286 ASP cc_start: 0.7807 (t0) cc_final: 0.7476 (t0) REVERT: E 363 ASP cc_start: 0.7764 (m-30) cc_final: 0.7516 (m-30) REVERT: F 28 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7687 (ttp-110) REVERT: F 44 MET cc_start: 0.8343 (mmm) cc_final: 0.8029 (mtt) REVERT: F 68 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8289 (mptt) REVERT: F 84 LYS cc_start: 0.8698 (ttmm) cc_final: 0.8485 (ttmm) REVERT: F 269 MET cc_start: 0.8415 (mtt) cc_final: 0.8159 (ttt) REVERT: G 19 LYS cc_start: 0.7787 (tttp) cc_final: 0.7536 (tttp) REVERT: G 33 PHE cc_start: 0.7522 (t80) cc_final: 0.7274 (t80) REVERT: G 34 ASN cc_start: 0.6986 (t0) cc_final: 0.6609 (t0) REVERT: G 72 ASP cc_start: 0.7223 (t0) cc_final: 0.7005 (t0) REVERT: G 85 SER cc_start: 0.7359 (t) cc_final: 0.7136 (t) REVERT: G 99 ASP cc_start: 0.6936 (t0) cc_final: 0.6436 (t0) REVERT: G 134 ASP cc_start: 0.7673 (t70) cc_final: 0.7411 (t0) REVERT: G 155 ILE cc_start: 0.7384 (mt) cc_final: 0.7088 (mt) REVERT: G 189 VAL cc_start: 0.7341 (OUTLIER) cc_final: 0.7114 (t) REVERT: G 214 ASP cc_start: 0.7282 (OUTLIER) cc_final: 0.6985 (t0) REVERT: G 266 ARG cc_start: 0.8492 (mpt-90) cc_final: 0.8164 (mmt-90) REVERT: G 270 ASP cc_start: 0.8404 (t0) cc_final: 0.7904 (t70) REVERT: H 11 ASP cc_start: 0.7629 (t0) cc_final: 0.7253 (t70) REVERT: H 13 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7879 (ttp) REVERT: H 15 ARG cc_start: 0.7977 (ptp90) cc_final: 0.7436 (ptp90) REVERT: H 23 LYS cc_start: 0.8045 (ttmt) cc_final: 0.7698 (tmmt) REVERT: H 31 LEU cc_start: 0.7299 (mm) cc_final: 0.6984 (mp) REVERT: H 139 ASP cc_start: 0.6866 (t0) cc_final: 0.6570 (t0) REVERT: H 222 ASN cc_start: 0.8823 (m-40) cc_final: 0.8375 (m110) REVERT: H 229 ASN cc_start: 0.8588 (OUTLIER) cc_final: 0.8381 (t0) REVERT: H 230 GLU cc_start: 0.7923 (mp0) cc_final: 0.7609 (mp0) REVERT: H 237 LYS cc_start: 0.8597 (tttm) cc_final: 0.8367 (tttp) REVERT: H 269 ARG cc_start: 0.7722 (tpp80) cc_final: 0.7192 (ttp80) outliers start: 92 outliers final: 59 residues processed: 726 average time/residue: 1.4702 time to fit residues: 1193.8458 Evaluate side-chains 739 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 670 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 369 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain G residue 162 GLN Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain H residue 13 MET Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 229 ASN Chi-restraints excluded: chain H residue 267 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 241 optimal weight: 1.9990 chunk 254 optimal weight: 0.5980 chunk 232 optimal weight: 2.9990 chunk 247 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 194 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 224 optimal weight: 0.8980 chunk 234 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN B 162 ASN C 12 ASN C 137 GLN C 353 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 ASN D 162 ASN E 297 ASN E 353 GLN F 246 GLN G 58 ASN G 162 GLN G 164 GLN G 195 GLN G 205 GLN G 240 GLN H 19 GLN H 241 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 22476 Z= 0.333 Angle : 0.623 12.267 30478 Z= 0.301 Chirality : 0.047 0.192 3367 Planarity : 0.005 0.087 3918 Dihedral : 7.286 103.548 3119 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.97 % Allowed : 21.36 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.16), residues: 2744 helix: 0.75 (0.16), residues: 1105 sheet: 0.93 (0.22), residues: 567 loop : -0.32 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 148 HIS 0.007 0.001 HIS B 161 PHE 0.026 0.002 PHE G 163 TYR 0.034 0.002 TYR E 143 ARG 0.020 0.001 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 673 time to evaluate : 2.697 Fit side-chains revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8717 (pt) cc_final: 0.8338 (mt) REVERT: A 92 ASN cc_start: 0.8547 (m-40) cc_final: 0.8287 (m-40) REVERT: A 195 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7530 (tp30) REVERT: A 207 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.8014 (mp0) REVERT: A 215 LYS cc_start: 0.8544 (mttm) cc_final: 0.8217 (mttm) REVERT: A 222 ASP cc_start: 0.8005 (t0) cc_final: 0.7675 (t0) REVERT: A 316 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8116 (mm-30) REVERT: A 363 ASP cc_start: 0.7219 (m-30) cc_final: 0.7001 (m-30) REVERT: A 364 GLU cc_start: 0.7257 (tm-30) cc_final: 0.7029 (tm-30) REVERT: B 99 GLU cc_start: 0.7972 (mp0) cc_final: 0.7754 (mp0) REVERT: B 153 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8623 (tp) REVERT: B 355 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8128 (mmm) REVERT: C 68 LYS cc_start: 0.8696 (mmtp) cc_final: 0.8452 (mttm) REVERT: C 91 TYR cc_start: 0.8832 (m-80) cc_final: 0.8487 (m-80) REVERT: C 128 ASN cc_start: 0.8257 (p0) cc_final: 0.7930 (p0) REVERT: C 143 TYR cc_start: 0.8644 (m-80) cc_final: 0.8402 (m-80) REVERT: C 222 ASP cc_start: 0.8208 (t0) cc_final: 0.7987 (t0) REVERT: C 269 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8392 (mtm) REVERT: C 284 LYS cc_start: 0.8680 (mtpm) cc_final: 0.8435 (mtpp) REVERT: C 297 ASN cc_start: 0.8700 (m110) cc_final: 0.8366 (m-40) REVERT: D 83 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: D 364 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7355 (tm-30) REVERT: E 44 MET cc_start: 0.8421 (mtp) cc_final: 0.8219 (mtm) REVERT: E 50 LYS cc_start: 0.8050 (ptpp) cc_final: 0.7775 (mtmt) REVERT: E 167 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7341 (mp0) REVERT: E 286 ASP cc_start: 0.7852 (t0) cc_final: 0.7512 (t0) REVERT: E 363 ASP cc_start: 0.7785 (m-30) cc_final: 0.7524 (m-30) REVERT: F 44 MET cc_start: 0.8336 (mmm) cc_final: 0.8116 (mtt) REVERT: F 68 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8283 (mptt) REVERT: F 84 LYS cc_start: 0.8718 (ttmm) cc_final: 0.8489 (ttmm) REVERT: F 215 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8044 (mppt) REVERT: G 19 LYS cc_start: 0.7811 (tttp) cc_final: 0.7569 (tttp) REVERT: G 33 PHE cc_start: 0.7583 (t80) cc_final: 0.7329 (t80) REVERT: G 34 ASN cc_start: 0.7118 (t0) cc_final: 0.6724 (t0) REVERT: G 59 MET cc_start: 0.7508 (mpp) cc_final: 0.7083 (mpp) REVERT: G 72 ASP cc_start: 0.7265 (t0) cc_final: 0.7045 (t0) REVERT: G 85 SER cc_start: 0.7347 (t) cc_final: 0.7132 (t) REVERT: G 89 ASP cc_start: 0.7059 (m-30) cc_final: 0.6656 (m-30) REVERT: G 99 ASP cc_start: 0.6962 (t0) cc_final: 0.6445 (t0) REVERT: G 134 ASP cc_start: 0.7731 (t70) cc_final: 0.7500 (t70) REVERT: G 189 VAL cc_start: 0.7446 (OUTLIER) cc_final: 0.7223 (t) REVERT: G 266 ARG cc_start: 0.8531 (mpt-90) cc_final: 0.8191 (mmt-90) REVERT: G 270 ASP cc_start: 0.8412 (t0) cc_final: 0.7924 (t70) REVERT: H 11 ASP cc_start: 0.7701 (t0) cc_final: 0.7292 (t70) REVERT: H 13 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7878 (ttp) REVERT: H 23 LYS cc_start: 0.8087 (ttmt) cc_final: 0.7720 (tmmt) REVERT: H 31 LEU cc_start: 0.7353 (mm) cc_final: 0.7055 (mp) REVERT: H 139 ASP cc_start: 0.6896 (t0) cc_final: 0.6581 (t0) REVERT: H 222 ASN cc_start: 0.8840 (m-40) cc_final: 0.8357 (m110) REVERT: H 230 GLU cc_start: 0.7927 (mp0) cc_final: 0.7548 (mp0) REVERT: H 269 ARG cc_start: 0.7752 (tpp80) cc_final: 0.7218 (ttp80) outliers start: 94 outliers final: 67 residues processed: 716 average time/residue: 1.4830 time to fit residues: 1188.7079 Evaluate side-chains 736 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 660 time to evaluate : 2.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 369 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain H residue 13 MET Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 267 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 262 optimal weight: 0.4980 chunk 159 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 182 optimal weight: 0.9990 chunk 274 optimal weight: 4.9990 chunk 253 optimal weight: 0.3980 chunk 218 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 169 optimal weight: 0.0870 chunk 134 optimal weight: 0.9980 chunk 173 optimal weight: 0.8980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN B 162 ASN C 137 GLN C 353 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN D 115 ASN D 162 ASN E 297 ASN E 353 GLN F 246 GLN G 58 ASN G 162 GLN G 164 GLN G 195 GLN G 205 GLN G 240 GLN H 19 GLN H 241 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22476 Z= 0.220 Angle : 0.588 8.840 30478 Z= 0.283 Chirality : 0.045 0.158 3367 Planarity : 0.004 0.062 3918 Dihedral : 7.184 102.115 3119 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.38 % Allowed : 22.29 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.16), residues: 2744 helix: 0.82 (0.16), residues: 1109 sheet: 0.96 (0.22), residues: 565 loop : -0.31 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 148 HIS 0.005 0.001 HIS B 161 PHE 0.029 0.001 PHE G 163 TYR 0.032 0.001 TYR E 143 ARG 0.011 0.001 ARG A 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 656 time to evaluate : 2.739 Fit side-chains revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8715 (pt) cc_final: 0.8348 (mt) REVERT: A 195 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7540 (tp30) REVERT: A 207 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.8008 (mp0) REVERT: A 215 LYS cc_start: 0.8534 (mttm) cc_final: 0.8284 (mttm) REVERT: A 222 ASP cc_start: 0.7980 (t0) cc_final: 0.7644 (t0) REVERT: A 316 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8106 (mm-30) REVERT: A 363 ASP cc_start: 0.7212 (m-30) cc_final: 0.7008 (m-30) REVERT: A 364 GLU cc_start: 0.7233 (tm-30) cc_final: 0.7006 (tm-30) REVERT: B 99 GLU cc_start: 0.7965 (mp0) cc_final: 0.7752 (mp0) REVERT: B 153 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8632 (tp) REVERT: B 355 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8114 (mmm) REVERT: C 68 LYS cc_start: 0.8696 (mmtp) cc_final: 0.8449 (mttm) REVERT: C 91 TYR cc_start: 0.8811 (m-80) cc_final: 0.8464 (m-80) REVERT: C 128 ASN cc_start: 0.8259 (p0) cc_final: 0.7930 (p0) REVERT: C 143 TYR cc_start: 0.8616 (m-80) cc_final: 0.8366 (m-80) REVERT: C 222 ASP cc_start: 0.8202 (t0) cc_final: 0.7965 (t0) REVERT: C 284 LYS cc_start: 0.8660 (mtpm) cc_final: 0.8420 (mtpp) REVERT: C 297 ASN cc_start: 0.8666 (m110) cc_final: 0.8174 (m-40) REVERT: D 83 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7350 (mp0) REVERT: D 286 ASP cc_start: 0.7975 (m-30) cc_final: 0.7736 (m-30) REVERT: D 364 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7341 (tm-30) REVERT: E 44 MET cc_start: 0.8390 (mtp) cc_final: 0.8188 (mtm) REVERT: E 50 LYS cc_start: 0.8029 (ptpp) cc_final: 0.7762 (mtmt) REVERT: E 167 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7323 (mp0) REVERT: E 286 ASP cc_start: 0.7818 (t0) cc_final: 0.7477 (t0) REVERT: E 363 ASP cc_start: 0.7763 (m-30) cc_final: 0.7521 (m-30) REVERT: F 44 MET cc_start: 0.8337 (mmm) cc_final: 0.8071 (mtt) REVERT: F 68 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8285 (mptt) REVERT: F 84 LYS cc_start: 0.8711 (ttmm) cc_final: 0.8482 (ttmm) REVERT: F 269 MET cc_start: 0.8436 (mtt) cc_final: 0.8187 (ttt) REVERT: G 19 LYS cc_start: 0.7806 (tttp) cc_final: 0.7547 (tttp) REVERT: G 33 PHE cc_start: 0.7559 (t80) cc_final: 0.7324 (t80) REVERT: G 34 ASN cc_start: 0.7084 (t0) cc_final: 0.6692 (t0) REVERT: G 59 MET cc_start: 0.7464 (mpp) cc_final: 0.7047 (mpp) REVERT: G 72 ASP cc_start: 0.7234 (t0) cc_final: 0.7031 (t0) REVERT: G 99 ASP cc_start: 0.6944 (t0) cc_final: 0.6443 (t0) REVERT: G 134 ASP cc_start: 0.7707 (t70) cc_final: 0.7468 (t0) REVERT: G 189 VAL cc_start: 0.7391 (OUTLIER) cc_final: 0.7176 (t) REVERT: G 214 ASP cc_start: 0.7308 (OUTLIER) cc_final: 0.7011 (t0) REVERT: G 266 ARG cc_start: 0.8512 (mpt-90) cc_final: 0.8159 (mmt-90) REVERT: G 270 ASP cc_start: 0.8408 (t0) cc_final: 0.7921 (t70) REVERT: H 11 ASP cc_start: 0.7668 (t0) cc_final: 0.7253 (t70) REVERT: H 13 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7868 (ttp) REVERT: H 23 LYS cc_start: 0.8054 (ttmt) cc_final: 0.7742 (tmmt) REVERT: H 31 LEU cc_start: 0.7371 (mm) cc_final: 0.7092 (mp) REVERT: H 139 ASP cc_start: 0.6869 (t0) cc_final: 0.6560 (t0) REVERT: H 222 ASN cc_start: 0.8828 (m-40) cc_final: 0.8340 (m110) REVERT: H 230 GLU cc_start: 0.7949 (mp0) cc_final: 0.7559 (mp0) REVERT: H 237 LYS cc_start: 0.8615 (tttm) cc_final: 0.8391 (tttp) REVERT: H 269 ARG cc_start: 0.7731 (tpp80) cc_final: 0.7191 (ttp80) outliers start: 80 outliers final: 59 residues processed: 695 average time/residue: 1.4837 time to fit residues: 1152.3570 Evaluate side-chains 723 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 656 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 369 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 207 VAL Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain H residue 13 MET Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 267 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 4.9990 chunk 67 optimal weight: 0.3980 chunk 201 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 219 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 192 optimal weight: 0.0980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN B 162 ASN C 137 GLN C 353 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 ASN E 353 GLN F 246 GLN G 58 ASN G 162 GLN G 164 GLN G 195 GLN G 205 GLN G 240 GLN H 19 GLN H 20 GLN H 241 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.110006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.092710 restraints weight = 31041.685| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.67 r_work: 0.3044 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22476 Z= 0.257 Angle : 0.615 13.037 30478 Z= 0.294 Chirality : 0.046 0.176 3367 Planarity : 0.005 0.100 3918 Dihedral : 7.236 102.845 3119 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.25 % Allowed : 22.41 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.16), residues: 2744 helix: 0.58 (0.16), residues: 1146 sheet: 0.94 (0.22), residues: 565 loop : -0.25 (0.20), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 148 HIS 0.006 0.001 HIS B 161 PHE 0.027 0.001 PHE G 163 TYR 0.033 0.001 TYR E 143 ARG 0.021 0.001 ARG A 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14827.17 seconds wall clock time: 258 minutes 26.76 seconds (15506.76 seconds total)