Starting phenix.real_space_refine on Sat Apr 6 19:55:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8trn_41584/04_2024/8trn_41584_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8trn_41584/04_2024/8trn_41584.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8trn_41584/04_2024/8trn_41584_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8trn_41584/04_2024/8trn_41584_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8trn_41584/04_2024/8trn_41584_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8trn_41584/04_2024/8trn_41584.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8trn_41584/04_2024/8trn_41584.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8trn_41584/04_2024/8trn_41584_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8trn_41584/04_2024/8trn_41584_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.344 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Br 3 7.06 5 P 6 5.49 5 Mg 3 5.21 5 S 54 5.16 5 C 5580 2.51 5 N 1458 2.21 5 O 1710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 26": "OD1" <-> "OD2" Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 57": "OD1" <-> "OD2" Residue "A ASP 81": "OD1" <-> "OD2" Residue "A GLU 84": "OE1" <-> "OE2" Residue "A GLU 108": "OE1" <-> "OE2" Residue "A GLU 126": "OE1" <-> "OE2" Residue "A TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 155": "OD1" <-> "OD2" Residue "A TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 168": "OE1" <-> "OE2" Residue "A GLU 206": "OE1" <-> "OE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A ASP 225": "OD1" <-> "OD2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 281": "OD1" <-> "OD2" Residue "A ASP 293": "OD1" <-> "OD2" Residue "A TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A GLU 317": "OE1" <-> "OE2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A GLU 361": "OE1" <-> "OE2" Residue "A TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 365": "OE1" <-> "OE2" Residue "B ASP 26": "OD1" <-> "OD2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 57": "OD1" <-> "OD2" Residue "B ASP 81": "OD1" <-> "OD2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 155": "OD1" <-> "OD2" Residue "B TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 168": "OE1" <-> "OE2" Residue "B GLU 206": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B ASP 225": "OD1" <-> "OD2" Residue "B GLU 238": "OE1" <-> "OE2" Residue "B TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 254": "OE1" <-> "OE2" Residue "B PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 281": "OD1" <-> "OD2" Residue "B ASP 293": "OD1" <-> "OD2" Residue "B TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 308": "OE1" <-> "OE2" Residue "B GLU 317": "OE1" <-> "OE2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "B GLU 361": "OE1" <-> "OE2" Residue "B TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 365": "OE1" <-> "OE2" Residue "C ASP 26": "OD1" <-> "OD2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 57": "OD1" <-> "OD2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 155": "OD1" <-> "OD2" Residue "C TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 168": "OE1" <-> "OE2" Residue "C GLU 206": "OE1" <-> "OE2" Residue "C GLU 215": "OE1" <-> "OE2" Residue "C ASP 225": "OD1" <-> "OD2" Residue "C GLU 238": "OE1" <-> "OE2" Residue "C TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 254": "OE1" <-> "OE2" Residue "C PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 281": "OD1" <-> "OD2" Residue "C ASP 293": "OD1" <-> "OD2" Residue "C TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 308": "OE1" <-> "OE2" Residue "C GLU 317": "OE1" <-> "OE2" Residue "C GLU 335": "OE1" <-> "OE2" Residue "C GLU 361": "OE1" <-> "OE2" Residue "C TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 365": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8814 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2863 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 19, 'TRANS': 347} Chain: "B" Number of atoms: 2863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2863 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 19, 'TRANS': 347} Chain: "C" Number of atoms: 2863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2863 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 19, 'TRANS': 347} Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.11, per 1000 atoms: 0.58 Number of scatterers: 8814 At special positions: 0 Unit cell: (77.43, 99.68, 139.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 3 34.99 S 54 16.00 P 6 15.00 Mg 3 11.99 O 1710 8.00 N 1458 7.00 C 5580 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: 3.33 Conformation dependent library (CDL) restraints added in 1.8 seconds 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2022 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 12 sheets defined 43.1% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 57 through 61 Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 80 through 92 Processing helix chain 'A' and resid 114 through 126 Processing helix chain 'A' and resid 138 through 145 Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 183 through 197 removed outlier: 3.906A pdb=" N HIS A 195 " --> pdb=" O MET A 191 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLU A 196 " --> pdb=" O LYS A 192 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ARG A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 217 removed outlier: 3.520A pdb=" N LYS A 216 " --> pdb=" O ASP A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 231 Processing helix chain 'A' and resid 253 through 262 removed outlier: 4.359A pdb=" N CYS A 258 " --> pdb=" O ARG A 255 " (cutoff:3.500A) Proline residue: A 259 - end of helix Processing helix chain 'A' and resid 265 through 268 Processing helix chain 'A' and resid 275 through 284 Processing helix chain 'A' and resid 288 through 295 removed outlier: 4.539A pdb=" N LYS A 292 " --> pdb=" O ASP A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 310 through 321 Processing helix chain 'A' and resid 336 through 349 removed outlier: 3.674A pdb=" N SER A 339 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N VAL A 340 " --> pdb=" O LYS A 337 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TRP A 341 " --> pdb=" O TYR A 338 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER A 348 " --> pdb=" O SER A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 355 removed outlier: 3.756A pdb=" N GLN A 355 " --> pdb=" O THR A 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 355' Processing helix chain 'A' and resid 360 through 366 Processing helix chain 'A' and resid 368 through 371 removed outlier: 3.603A pdb=" N VAL A 371 " --> pdb=" O PRO A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 368 through 371' Processing helix chain 'B' and resid 57 through 61 Processing helix chain 'B' and resid 63 through 65 No H-bonds generated for 'chain 'B' and resid 63 through 65' Processing helix chain 'B' and resid 80 through 92 Processing helix chain 'B' and resid 114 through 126 Processing helix chain 'B' and resid 138 through 145 Processing helix chain 'B' and resid 173 through 175 No H-bonds generated for 'chain 'B' and resid 173 through 175' Processing helix chain 'B' and resid 183 through 197 removed outlier: 3.905A pdb=" N HIS B 195 " --> pdb=" O MET B 191 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLU B 196 " --> pdb=" O LYS B 192 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ARG B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 217 removed outlier: 3.521A pdb=" N LYS B 216 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 231 Processing helix chain 'B' and resid 253 through 262 removed outlier: 4.359A pdb=" N CYS B 258 " --> pdb=" O ARG B 255 " (cutoff:3.500A) Proline residue: B 259 - end of helix Processing helix chain 'B' and resid 265 through 268 Processing helix chain 'B' and resid 275 through 284 Processing helix chain 'B' and resid 288 through 295 removed outlier: 4.540A pdb=" N LYS B 292 " --> pdb=" O ASP B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'B' and resid 310 through 321 Processing helix chain 'B' and resid 336 through 349 removed outlier: 3.674A pdb=" N SER B 339 " --> pdb=" O ARG B 336 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL B 340 " --> pdb=" O LYS B 337 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TRP B 341 " --> pdb=" O TYR B 338 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER B 348 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 355 removed outlier: 3.757A pdb=" N GLN B 355 " --> pdb=" O THR B 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 352 through 355' Processing helix chain 'B' and resid 360 through 366 Processing helix chain 'B' and resid 368 through 371 removed outlier: 3.603A pdb=" N VAL B 371 " --> pdb=" O PRO B 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 368 through 371' Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'C' and resid 63 through 65 No H-bonds generated for 'chain 'C' and resid 63 through 65' Processing helix chain 'C' and resid 80 through 92 Processing helix chain 'C' and resid 114 through 126 Processing helix chain 'C' and resid 138 through 145 Processing helix chain 'C' and resid 173 through 175 No H-bonds generated for 'chain 'C' and resid 173 through 175' Processing helix chain 'C' and resid 183 through 197 removed outlier: 3.905A pdb=" N HIS C 195 " --> pdb=" O MET C 191 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLU C 196 " --> pdb=" O LYS C 192 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ARG C 197 " --> pdb=" O ILE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 217 removed outlier: 3.520A pdb=" N LYS C 216 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 231 Processing helix chain 'C' and resid 253 through 262 removed outlier: 4.360A pdb=" N CYS C 258 " --> pdb=" O ARG C 255 " (cutoff:3.500A) Proline residue: C 259 - end of helix Processing helix chain 'C' and resid 265 through 268 Processing helix chain 'C' and resid 275 through 284 Processing helix chain 'C' and resid 288 through 295 removed outlier: 4.540A pdb=" N LYS C 292 " --> pdb=" O ASP C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 310 through 321 Processing helix chain 'C' and resid 336 through 349 removed outlier: 3.674A pdb=" N SER C 339 " --> pdb=" O ARG C 336 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N VAL C 340 " --> pdb=" O LYS C 337 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TRP C 341 " --> pdb=" O TYR C 338 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER C 348 " --> pdb=" O SER C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 355 removed outlier: 3.757A pdb=" N GLN C 355 " --> pdb=" O THR C 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 352 through 355' Processing helix chain 'C' and resid 360 through 366 Processing helix chain 'C' and resid 368 through 371 removed outlier: 3.603A pdb=" N VAL C 371 " --> pdb=" O PRO C 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 368 through 371' Processing sheet with id= A, first strand: chain 'A' and resid 133 through 137 removed outlier: 6.866A pdb=" N VAL A 104 " --> pdb=" O TYR A 134 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ALA A 136 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU A 106 " --> pdb=" O ALA A 136 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU A 9 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N THR A 107 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N VAL A 11 " --> pdb=" O THR A 107 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 36 through 39 Processing sheet with id= C, first strand: chain 'A' and resid 298 through 301 removed outlier: 6.581A pdb=" N ILE A 152 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N SER A 301 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU A 154 " --> pdb=" O SER A 301 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 239 through 242 Processing sheet with id= E, first strand: chain 'B' and resid 133 through 137 removed outlier: 6.865A pdb=" N VAL B 104 " --> pdb=" O TYR B 134 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ALA B 136 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU B 106 " --> pdb=" O ALA B 136 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU B 9 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N THR B 107 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N VAL B 11 " --> pdb=" O THR B 107 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 36 through 39 Processing sheet with id= G, first strand: chain 'B' and resid 298 through 301 removed outlier: 6.581A pdb=" N ILE B 152 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N SER B 301 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU B 154 " --> pdb=" O SER B 301 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 239 through 242 Processing sheet with id= I, first strand: chain 'C' and resid 133 through 137 removed outlier: 6.865A pdb=" N VAL C 104 " --> pdb=" O TYR C 134 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ALA C 136 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU C 106 " --> pdb=" O ALA C 136 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU C 9 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N THR C 107 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N VAL C 11 " --> pdb=" O THR C 107 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 36 through 39 Processing sheet with id= K, first strand: chain 'C' and resid 298 through 301 removed outlier: 6.582A pdb=" N ILE C 152 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N SER C 301 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU C 154 " --> pdb=" O SER C 301 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 239 through 242 306 hydrogen bonds defined for protein. 729 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.68 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 2841 1.34 - 1.48: 2205 1.48 - 1.62: 3864 1.62 - 1.75: 0 1.75 - 1.89: 99 Bond restraints: 9009 Sorted by residual: bond pdb=" C4 9UE C 403 " pdb=" C5 9UE C 403 " ideal model delta sigma weight residual 0.880 1.499 -0.619 2.00e-02 2.50e+03 9.58e+02 bond pdb=" C4 9UE B 403 " pdb=" C5 9UE B 403 " ideal model delta sigma weight residual 0.880 1.499 -0.619 2.00e-02 2.50e+03 9.57e+02 bond pdb=" C4 9UE A 403 " pdb=" C5 9UE A 403 " ideal model delta sigma weight residual 0.880 1.499 -0.619 2.00e-02 2.50e+03 9.57e+02 bond pdb=" C11 9UE C 403 " pdb=" C12 9UE C 403 " ideal model delta sigma weight residual 2.064 1.505 0.559 2.00e-02 2.50e+03 7.81e+02 bond pdb=" C11 9UE B 403 " pdb=" C12 9UE B 403 " ideal model delta sigma weight residual 2.064 1.505 0.559 2.00e-02 2.50e+03 7.80e+02 ... (remaining 9004 not shown) Histogram of bond angle deviations from ideal: 98.58 - 106.07: 278 106.07 - 113.55: 4992 113.55 - 121.03: 4445 121.03 - 128.52: 2443 128.52 - 136.00: 70 Bond angle restraints: 12228 Sorted by residual: angle pdb=" C20 9UE A 403 " pdb=" C21 9UE A 403 " pdb=" C28 9UE A 403 " ideal model delta sigma weight residual 73.46 127.01 -53.55 3.00e+00 1.11e-01 3.19e+02 angle pdb=" C20 9UE B 403 " pdb=" C21 9UE B 403 " pdb=" C28 9UE B 403 " ideal model delta sigma weight residual 73.46 126.98 -53.52 3.00e+00 1.11e-01 3.18e+02 angle pdb=" C20 9UE C 403 " pdb=" C21 9UE C 403 " pdb=" C28 9UE C 403 " ideal model delta sigma weight residual 73.46 126.96 -53.50 3.00e+00 1.11e-01 3.18e+02 angle pdb=" C13 9UE C 403 " pdb=" C14 9UE C 403 " pdb=" C16 9UE C 403 " ideal model delta sigma weight residual 67.70 118.96 -51.26 3.00e+00 1.11e-01 2.92e+02 angle pdb=" C13 9UE B 403 " pdb=" C14 9UE B 403 " pdb=" C16 9UE B 403 " ideal model delta sigma weight residual 67.70 118.91 -51.21 3.00e+00 1.11e-01 2.91e+02 ... (remaining 12223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.06: 5142 33.06 - 66.12: 177 66.12 - 99.18: 42 99.18 - 132.24: 15 132.24 - 165.30: 6 Dihedral angle restraints: 5382 sinusoidal: 2217 harmonic: 3165 Sorted by residual: dihedral pdb=" C5' ADP B 402 " pdb=" O5' ADP B 402 " pdb=" PA ADP B 402 " pdb=" O2A ADP B 402 " ideal model delta sinusoidal sigma weight residual -60.00 105.30 -165.30 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C5' ADP C 402 " pdb=" O5' ADP C 402 " pdb=" PA ADP C 402 " pdb=" O2A ADP C 402 " ideal model delta sinusoidal sigma weight residual -60.00 105.30 -165.29 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C5' ADP A 402 " pdb=" O5' ADP A 402 " pdb=" PA ADP A 402 " pdb=" O2A ADP A 402 " ideal model delta sinusoidal sigma weight residual -60.00 105.29 -165.28 1 2.00e+01 2.50e-03 4.72e+01 ... (remaining 5379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1206 0.086 - 0.171: 138 0.171 - 0.257: 3 0.257 - 0.342: 0 0.342 - 0.428: 3 Chirality restraints: 1350 Sorted by residual: chirality pdb=" C12 9UE C 403 " pdb=" C11 9UE C 403 " pdb=" C13 9UE C 403 " pdb=" C17 9UE C 403 " both_signs ideal model delta sigma weight residual False 2.99 2.56 0.43 2.00e-01 2.50e+01 4.57e+00 chirality pdb=" C12 9UE A 403 " pdb=" C11 9UE A 403 " pdb=" C13 9UE A 403 " pdb=" C17 9UE A 403 " both_signs ideal model delta sigma weight residual False 2.99 2.56 0.43 2.00e-01 2.50e+01 4.53e+00 chirality pdb=" C12 9UE B 403 " pdb=" C11 9UE B 403 " pdb=" C13 9UE B 403 " pdb=" C17 9UE B 403 " both_signs ideal model delta sigma weight residual False 2.99 2.56 0.43 2.00e-01 2.50e+01 4.53e+00 ... (remaining 1347 not shown) Planarity restraints: 1560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 367 " 0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO A 368 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 368 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 368 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 367 " 0.019 5.00e-02 4.00e+02 2.95e-02 1.39e+00 pdb=" N PRO B 368 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 368 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 368 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 367 " 0.019 5.00e-02 4.00e+02 2.95e-02 1.39e+00 pdb=" N PRO C 368 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO C 368 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 368 " 0.016 5.00e-02 4.00e+02 ... (remaining 1557 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 36 2.58 - 3.16: 6993 3.16 - 3.74: 12791 3.74 - 4.32: 19297 4.32 - 4.90: 32147 Nonbonded interactions: 71264 Sorted by model distance: nonbonded pdb="MG MG C 401 " pdb=" O1B ADP C 402 " model vdw 1.995 2.170 nonbonded pdb="MG MG A 401 " pdb=" O1B ADP A 402 " model vdw 1.996 2.170 nonbonded pdb="MG MG B 401 " pdb=" O1B ADP B 402 " model vdw 1.996 2.170 nonbonded pdb=" OD1 ASP C 158 " pdb=" O3' ADP C 402 " model vdw 2.204 2.440 nonbonded pdb=" OD1 ASP A 158 " pdb=" O3' ADP A 402 " model vdw 2.204 2.440 ... (remaining 71259 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' selection = chain 'B' selection = chain 'C' } 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: 2.950 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: 11.630 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 27.100 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 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:12.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 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 : 0.025 0.619 9009 Z= 1.520 Angle : 2.230 53.546 12228 Z= 0.794 Chirality : 0.054 0.428 1350 Planarity : 0.004 0.030 1560 Dihedral : 20.193 165.299 3360 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.64 % Allowed : 13.10 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.25), residues: 1095 helix: 0.03 (0.24), residues: 462 sheet: 0.51 (0.35), residues: 201 loop : 0.45 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 357 HIS 0.004 0.001 HIS C 162 PHE 0.010 0.002 PHE B 224 TYR 0.010 0.001 TYR C 295 ARG 0.004 0.001 ARG C 211 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 194 time to evaluate : 1.003 Fit side-chains REVERT: A 70 TYR cc_start: 0.9069 (m-80) cc_final: 0.8739 (m-80) REVERT: A 168 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8406 (mt-10) REVERT: A 202 THR cc_start: 0.9017 (m) cc_final: 0.8762 (t) REVERT: A 208 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7864 (mm-30) REVERT: A 327 LYS cc_start: 0.8277 (ptpt) cc_final: 0.7794 (mtmm) REVERT: B 13 ASN cc_start: 0.8287 (OUTLIER) cc_final: 0.8085 (t0) REVERT: B 38 LYS cc_start: 0.8515 (mtmm) cc_final: 0.8270 (mttp) REVERT: B 48 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7491 (ptt) REVERT: B 69 LYS cc_start: 0.8540 (ttmm) cc_final: 0.8231 (mmmm) REVERT: B 327 LYS cc_start: 0.8025 (ptpt) cc_final: 0.7599 (mtmm) REVERT: B 356 MET cc_start: 0.8710 (mtm) cc_final: 0.8430 (mtt) REVERT: C 38 LYS cc_start: 0.8537 (mtmm) cc_final: 0.8292 (mttp) REVERT: C 69 LYS cc_start: 0.8295 (ttmm) cc_final: 0.7994 (mttm) REVERT: C 83 MET cc_start: 0.8981 (tpt) cc_final: 0.8619 (tpt) REVERT: C 97 VAL cc_start: 0.8981 (m) cc_final: 0.8766 (p) REVERT: C 134 TYR cc_start: 0.9083 (t80) cc_final: 0.8804 (t80) REVERT: C 289 ASP cc_start: 0.8459 (m-30) cc_final: 0.8223 (m-30) REVERT: C 327 LYS cc_start: 0.8006 (ptpt) cc_final: 0.7653 (mtmm) REVERT: C 364 ASP cc_start: 0.7905 (m-30) cc_final: 0.7666 (m-30) outliers start: 6 outliers final: 0 residues processed: 197 average time/residue: 1.4611 time to fit residues: 303.9817 Evaluate side-chains 160 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 158 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 48 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 32 optimal weight: 0.0020 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN C 13 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9009 Z= 0.209 Angle : 1.250 49.111 12228 Z= 0.456 Chirality : 0.050 0.399 1350 Planarity : 0.004 0.030 1560 Dihedral : 19.387 156.805 1277 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.51 % Allowed : 16.29 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.25), residues: 1095 helix: 0.36 (0.24), residues: 444 sheet: 0.78 (0.35), residues: 216 loop : 0.39 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 357 HIS 0.007 0.001 HIS A 74 PHE 0.011 0.001 PHE B 32 TYR 0.011 0.001 TYR A 295 ARG 0.002 0.000 ARG C 211 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 160 time to evaluate : 1.130 Fit side-chains REVERT: A 70 TYR cc_start: 0.9054 (m-80) cc_final: 0.8695 (m-80) REVERT: A 108 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7914 (tt0) REVERT: A 168 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8466 (mt-10) REVERT: A 202 THR cc_start: 0.8985 (m) cc_final: 0.8728 (t) REVERT: A 208 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7342 (mm-30) REVERT: A 327 LYS cc_start: 0.8374 (ptpt) cc_final: 0.7868 (mtmm) REVERT: B 38 LYS cc_start: 0.8270 (mtmm) cc_final: 0.8040 (mtmt) REVERT: B 48 MET cc_start: 0.8008 (mmm) cc_final: 0.7428 (ptt) REVERT: B 69 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8160 (mmmm) REVERT: B 327 LYS cc_start: 0.8124 (ptpt) cc_final: 0.7683 (mtmm) REVERT: C 38 LYS cc_start: 0.8277 (mtmm) cc_final: 0.8036 (mttp) REVERT: C 44 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.8011 (tt) REVERT: C 69 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7901 (mttm) REVERT: C 83 MET cc_start: 0.8989 (tpt) cc_final: 0.8712 (tpt) REVERT: C 126 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7519 (mm-30) REVERT: C 229 LYS cc_start: 0.7900 (tttt) cc_final: 0.7344 (ttmm) REVERT: C 289 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.8109 (m-30) REVERT: C 327 LYS cc_start: 0.8128 (ptpt) cc_final: 0.7748 (mtmm) REVERT: C 356 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8071 (mtm) outliers start: 33 outliers final: 15 residues processed: 175 average time/residue: 1.3706 time to fit residues: 254.4233 Evaluate side-chains 174 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 153 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 371 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 81 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9009 Z= 0.256 Angle : 1.236 47.759 12228 Z= 0.450 Chirality : 0.048 0.271 1350 Planarity : 0.004 0.039 1560 Dihedral : 19.213 157.150 1274 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 5.01 % Allowed : 16.29 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.25), residues: 1095 helix: 0.16 (0.24), residues: 459 sheet: 0.55 (0.36), residues: 201 loop : 0.37 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 357 HIS 0.004 0.001 HIS A 162 PHE 0.010 0.001 PHE B 32 TYR 0.013 0.001 TYR A 295 ARG 0.006 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 153 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: A 108 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7910 (tt0) REVERT: A 134 TYR cc_start: 0.9193 (t80) cc_final: 0.8956 (t80) REVERT: A 168 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8477 (mt-10) REVERT: A 327 LYS cc_start: 0.8419 (ptpt) cc_final: 0.7913 (mtmm) REVERT: B 48 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7403 (ptt) REVERT: B 69 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8158 (mmmm) REVERT: B 81 ASP cc_start: 0.7802 (m-30) cc_final: 0.7555 (m-30) REVERT: B 225 ASP cc_start: 0.7960 (m-30) cc_final: 0.7753 (m-30) REVERT: B 308 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7550 (tm-30) REVERT: B 327 LYS cc_start: 0.8173 (ptpt) cc_final: 0.7751 (mtmm) REVERT: C 38 LYS cc_start: 0.8321 (mtmm) cc_final: 0.8056 (mttp) REVERT: C 44 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.8026 (tt) REVERT: C 65 ILE cc_start: 0.9405 (OUTLIER) cc_final: 0.9032 (pp) REVERT: C 69 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7898 (mttm) REVERT: C 73 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7362 (tt0) REVERT: C 83 MET cc_start: 0.8964 (tpt) cc_final: 0.8760 (tpt) REVERT: C 126 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7554 (mm-30) REVERT: C 229 LYS cc_start: 0.7934 (tttt) cc_final: 0.7366 (ttmm) REVERT: C 289 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.8092 (m-30) REVERT: C 327 LYS cc_start: 0.8185 (ptpt) cc_final: 0.7757 (mtmm) REVERT: C 356 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8139 (mtm) outliers start: 47 outliers final: 20 residues processed: 176 average time/residue: 1.4171 time to fit residues: 264.0390 Evaluate side-chains 177 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 148 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 371 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 98 optimal weight: 0.0010 chunk 104 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 162 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9009 Z= 0.233 Angle : 1.225 47.952 12228 Z= 0.443 Chirality : 0.048 0.272 1350 Planarity : 0.004 0.033 1560 Dihedral : 19.094 156.941 1272 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.73 % Allowed : 18.10 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.25), residues: 1095 helix: 0.55 (0.25), residues: 426 sheet: 0.75 (0.35), residues: 216 loop : 0.50 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 357 HIS 0.003 0.001 HIS B 162 PHE 0.010 0.001 PHE A 32 TYR 0.013 0.001 TYR A 295 ARG 0.006 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 153 time to evaluate : 1.046 Fit side-chains REVERT: A 73 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7665 (tt0) REVERT: A 108 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7878 (tt0) REVERT: A 134 TYR cc_start: 0.9228 (t80) cc_final: 0.8972 (t80) REVERT: A 168 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8475 (mt-10) REVERT: A 208 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7438 (mm-30) REVERT: A 327 LYS cc_start: 0.8522 (ptpt) cc_final: 0.8003 (mtmm) REVERT: B 48 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7505 (ptt) REVERT: B 69 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8164 (mmmm) REVERT: B 81 ASP cc_start: 0.7785 (m-30) cc_final: 0.7584 (m-30) REVERT: B 225 ASP cc_start: 0.8043 (m-30) cc_final: 0.7796 (m-30) REVERT: B 226 GLU cc_start: 0.7963 (tp30) cc_final: 0.7683 (mm-30) REVERT: B 308 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7510 (tm-30) REVERT: B 327 LYS cc_start: 0.8214 (ptpt) cc_final: 0.7832 (mtmm) REVERT: B 365 GLU cc_start: 0.7654 (tp30) cc_final: 0.7365 (tp30) REVERT: C 44 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.8077 (tt) REVERT: C 65 ILE cc_start: 0.9413 (OUTLIER) cc_final: 0.9017 (pp) REVERT: C 69 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7870 (mttm) REVERT: C 73 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7334 (tt0) REVERT: C 83 MET cc_start: 0.8932 (tpt) cc_final: 0.8713 (tpt) REVERT: C 126 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7510 (mm-30) REVERT: C 229 LYS cc_start: 0.8024 (tttt) cc_final: 0.7450 (ttmm) REVERT: C 289 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.8135 (m-30) REVERT: C 327 LYS cc_start: 0.8259 (ptpt) cc_final: 0.7824 (mtmm) REVERT: C 356 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8195 (mtm) REVERT: C 364 ASP cc_start: 0.7934 (m-30) cc_final: 0.7641 (m-30) outliers start: 35 outliers final: 18 residues processed: 168 average time/residue: 1.4283 time to fit residues: 253.8555 Evaluate side-chains 173 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 145 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 371 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 0 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 93 optimal weight: 0.0970 chunk 26 optimal weight: 0.7980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9009 Z= 0.282 Angle : 1.233 47.995 12228 Z= 0.448 Chirality : 0.048 0.261 1350 Planarity : 0.004 0.036 1560 Dihedral : 19.141 157.828 1272 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.47 % Allowed : 17.68 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.25), residues: 1095 helix: 0.61 (0.25), residues: 420 sheet: 0.69 (0.35), residues: 216 loop : 0.54 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 357 HIS 0.003 0.001 HIS A 74 PHE 0.011 0.002 PHE B 32 TYR 0.015 0.001 TYR A 295 ARG 0.006 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 149 time to evaluate : 1.242 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7667 (tt0) REVERT: A 108 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7947 (tt0) REVERT: A 134 TYR cc_start: 0.9220 (t80) cc_final: 0.9003 (t80) REVERT: A 168 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8486 (mt-10) REVERT: A 327 LYS cc_start: 0.8545 (ptpt) cc_final: 0.8041 (mtmm) REVERT: B 48 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7534 (ptt) REVERT: B 69 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8155 (mmmm) REVERT: B 225 ASP cc_start: 0.8070 (m-30) cc_final: 0.7799 (m-30) REVERT: B 226 GLU cc_start: 0.7974 (tp30) cc_final: 0.7694 (mm-30) REVERT: B 308 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7504 (tm-30) REVERT: B 327 LYS cc_start: 0.8187 (ptpt) cc_final: 0.7777 (mtmm) REVERT: B 365 GLU cc_start: 0.7678 (tp30) cc_final: 0.7409 (tp30) REVERT: C 44 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.8127 (tt) REVERT: C 65 ILE cc_start: 0.9423 (OUTLIER) cc_final: 0.9026 (pp) REVERT: C 69 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7860 (mttm) REVERT: C 73 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7358 (tt0) REVERT: C 83 MET cc_start: 0.8902 (tpt) cc_final: 0.8701 (tpt) REVERT: C 126 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7598 (mm-30) REVERT: C 229 LYS cc_start: 0.8092 (tttt) cc_final: 0.7620 (ttmp) REVERT: C 289 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.8133 (m-30) REVERT: C 327 LYS cc_start: 0.8323 (ptpt) cc_final: 0.7889 (mtmm) REVERT: C 356 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8176 (mtm) REVERT: C 364 ASP cc_start: 0.8014 (m-30) cc_final: 0.7748 (m-30) outliers start: 42 outliers final: 24 residues processed: 169 average time/residue: 1.4714 time to fit residues: 262.8473 Evaluate side-chains 177 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 143 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 371 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 264 GLN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9009 Z= 0.228 Angle : 1.220 47.876 12228 Z= 0.440 Chirality : 0.047 0.263 1350 Planarity : 0.004 0.033 1560 Dihedral : 19.134 157.717 1272 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.83 % Allowed : 18.00 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.25), residues: 1095 helix: 0.59 (0.25), residues: 426 sheet: 0.69 (0.35), residues: 216 loop : 0.57 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 357 HIS 0.004 0.001 HIS B 162 PHE 0.009 0.001 PHE A 32 TYR 0.013 0.001 TYR A 295 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 145 time to evaluate : 0.972 Fit side-chains REVERT: A 73 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7642 (tt0) REVERT: A 108 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.7918 (tt0) REVERT: A 134 TYR cc_start: 0.9219 (t80) cc_final: 0.8995 (t80) REVERT: A 168 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8488 (mt-10) REVERT: A 327 LYS cc_start: 0.8538 (ptpt) cc_final: 0.8036 (mtmm) REVERT: B 48 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7525 (ptt) REVERT: B 69 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8164 (mmmm) REVERT: B 225 ASP cc_start: 0.8053 (m-30) cc_final: 0.7767 (m-30) REVERT: B 226 GLU cc_start: 0.7946 (tp30) cc_final: 0.7676 (mm-30) REVERT: B 308 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7512 (tm-30) REVERT: B 327 LYS cc_start: 0.8198 (ptpt) cc_final: 0.7787 (mtmm) REVERT: B 365 GLU cc_start: 0.7679 (tp30) cc_final: 0.7413 (tp30) REVERT: C 44 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8166 (tt) REVERT: C 65 ILE cc_start: 0.9421 (OUTLIER) cc_final: 0.9015 (pp) REVERT: C 69 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7864 (mttm) REVERT: C 73 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7381 (tt0) REVERT: C 126 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7513 (mm-30) REVERT: C 229 LYS cc_start: 0.8095 (tttt) cc_final: 0.7620 (ttmp) REVERT: C 289 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8142 (m-30) REVERT: C 327 LYS cc_start: 0.8342 (ptpt) cc_final: 0.7905 (mtmm) REVERT: C 356 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8206 (mtm) REVERT: C 364 ASP cc_start: 0.8019 (m-30) cc_final: 0.7768 (m-30) outliers start: 36 outliers final: 22 residues processed: 161 average time/residue: 1.4877 time to fit residues: 252.8951 Evaluate side-chains 173 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 141 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 371 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 76 optimal weight: 0.0000 chunk 87 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 65 optimal weight: 0.0670 chunk 63 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 overall best weight: 0.4522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9009 Z= 0.151 Angle : 1.202 47.688 12228 Z= 0.430 Chirality : 0.045 0.262 1350 Planarity : 0.004 0.031 1560 Dihedral : 19.117 156.717 1272 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.98 % Allowed : 19.17 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.26), residues: 1095 helix: 0.62 (0.25), residues: 441 sheet: 0.79 (0.36), residues: 216 loop : 0.73 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 87 HIS 0.003 0.001 HIS A 74 PHE 0.009 0.001 PHE B 256 TYR 0.008 0.001 TYR A 295 ARG 0.006 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 148 time to evaluate : 1.036 Fit side-chains REVERT: A 73 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7610 (tt0) REVERT: A 134 TYR cc_start: 0.9212 (t80) cc_final: 0.8948 (t80) REVERT: A 168 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8493 (mt-10) REVERT: A 327 LYS cc_start: 0.8521 (ptpt) cc_final: 0.8018 (mtmm) REVERT: B 48 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7581 (ptt) REVERT: B 69 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8180 (mmmm) REVERT: B 225 ASP cc_start: 0.8043 (m-30) cc_final: 0.7745 (m-30) REVERT: B 226 GLU cc_start: 0.7933 (tp30) cc_final: 0.7678 (mm-30) REVERT: B 297 ASN cc_start: 0.8604 (t0) cc_final: 0.8367 (t0) REVERT: B 308 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7491 (tm-30) REVERT: B 327 LYS cc_start: 0.8211 (ptpt) cc_final: 0.7797 (mtmm) REVERT: B 365 GLU cc_start: 0.7657 (tp30) cc_final: 0.7408 (tp30) REVERT: C 44 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8125 (tt) REVERT: C 69 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7889 (mttm) REVERT: C 73 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7347 (tt0) REVERT: C 126 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7523 (mm-30) REVERT: C 229 LYS cc_start: 0.8105 (tttt) cc_final: 0.7631 (ttmp) REVERT: C 289 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.8080 (m-30) REVERT: C 327 LYS cc_start: 0.8318 (ptpt) cc_final: 0.7882 (mtmm) REVERT: C 364 ASP cc_start: 0.7995 (m-30) cc_final: 0.7734 (m-30) outliers start: 28 outliers final: 14 residues processed: 160 average time/residue: 1.4938 time to fit residues: 252.1962 Evaluate side-chains 164 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 142 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 289 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.7980 chunk 62 optimal weight: 0.0570 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.8902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9009 Z= 0.227 Angle : 1.215 47.935 12228 Z= 0.437 Chirality : 0.047 0.253 1350 Planarity : 0.004 0.033 1560 Dihedral : 19.168 157.423 1272 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.41 % Allowed : 18.85 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.25), residues: 1095 helix: 0.51 (0.25), residues: 444 sheet: 0.61 (0.37), residues: 201 loop : 0.78 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 87 HIS 0.004 0.001 HIS B 162 PHE 0.009 0.001 PHE A 32 TYR 0.011 0.001 TYR A 295 ARG 0.006 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 142 time to evaluate : 1.003 Fit side-chains REVERT: A 38 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7903 (mppt) REVERT: A 73 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7638 (tt0) REVERT: A 134 TYR cc_start: 0.9219 (t80) cc_final: 0.9008 (t80) REVERT: A 168 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8494 (mt-10) REVERT: A 327 LYS cc_start: 0.8526 (ptpt) cc_final: 0.8017 (mtmm) REVERT: B 48 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7544 (ptt) REVERT: B 69 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8189 (mmmm) REVERT: B 225 ASP cc_start: 0.8016 (m-30) cc_final: 0.7717 (m-30) REVERT: B 226 GLU cc_start: 0.7947 (tp30) cc_final: 0.7699 (mm-30) REVERT: B 308 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7490 (tm-30) REVERT: B 327 LYS cc_start: 0.8156 (ptpt) cc_final: 0.7729 (mtmm) REVERT: B 365 GLU cc_start: 0.7674 (tp30) cc_final: 0.7432 (tp30) REVERT: C 44 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.8126 (tt) REVERT: C 65 ILE cc_start: 0.9410 (OUTLIER) cc_final: 0.8975 (pp) REVERT: C 69 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7877 (mttm) REVERT: C 73 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7382 (tt0) REVERT: C 126 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7571 (mm-30) REVERT: C 229 LYS cc_start: 0.8114 (tttt) cc_final: 0.7641 (ttmp) REVERT: C 289 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.8123 (m-30) REVERT: C 327 LYS cc_start: 0.8318 (ptpt) cc_final: 0.7894 (mtmm) REVERT: C 356 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8253 (mtm) REVERT: C 364 ASP cc_start: 0.8044 (m-30) cc_final: 0.7786 (m-30) outliers start: 32 outliers final: 19 residues processed: 156 average time/residue: 1.5061 time to fit residues: 247.8290 Evaluate side-chains 171 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 141 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 356 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 99 optimal weight: 0.3980 chunk 58 optimal weight: 6.9990 chunk 42 optimal weight: 0.0170 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9009 Z= 0.164 Angle : 1.202 47.727 12228 Z= 0.430 Chirality : 0.045 0.251 1350 Planarity : 0.004 0.032 1560 Dihedral : 19.162 157.109 1272 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.19 % Allowed : 19.38 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.26), residues: 1095 helix: 0.63 (0.25), residues: 444 sheet: 0.65 (0.37), residues: 201 loop : 0.88 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 87 HIS 0.003 0.001 HIS A 74 PHE 0.009 0.001 PHE B 256 TYR 0.011 0.001 TYR A 295 ARG 0.007 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 146 time to evaluate : 1.186 Fit side-chains REVERT: A 73 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7617 (tt0) REVERT: A 134 TYR cc_start: 0.9207 (t80) cc_final: 0.8963 (t80) REVERT: A 168 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8489 (mt-10) REVERT: A 327 LYS cc_start: 0.8489 (ptpt) cc_final: 0.7977 (mtmm) REVERT: B 48 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7597 (ptt) REVERT: B 69 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8186 (mmmm) REVERT: B 225 ASP cc_start: 0.8005 (m-30) cc_final: 0.7709 (m-30) REVERT: B 226 GLU cc_start: 0.7936 (tp30) cc_final: 0.7708 (mm-30) REVERT: B 308 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7501 (tm-30) REVERT: B 327 LYS cc_start: 0.8165 (ptpt) cc_final: 0.7734 (mtmm) REVERT: B 365 GLU cc_start: 0.7653 (tp30) cc_final: 0.7408 (tp30) REVERT: C 44 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8155 (tt) REVERT: C 65 ILE cc_start: 0.9397 (OUTLIER) cc_final: 0.8965 (pp) REVERT: C 69 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7876 (mttm) REVERT: C 73 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7366 (tt0) REVERT: C 126 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7551 (mm-30) REVERT: C 229 LYS cc_start: 0.8142 (tttt) cc_final: 0.7654 (ttmp) REVERT: C 289 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.8064 (m-30) REVERT: C 327 LYS cc_start: 0.8323 (ptpt) cc_final: 0.7894 (mtmm) REVERT: C 356 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8230 (mtm) REVERT: C 364 ASP cc_start: 0.8067 (m-30) cc_final: 0.7801 (m-30) outliers start: 30 outliers final: 17 residues processed: 158 average time/residue: 1.5085 time to fit residues: 251.4878 Evaluate side-chains 169 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 142 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 356 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 68 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9009 Z= 0.199 Angle : 1.208 47.856 12228 Z= 0.434 Chirality : 0.046 0.245 1350 Planarity : 0.004 0.036 1560 Dihedral : 19.193 157.292 1272 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.30 % Allowed : 19.06 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.26), residues: 1095 helix: 0.66 (0.25), residues: 441 sheet: 0.79 (0.36), residues: 216 loop : 0.78 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 87 HIS 0.004 0.001 HIS A 74 PHE 0.009 0.001 PHE A 256 TYR 0.009 0.001 TYR A 295 ARG 0.008 0.000 ARG A 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 143 time to evaluate : 1.059 Fit side-chains REVERT: A 73 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7636 (tt0) REVERT: A 134 TYR cc_start: 0.9208 (t80) cc_final: 0.8997 (t80) REVERT: A 148 ARG cc_start: 0.7844 (mtp180) cc_final: 0.7522 (mtp180) REVERT: A 168 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8471 (mt-10) REVERT: A 327 LYS cc_start: 0.8495 (ptpt) cc_final: 0.7981 (mtmm) REVERT: B 48 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7588 (ptt) REVERT: B 69 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8187 (mmmm) REVERT: B 225 ASP cc_start: 0.8003 (m-30) cc_final: 0.7664 (m-30) REVERT: B 226 GLU cc_start: 0.7929 (tp30) cc_final: 0.7712 (mm-30) REVERT: B 308 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7501 (tm-30) REVERT: B 327 LYS cc_start: 0.8166 (ptpt) cc_final: 0.7721 (mtmm) REVERT: B 365 GLU cc_start: 0.7655 (tp30) cc_final: 0.7406 (tp30) REVERT: C 44 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8157 (tt) REVERT: C 65 ILE cc_start: 0.9404 (OUTLIER) cc_final: 0.8961 (pp) REVERT: C 69 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7877 (mttm) REVERT: C 73 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7385 (tt0) REVERT: C 126 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7552 (mm-30) REVERT: C 229 LYS cc_start: 0.8143 (tttt) cc_final: 0.7677 (ttmp) REVERT: C 289 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.8087 (m-30) REVERT: C 327 LYS cc_start: 0.8340 (ptpt) cc_final: 0.7911 (mtmm) REVERT: C 356 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8237 (mtm) REVERT: C 364 ASP cc_start: 0.8091 (m-30) cc_final: 0.7822 (m-30) outliers start: 31 outliers final: 17 residues processed: 155 average time/residue: 1.5141 time to fit residues: 247.8098 Evaluate side-chains 169 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 142 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 356 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.0980 chunk 26 optimal weight: 0.0570 chunk 79 optimal weight: 0.7980 chunk 12 optimal weight: 0.3980 chunk 23 optimal weight: 0.2980 chunk 85 optimal weight: 0.0670 chunk 35 optimal weight: 0.8980 chunk 88 optimal weight: 0.0970 chunk 10 optimal weight: 0.0060 chunk 15 optimal weight: 6.9990 chunk 75 optimal weight: 0.3980 overall best weight: 0.0650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 HIS C 355 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.112391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.096873 restraints weight = 9220.914| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.64 r_work: 0.2884 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9009 Z= 0.123 Angle : 1.185 47.459 12228 Z= 0.423 Chirality : 0.044 0.220 1350 Planarity : 0.003 0.032 1560 Dihedral : 19.210 160.822 1272 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.81 % Allowed : 20.45 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.26), residues: 1095 helix: 0.98 (0.25), residues: 435 sheet: 0.93 (0.37), residues: 216 loop : 0.88 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 87 HIS 0.003 0.001 HIS A 74 PHE 0.009 0.001 PHE C 256 TYR 0.007 0.001 TYR C 307 ARG 0.008 0.000 ARG A 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4271.86 seconds wall clock time: 76 minutes 45.10 seconds (4605.10 seconds total)