Starting phenix.real_space_refine on Thu Jun 27 03:52:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ru0_19501/06_2024/8ru0_19501_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ru0_19501/06_2024/8ru0_19501.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ru0_19501/06_2024/8ru0_19501.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ru0_19501/06_2024/8ru0_19501.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ru0_19501/06_2024/8ru0_19501_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ru0_19501/06_2024/8ru0_19501_updated.pdb" } resolution = 3.08 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= 0.002 sd= 0.092 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 4 5.21 5 S 83 5.16 5 C 7343 2.51 5 N 1964 2.21 5 O 2254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 80": "OD1" <-> "OD2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 51": "OD1" <-> "OD2" Residue "A TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 363": "OD1" <-> "OD2" Residue "C ASP 25": "OD1" <-> "OD2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 292": "OD1" <-> "OD2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "D ASP 80": "OD1" <-> "OD2" Residue "D TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 286": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 11660 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: "A" 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: "C" Number of atoms: 2881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2881 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 19, 'TRANS': 349} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2855 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 19, 'TRANS': 346} 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.51, per 1000 atoms: 0.56 Number of scatterers: 11660 At special positions: 0 Unit cell: (77.4, 99, 165.6, 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 83 16.00 P 12 15.00 Mg 4 11.99 O 2254 8.00 N 1964 7.00 C 7343 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: 4.49 Conformation dependent library (CDL) restraints added in 2.1 seconds 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2728 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 75 helices and 18 sheets defined 42.8% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'B' and resid 55 through 60 removed outlier: 3.556A pdb=" N SER B 60 " --> pdb=" O GLU B 57 " (cutoff:3.500A) 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 81 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 196 removed outlier: 3.754A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.761A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.521A 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 254 through 260 Proline residue: B 258 - end of helix No H-bonds generated for 'chain 'B' and resid 254 through 260' 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 295 Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 335 through 348 removed outlier: 3.517A pdb=" N SER B 338 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY B 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 354 No H-bonds generated for 'chain 'B' and resid 352 through 354' Processing helix chain 'B' and resid 359 through 373 Proline residue: B 367 - end of helix removed outlier: 5.588A pdb=" N VAL B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N HIS B 371 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 60 removed outlier: 3.555A pdb=" N SER A 60 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 91 Processing helix chain 'A' and resid 113 through 125 removed outlier: 3.581A pdb=" N GLU A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 144 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 195 removed outlier: 3.980A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 215 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.564A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N CYS A 257 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 287 through 295 removed outlier: 4.331A pdb=" N LYS A 291 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR A 294 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 335 through 348 removed outlier: 3.690A pdb=" N SER A 338 " --> pdb=" O ARG A 335 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'C' and resid 55 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 113 through 125 removed outlier: 3.632A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) 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: 4.052A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 254 through 262 Proline residue: C 258 - end of helix removed outlier: 4.734A pdb=" N LEU C 261 " --> pdb=" O CYS C 257 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 254 through 262' 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 295 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 Processing helix chain 'C' and resid 351 through 354 removed outlier: 3.574A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 351 through 354' Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 373 removed outlier: 3.522A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 removed outlier: 3.512A pdb=" N SER D 60 " --> pdb=" O GLU D 57 " (cutoff:3.500A) 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 126 Processing helix chain 'D' and resid 137 through 144 Processing helix chain 'D' and resid 182 through 194 removed outlier: 4.136A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 removed outlier: 3.520A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 254 through 261 Proline residue: D 258 - end of helix removed outlier: 4.907A pdb=" N LEU D 261 " --> pdb=" O CYS D 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 254 through 261' 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 295 removed outlier: 4.044A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 305 No H-bonds generated for 'chain 'D' and resid 303 through 305' Processing helix chain 'D' and resid 309 through 319 Processing helix chain 'D' and resid 335 through 348 removed outlier: 3.679A pdb=" N SER D 338 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY D 342 " --> pdb=" O VAL D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 354 removed outlier: 3.741A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 351 through 354' Processing helix chain 'D' and resid 359 through 363 Processing helix chain 'D' and resid 367 through 370 removed outlier: 3.977A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 367 through 370' Processing sheet with id= A, first strand: chain 'B' and resid 8 through 11 Processing sheet with id= B, first strand: chain 'B' and resid 35 through 37 Processing sheet with id= C, first strand: chain 'B' and resid 103 through 107 Processing sheet with id= D, first strand: chain 'B' and resid 297 through 299 removed outlier: 6.406A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= F, first strand: chain 'A' and resid 8 through 10 Processing sheet with id= G, first strand: chain 'A' and resid 52 through 54 removed outlier: 3.572A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 103 through 107 Processing sheet with id= I, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.532A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= K, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.691A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.321A 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 37 Processing sheet with id= M, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.217A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 5.757A 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 133 through 136 removed outlier: 3.670A pdb=" N TYR D 133 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY D 20 " --> pdb=" O VAL D 9 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 35 through 38 removed outlier: 3.834A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 298 through 300 removed outlier: 3.517A pdb=" N SER D 155 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN D 162 " --> pdb=" O MET D 176 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N MET D 176 " --> pdb=" O ASN D 162 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 238 through 241 410 hydrogen bonds defined for protein. 1035 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: 3.41 Time building geometry restraints manager: 4.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3790 1.34 - 1.46: 2500 1.46 - 1.58: 5460 1.58 - 1.69: 14 1.69 - 1.81: 147 Bond restraints: 11911 Sorted by residual: bond pdb=" CA ASP D 222 " pdb=" CB ASP D 222 " ideal model delta sigma weight residual 1.527 1.545 -0.018 1.75e-02 3.27e+03 1.09e+00 bond pdb=" C4 ADP B 401 " pdb=" C5 ADP B 401 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.01e+00 bond pdb=" N GLY B 48 " pdb=" CA GLY B 48 " ideal model delta sigma weight residual 1.449 1.464 -0.014 1.45e-02 4.76e+03 9.95e-01 bond pdb=" C4 ADP A 401 " pdb=" C5 ADP A 401 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 9.93e-01 bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.471 0.019 2.00e-02 2.50e+03 9.33e-01 ... (remaining 11906 not shown) Histogram of bond angle deviations from ideal: 100.55 - 108.42: 696 108.42 - 116.28: 7345 116.28 - 124.15: 7850 124.15 - 132.01: 254 132.01 - 139.88: 25 Bond angle restraints: 16170 Sorted by residual: angle pdb=" N VAL D 45 " pdb=" CA VAL D 45 " pdb=" C VAL D 45 " ideal model delta sigma weight residual 113.39 109.25 4.14 1.47e+00 4.63e-01 7.94e+00 angle pdb=" C ASP D 222 " pdb=" CA ASP D 222 " pdb=" CB ASP D 222 " ideal model delta sigma weight residual 111.23 115.85 -4.62 1.68e+00 3.54e-01 7.58e+00 angle pdb=" CA GLN D 360 " pdb=" CB GLN D 360 " pdb=" CG GLN D 360 " ideal model delta sigma weight residual 114.10 119.09 -4.99 2.00e+00 2.50e-01 6.23e+00 angle pdb=" CA ASP D 222 " pdb=" CB ASP D 222 " pdb=" CG ASP D 222 " ideal model delta sigma weight residual 112.60 114.93 -2.33 1.00e+00 1.00e+00 5.41e+00 angle pdb=" C GLY D 150 " pdb=" N ILE D 151 " pdb=" CA ILE D 151 " ideal model delta sigma weight residual 121.97 126.14 -4.17 1.80e+00 3.09e-01 5.36e+00 ... (remaining 16165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.20: 6948 35.20 - 70.40: 215 70.40 - 105.60: 8 105.60 - 140.80: 2 140.80 - 176.00: 3 Dihedral angle restraints: 7176 sinusoidal: 2912 harmonic: 4264 Sorted by residual: dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 116.00 -176.00 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 115.04 -175.04 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 108.38 -168.38 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 7173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1226 0.035 - 0.070: 386 0.070 - 0.105: 133 0.105 - 0.140: 45 0.140 - 0.175: 3 Chirality restraints: 1793 Sorted by residual: chirality pdb=" CA ASP D 222 " pdb=" N ASP D 222 " pdb=" C ASP D 222 " pdb=" CB ASP D 222 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.69e-01 chirality pdb=" CB ILE D 151 " pdb=" CA ILE D 151 " pdb=" CG1 ILE D 151 " pdb=" CG2 ILE D 151 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.07e-01 chirality pdb=" CB THR B 202 " pdb=" CA THR B 202 " pdb=" OG1 THR B 202 " pdb=" CG2 THR B 202 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.76e-01 ... (remaining 1790 not shown) Planarity restraints: 2063 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 366 " 0.026 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO C 367 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 367 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 367 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 222 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.54e+00 pdb=" C ASP C 222 " -0.028 2.00e-02 2.50e+03 pdb=" O ASP C 222 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE C 223 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 242 " -0.021 5.00e-02 4.00e+02 3.13e-02 1.57e+00 pdb=" N PRO B 243 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 243 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 243 " -0.017 5.00e-02 4.00e+02 ... (remaining 2060 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 110 2.63 - 3.20: 10154 3.20 - 3.77: 17235 3.77 - 4.33: 25428 4.33 - 4.90: 41981 Nonbonded interactions: 94908 Sorted by model distance: nonbonded pdb="MG MG C 402 " pdb=" O2 PO4 C 403 " model vdw 2.068 2.170 nonbonded pdb="MG MG D 401 " pdb=" O1G ATP D 402 " model vdw 2.148 2.170 nonbonded pdb=" OD1 ASP A 157 " pdb=" O3' ADP A 401 " model vdw 2.210 2.440 nonbonded pdb=" OD1 ASP B 157 " pdb=" O3' ADP B 401 " model vdw 2.249 2.440 nonbonded pdb=" O GLY B 156 " pdb=" OG1 THR B 303 " model vdw 2.253 2.440 ... (remaining 94903 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 371 or resid 402)) selection = (chain 'B' and (resid 6 through 371 or resid 402)) selection = (chain 'C' and (resid 6 through 371 or resid 402)) selection = (chain 'D' and (resid 6 through 371 or resid 401)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 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: 9.860 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 32.980 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 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 : 0.002 0.023 11911 Z= 0.116 Angle : 0.490 6.327 16170 Z= 0.244 Chirality : 0.041 0.175 1793 Planarity : 0.003 0.040 2063 Dihedral : 16.571 176.002 4448 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.13 % Favored : 97.80 % Rotamer: Outliers : 0.24 % Allowed : 17.20 % Favored : 82.56 % 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: -0.20 (0.22), residues: 1456 helix: 0.31 (0.21), residues: 598 sheet: -0.48 (0.32), residues: 266 loop : -0.21 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 356 HIS 0.009 0.001 HIS D 87 PHE 0.010 0.001 PHE C 223 TYR 0.005 0.001 TYR C 218 ARG 0.002 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 140 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 141 average time/residue: 0.2295 time to fit residues: 46.9778 Evaluate side-chains 139 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 137 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain C residue 355 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 7.9990 chunk 110 optimal weight: 8.9990 chunk 61 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 69 optimal weight: 0.0030 chunk 85 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 overall best weight: 3.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS C 49 GLN D 87 HIS D 296 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.055 11911 Z= 0.597 Angle : 0.700 7.648 16170 Z= 0.356 Chirality : 0.053 0.156 1793 Planarity : 0.006 0.048 2063 Dihedral : 9.612 142.397 1685 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.98 % Favored : 95.95 % Rotamer: Outliers : 3.05 % Allowed : 17.68 % Favored : 79.26 % 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: -0.90 (0.21), residues: 1456 helix: -0.10 (0.21), residues: 598 sheet: -0.88 (0.32), residues: 258 loop : -0.80 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 340 HIS 0.009 0.002 HIS D 87 PHE 0.019 0.002 PHE B 352 TYR 0.018 0.002 TYR C 294 ARG 0.005 0.001 ARG D 335 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 138 time to evaluate : 1.225 Fit side-chains revert: symmetry clash REVERT: B 111 ASN cc_start: 0.9009 (OUTLIER) cc_final: 0.8496 (t0) REVERT: C 49 GLN cc_start: 0.6563 (OUTLIER) cc_final: 0.4903 (mp-120) REVERT: C 225 ASN cc_start: 0.6741 (m-40) cc_final: 0.6301 (t0) outliers start: 38 outliers final: 21 residues processed: 166 average time/residue: 0.2049 time to fit residues: 50.2933 Evaluate side-chains 152 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 357 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 0.0770 chunk 41 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 132 optimal weight: 0.7980 chunk 143 optimal weight: 0.0980 chunk 118 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 161 HIS ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN D 87 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11911 Z= 0.139 Angle : 0.507 6.534 16170 Z= 0.246 Chirality : 0.043 0.170 1793 Planarity : 0.004 0.036 2063 Dihedral : 8.615 130.635 1682 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.34 % Favored : 97.60 % Rotamer: Outliers : 2.49 % Allowed : 18.73 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.22), residues: 1456 helix: 0.32 (0.22), residues: 591 sheet: -0.52 (0.33), residues: 257 loop : -0.57 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 340 HIS 0.010 0.001 HIS D 87 PHE 0.009 0.001 PHE A 255 TYR 0.008 0.001 TYR A 143 ARG 0.001 0.000 ARG C 335 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 141 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 111 ASN cc_start: 0.8958 (OUTLIER) cc_final: 0.8460 (t0) REVERT: C 49 GLN cc_start: 0.6709 (OUTLIER) cc_final: 0.5259 (mp-120) REVERT: C 355 MET cc_start: 0.7590 (mtp) cc_final: 0.7067 (mtp) REVERT: D 47 MET cc_start: 0.5322 (OUTLIER) cc_final: 0.3864 (tmm) outliers start: 31 outliers final: 21 residues processed: 165 average time/residue: 0.2162 time to fit residues: 52.7201 Evaluate side-chains 162 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 138 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 370 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 0.2980 chunk 99 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 141 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 126 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN D 87 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11911 Z= 0.316 Angle : 0.562 6.448 16170 Z= 0.275 Chirality : 0.046 0.138 1793 Planarity : 0.004 0.036 2063 Dihedral : 8.052 122.788 1682 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.43 % Favored : 96.50 % Rotamer: Outliers : 3.54 % Allowed : 18.33 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.22), residues: 1456 helix: 0.29 (0.22), residues: 583 sheet: -0.59 (0.32), residues: 256 loop : -0.69 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 340 HIS 0.009 0.001 HIS D 87 PHE 0.011 0.001 PHE B 352 TYR 0.016 0.001 TYR C 294 ARG 0.002 0.000 ARG D 335 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 140 time to evaluate : 1.308 Fit side-chains revert: symmetry clash REVERT: B 72 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7942 (mt-10) REVERT: B 111 ASN cc_start: 0.8991 (OUTLIER) cc_final: 0.8511 (t0) REVERT: C 225 ASN cc_start: 0.6726 (m-40) cc_final: 0.6289 (t0) REVERT: C 314 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.6323 (tp40) REVERT: D 72 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7299 (mm-30) outliers start: 44 outliers final: 33 residues processed: 173 average time/residue: 0.2126 time to fit residues: 54.3248 Evaluate side-chains 173 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 137 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 370 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11911 Z= 0.184 Angle : 0.508 5.966 16170 Z= 0.245 Chirality : 0.044 0.149 1793 Planarity : 0.004 0.034 2063 Dihedral : 7.402 107.465 1682 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.61 % Favored : 97.32 % Rotamer: Outliers : 3.14 % Allowed : 19.45 % Favored : 77.41 % 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: -0.34 (0.22), residues: 1456 helix: 0.42 (0.22), residues: 583 sheet: -0.45 (0.32), residues: 262 loop : -0.60 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 340 HIS 0.010 0.001 HIS D 87 PHE 0.009 0.001 PHE A 255 TYR 0.011 0.001 TYR C 294 ARG 0.002 0.000 ARG C 335 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 141 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 72 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: B 111 ASN cc_start: 0.8964 (OUTLIER) cc_final: 0.8450 (t0) REVERT: C 11 ASP cc_start: 0.8084 (t0) cc_final: 0.7831 (t70) REVERT: C 64 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8395 (pp) REVERT: C 222 ASP cc_start: 0.7282 (OUTLIER) cc_final: 0.7033 (p0) REVERT: C 225 ASN cc_start: 0.6587 (m-40) cc_final: 0.6144 (t0) REVERT: D 47 MET cc_start: 0.5519 (OUTLIER) cc_final: 0.4108 (tmm) outliers start: 39 outliers final: 28 residues processed: 170 average time/residue: 0.2095 time to fit residues: 52.7070 Evaluate side-chains 171 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 138 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 370 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 1.9990 chunk 127 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 ASN B 115 ASN ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS D 87 HIS D 161 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 11911 Z= 0.393 Angle : 0.604 6.608 16170 Z= 0.298 Chirality : 0.048 0.144 1793 Planarity : 0.005 0.040 2063 Dihedral : 7.323 108.222 1682 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.91 % Favored : 96.02 % Rotamer: Outliers : 4.66 % Allowed : 18.17 % Favored : 77.17 % 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 (0.22), residues: 1456 helix: 0.15 (0.22), residues: 583 sheet: -0.62 (0.32), residues: 258 loop : -0.91 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 340 HIS 0.010 0.002 HIS D 87 PHE 0.012 0.001 PHE B 352 TYR 0.020 0.002 TYR C 294 ARG 0.003 0.000 ARG D 335 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 141 time to evaluate : 1.256 Fit side-chains revert: symmetry clash REVERT: B 72 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8022 (mt-10) REVERT: A 206 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7328 (ttt180) REVERT: C 64 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8481 (pp) REVERT: C 222 ASP cc_start: 0.7493 (OUTLIER) cc_final: 0.7259 (p0) REVERT: C 225 ASN cc_start: 0.6603 (m-40) cc_final: 0.6206 (t0) REVERT: C 325 MET cc_start: 0.6772 (OUTLIER) cc_final: 0.6164 (mmt) outliers start: 58 outliers final: 42 residues processed: 184 average time/residue: 0.2217 time to fit residues: 59.2248 Evaluate side-chains 184 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 137 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 370 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 87 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11911 Z= 0.212 Angle : 0.530 6.182 16170 Z= 0.258 Chirality : 0.045 0.151 1793 Planarity : 0.004 0.035 2063 Dihedral : 6.943 103.794 1682 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.95 % Favored : 96.98 % Rotamer: Outliers : 3.78 % Allowed : 19.21 % Favored : 77.01 % 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: -0.50 (0.22), residues: 1456 helix: 0.31 (0.22), residues: 582 sheet: -0.43 (0.32), residues: 257 loop : -0.79 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 340 HIS 0.010 0.001 HIS D 87 PHE 0.010 0.001 PHE A 255 TYR 0.013 0.001 TYR C 294 ARG 0.003 0.000 ARG A 335 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 143 time to evaluate : 1.296 Fit side-chains revert: symmetry clash REVERT: B 72 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7930 (mt-10) REVERT: B 104 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8186 (tp) REVERT: B 111 ASN cc_start: 0.8955 (OUTLIER) cc_final: 0.8432 (t0) REVERT: A 206 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7309 (ttt180) REVERT: C 11 ASP cc_start: 0.8062 (t0) cc_final: 0.7806 (t70) REVERT: C 64 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8414 (pp) REVERT: C 222 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.7161 (p0) REVERT: C 225 ASN cc_start: 0.6593 (m-40) cc_final: 0.6136 (t0) REVERT: C 325 MET cc_start: 0.6717 (OUTLIER) cc_final: 0.6132 (mmt) outliers start: 47 outliers final: 37 residues processed: 177 average time/residue: 0.2037 time to fit residues: 53.2308 Evaluate side-chains 182 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 138 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 370 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 42 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 chunk 69 optimal weight: 0.0980 chunk 13 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 128 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 87 HIS ** D 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11911 Z= 0.142 Angle : 0.494 6.128 16170 Z= 0.238 Chirality : 0.043 0.155 1793 Planarity : 0.004 0.034 2063 Dihedral : 6.367 89.898 1682 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.82 % Favored : 97.12 % Rotamer: Outliers : 2.89 % Allowed : 20.26 % Favored : 76.85 % 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: -0.21 (0.22), residues: 1456 helix: 0.53 (0.22), residues: 584 sheet: -0.23 (0.33), residues: 263 loop : -0.63 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 356 HIS 0.010 0.001 HIS D 87 PHE 0.009 0.001 PHE A 255 TYR 0.011 0.001 TYR C 294 ARG 0.002 0.000 ARG C 335 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 143 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 72 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7795 (mt-10) REVERT: A 206 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7214 (ttt180) REVERT: C 11 ASP cc_start: 0.8009 (t0) cc_final: 0.7765 (t70) REVERT: C 64 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8382 (pp) REVERT: C 222 ASP cc_start: 0.7367 (OUTLIER) cc_final: 0.7115 (p0) REVERT: C 225 ASN cc_start: 0.6658 (m-40) cc_final: 0.6104 (t0) REVERT: D 47 MET cc_start: 0.5520 (OUTLIER) cc_final: 0.4115 (tmm) outliers start: 36 outliers final: 26 residues processed: 168 average time/residue: 0.1984 time to fit residues: 49.4168 Evaluate side-chains 167 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 136 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 370 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 131 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 118 optimal weight: 0.0670 chunk 124 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 overall best weight: 1.0920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 87 HIS D 161 HIS ** D 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11911 Z= 0.203 Angle : 0.518 6.373 16170 Z= 0.251 Chirality : 0.044 0.152 1793 Planarity : 0.004 0.034 2063 Dihedral : 6.338 86.361 1682 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.95 % Favored : 96.98 % Rotamer: Outliers : 3.46 % Allowed : 19.77 % Favored : 76.77 % 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: -0.23 (0.22), residues: 1456 helix: 0.48 (0.22), residues: 584 sheet: -0.19 (0.33), residues: 257 loop : -0.63 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 340 HIS 0.010 0.001 HIS D 87 PHE 0.010 0.001 PHE A 255 TYR 0.010 0.001 TYR A 143 ARG 0.005 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 135 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 72 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7854 (mt-10) REVERT: B 104 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8159 (tp) REVERT: A 206 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.7188 (ttt180) REVERT: C 11 ASP cc_start: 0.8008 (t0) cc_final: 0.7770 (t70) REVERT: C 64 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8389 (pp) REVERT: C 222 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.7152 (p0) REVERT: C 225 ASN cc_start: 0.6665 (m-40) cc_final: 0.6122 (t0) REVERT: C 294 TYR cc_start: 0.8623 (m-10) cc_final: 0.8421 (m-80) REVERT: D 47 MET cc_start: 0.5571 (OUTLIER) cc_final: 0.4148 (tmm) outliers start: 43 outliers final: 33 residues processed: 168 average time/residue: 0.2057 time to fit residues: 51.3089 Evaluate side-chains 176 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 137 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 145 optimal weight: 8.9990 chunk 133 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN D 87 HIS ** D 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11911 Z= 0.282 Angle : 0.555 6.450 16170 Z= 0.273 Chirality : 0.046 0.158 1793 Planarity : 0.004 0.035 2063 Dihedral : 6.565 93.582 1682 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.64 % Favored : 96.29 % Rotamer: Outliers : 3.62 % Allowed : 19.94 % Favored : 76.45 % 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: -0.41 (0.22), residues: 1456 helix: 0.37 (0.22), residues: 581 sheet: -0.31 (0.33), residues: 257 loop : -0.75 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 340 HIS 0.010 0.001 HIS D 87 PHE 0.010 0.001 PHE D 223 TYR 0.012 0.001 TYR A 143 ARG 0.005 0.000 ARG B 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 136 time to evaluate : 1.424 Fit side-chains revert: symmetry clash REVERT: B 72 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7956 (mt-10) REVERT: B 104 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8148 (tp) REVERT: B 115 ASN cc_start: 0.8015 (OUTLIER) cc_final: 0.7770 (t0) REVERT: A 206 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.7306 (ttt180) REVERT: C 11 ASP cc_start: 0.8037 (t0) cc_final: 0.7793 (t70) REVERT: C 64 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8437 (pp) REVERT: C 222 ASP cc_start: 0.7478 (OUTLIER) cc_final: 0.7222 (p0) REVERT: C 225 ASN cc_start: 0.6677 (m-40) cc_final: 0.6159 (t0) outliers start: 45 outliers final: 36 residues processed: 170 average time/residue: 0.2195 time to fit residues: 55.5946 Evaluate side-chains 176 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 134 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 106 optimal weight: 0.0870 chunk 17 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 87 HIS ** D 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.134466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.109645 restraints weight = 14964.391| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.11 r_work: 0.3162 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 11911 Z= 0.259 Angle : 0.803 59.199 16170 Z= 0.461 Chirality : 0.046 0.472 1793 Planarity : 0.004 0.047 2063 Dihedral : 6.576 93.412 1682 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.71 % Favored : 96.22 % Rotamer: Outliers : 3.70 % Allowed : 19.86 % Favored : 76.45 % Cbeta Deviations : 0.07 % 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: -0.40 (0.22), residues: 1456 helix: 0.39 (0.22), residues: 581 sheet: -0.31 (0.33), residues: 257 loop : -0.75 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 340 HIS 0.009 0.001 HIS D 87 PHE 0.010 0.001 PHE A 255 TYR 0.011 0.001 TYR A 143 ARG 0.004 0.000 ARG B 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2481.67 seconds wall clock time: 44 minutes 59.14 seconds (2699.14 seconds total)