Starting phenix.real_space_refine on Sat Jul 20 18:31:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ru0_19501/07_2024/8ru0_19501_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ru0_19501/07_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_19501/07_2024/8ru0_19501.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ru0_19501/07_2024/8ru0_19501.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ru0_19501/07_2024/8ru0_19501_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ru0_19501/07_2024/8ru0_19501_neut.cif" } 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 6.83, per 1000 atoms: 0.59 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: 5.19 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... Secondary structure from input PDB file: 82 helices and 23 sheets defined 49.9% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 62 through 65 removed outlier: 3.516A pdb=" N LEU B 65 " --> pdb=" O ARG B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 65' Processing helix chain 'B' and resid 80 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.539A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.120A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.767A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 194 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 202 through 217 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 222 through 233 Processing helix chain 'B' and resid 257 through 261 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 302 through 306 removed outlier: 4.022A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 374 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 61 Processing helix chain 'A' and resid 80 through 92 Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.317A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) 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 145 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 296 removed outlier: 3.555A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.890A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 355 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 368 through 374 removed outlier: 4.526A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.785A pdb=" N GLN C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.332A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) 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 146 Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.941A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 257 through 261 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 302 through 306 removed outlier: 4.349A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.574A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.939A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.593A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 112 through 127 Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.520A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 257 through 262 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 296 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 302 through 306 removed outlier: 4.132A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 320 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 350 through 355 removed outlier: 3.741A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 364 Processing helix chain 'D' and resid 366 through 371 removed outlier: 3.977A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.907A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.261A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 176 through 178 removed outlier: 4.090A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.811A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.572A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'A' and resid 176 through 178 Processing sheet with id=AB2, first strand: chain 'A' and resid 176 through 178 removed outlier: 4.068A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 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=AB5, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.531A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 5.927A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.586A pdb=" N GLY D 20 " --> pdb=" O VAL D 9 " (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: 3.670A pdb=" N TYR D 133 " --> pdb=" O THR D 103 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.834A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 176 through 178 removed outlier: 4.022A pdb=" N MET D 176 " --> pdb=" O ASN D 162 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN D 162 " --> pdb=" O MET D 176 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 165 through 166 Processing sheet with id=AC5, first strand: chain 'D' and resid 238 through 241 570 hydrogen bonds defined for protein. 1458 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: 4.26 Time building geometry restraints manager: 5.12 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: 109 2.63 - 3.20: 10032 3.20 - 3.77: 17143 3.77 - 4.33: 25091 4.33 - 4.90: 41933 Nonbonded interactions: 94308 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 94303 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: 4.830 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 34.110 Find NCS groups from input model: 0.820 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: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.200 ------------------------------------------------------------------------------- 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= 0.115 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 : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 141 average time/residue: 0.2380 time to fit residues: 48.7790 Evaluate side-chains 139 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 137 time to evaluate : 1.311 ------------------------------------------------------------------------------- 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: 7.9990 chunk 74 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 69 optimal weight: 0.0030 chunk 85 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 overall best weight: 2.7996 ------------------------------------------------------------------------------- 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 ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 HIS D 296 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 11911 Z= 0.461 Angle : 0.665 7.303 16170 Z= 0.337 Chirality : 0.050 0.151 1793 Planarity : 0.005 0.044 2063 Dihedral : 9.464 138.116 1685 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.78 % Favored : 96.15 % Rotamer: Outliers : 2.57 % Allowed : 17.68 % Favored : 79.74 % 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: -0.29 (0.22), residues: 1456 helix: 0.45 (0.21), residues: 590 sheet: -0.58 (0.32), residues: 258 loop : -0.49 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 340 HIS 0.009 0.002 HIS D 87 PHE 0.015 0.002 PHE B 352 TYR 0.016 0.002 TYR C 294 ARG 0.004 0.000 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 175 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 143 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 111 ASN cc_start: 0.9003 (OUTLIER) cc_final: 0.8503 (t0) REVERT: C 49 GLN cc_start: 0.6516 (OUTLIER) cc_final: 0.4862 (mp-120) outliers start: 32 outliers final: 16 residues processed: 165 average time/residue: 0.2113 time to fit residues: 52.4437 Evaluate side-chains 153 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 135 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASP 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 A residue 25 ASP Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 49 GLN 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 106 optimal weight: 0.0270 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 161 HIS C 49 GLN C 297 ASN D 87 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11911 Z= 0.155 Angle : 0.522 6.450 16170 Z= 0.257 Chirality : 0.044 0.165 1793 Planarity : 0.004 0.041 2063 Dihedral : 8.591 129.899 1682 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.47 % Favored : 97.46 % Rotamer: Outliers : 2.41 % Allowed : 18.49 % Favored : 79.10 % 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: 0.18 (0.22), residues: 1456 helix: 0.95 (0.22), residues: 581 sheet: -0.36 (0.33), residues: 245 loop : -0.36 (0.25), residues: 630 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 0.007 0.001 PHE D 31 TYR 0.012 0.001 TYR C 294 ARG 0.003 0.000 ARG B 95 *********************** 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 169 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 139 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 111 ASN cc_start: 0.8977 (OUTLIER) cc_final: 0.8469 (t0) REVERT: C 49 GLN cc_start: 0.6728 (OUTLIER) cc_final: 0.5283 (mp-120) REVERT: C 222 ASP cc_start: 0.7005 (OUTLIER) cc_final: 0.6594 (p0) outliers start: 30 outliers final: 19 residues processed: 160 average time/residue: 0.2156 time to fit residues: 51.4603 Evaluate side-chains 158 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 136 time to evaluate : 1.354 ------------------------------------------------------------------------------- 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 A residue 25 ASP Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain C residue 49 GLN 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 324 THR Chi-restraints excluded: chain C residue 349 LEU 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 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: 2.9990 chunk 99 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 133 optimal weight: 0.0370 chunk 141 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.7664 ------------------------------------------------------------------------------- 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: 0.7990 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11911 Z= 0.307 Angle : 0.570 6.410 16170 Z= 0.283 Chirality : 0.046 0.142 1793 Planarity : 0.004 0.043 2063 Dihedral : 8.021 121.619 1682 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.37 % Favored : 96.57 % Rotamer: Outliers : 3.86 % Allowed : 17.60 % Favored : 78.54 % 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: 0.02 (0.22), residues: 1456 helix: 0.88 (0.22), residues: 583 sheet: -0.36 (0.32), residues: 250 loop : -0.56 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 340 HIS 0.010 0.001 HIS D 87 PHE 0.011 0.001 PHE B 352 TYR 0.013 0.001 TYR C 294 ARG 0.003 0.000 ARG B 95 *********************** 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 187 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 139 time to evaluate : 1.478 Fit side-chains revert: symmetry clash REVERT: B 72 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7503 (mt-10) REVERT: B 111 ASN cc_start: 0.8995 (OUTLIER) cc_final: 0.8514 (t0) REVERT: B 180 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8814 (tp) REVERT: A 222 ASP cc_start: 0.6877 (m-30) cc_final: 0.5971 (p0) REVERT: C 64 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8428 (pp) outliers start: 48 outliers final: 36 residues processed: 178 average time/residue: 0.2345 time to fit residues: 63.1284 Evaluate side-chains 176 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 136 time to evaluate : 1.298 ------------------------------------------------------------------------------- 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 180 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 286 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 226 GLU Chi-restraints excluded: chain A residue 292 ASP 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 139 VAL 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 349 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 57 GLU 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 338 SER 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: 3.9990 chunk 80 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 120 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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** D 87 HIS D 161 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 11911 Z= 0.417 Angle : 0.629 6.894 16170 Z= 0.317 Chirality : 0.049 0.146 1793 Planarity : 0.005 0.048 2063 Dihedral : 7.734 113.895 1682 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.33 % Favored : 95.60 % Rotamer: Outliers : 4.50 % Allowed : 18.25 % Favored : 77.25 % 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: 0.59 (0.22), residues: 588 sheet: -0.49 (0.31), residues: 254 loop : -0.90 (0.24), residues: 614 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 0.015 0.002 PHE B 352 TYR 0.019 0.002 TYR C 294 ARG 0.002 0.000 ARG B 95 *********************** 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 193 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 137 time to evaluate : 1.326 Fit side-chains revert: symmetry clash REVERT: B 72 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7525 (mt-10) REVERT: B 111 ASN cc_start: 0.8996 (OUTLIER) cc_final: 0.8487 (t0) REVERT: B 180 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8800 (tp) REVERT: B 355 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8204 (mtm) REVERT: C 64 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8481 (pp) REVERT: C 314 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.6370 (tp40) REVERT: C 325 MET cc_start: 0.6800 (OUTLIER) cc_final: 0.6171 (mmt) outliers start: 56 outliers final: 38 residues processed: 180 average time/residue: 0.2092 time to fit residues: 56.2686 Evaluate side-chains 179 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 134 time to evaluate : 1.425 ------------------------------------------------------------------------------- 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 111 ASN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 292 ASP 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 139 VAL 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 314 GLN 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 351 THR Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 57 GLU 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 338 SER Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 0.0370 chunk 127 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 141 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 chunk 65 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN C 101 HIS D 87 HIS ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11911 Z= 0.145 Angle : 0.515 6.050 16170 Z= 0.253 Chirality : 0.043 0.166 1793 Planarity : 0.004 0.043 2063 Dihedral : 6.958 101.035 1682 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.61 % Favored : 97.32 % Rotamer: Outliers : 2.73 % Allowed : 20.18 % Favored : 77.09 % 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: 0.16 (0.22), residues: 1456 helix: 1.07 (0.22), residues: 587 sheet: -0.25 (0.32), residues: 250 loop : -0.58 (0.24), residues: 619 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 0.008 0.001 PHE A 255 TYR 0.011 0.001 TYR C 294 ARG 0.002 0.000 ARG B 95 *********************** 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 179 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 145 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 72 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7449 (mt-10) REVERT: B 104 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8178 (tp) REVERT: B 111 ASN cc_start: 0.8964 (OUTLIER) cc_final: 0.8471 (t0) REVERT: B 180 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8723 (tp) REVERT: C 11 ASP cc_start: 0.8068 (t0) cc_final: 0.7828 (t70) REVERT: C 64 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8413 (pp) REVERT: D 184 ASP cc_start: 0.7138 (m-30) cc_final: 0.6893 (m-30) outliers start: 34 outliers final: 19 residues processed: 170 average time/residue: 0.2054 time to fit residues: 53.0008 Evaluate side-chains 161 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 137 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 153 LEU Chi-restraints excluded: chain B residue 180 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 A residue 226 GLU Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 323 SER 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 201 VAL Chi-restraints excluded: chain D residue 202 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 118 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 297 ASN D 87 HIS ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11911 Z= 0.180 Angle : 0.521 6.302 16170 Z= 0.255 Chirality : 0.044 0.153 1793 Planarity : 0.004 0.040 2063 Dihedral : 6.589 94.781 1682 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.02 % Favored : 96.91 % Rotamer: Outliers : 2.73 % Allowed : 20.42 % 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: 0.24 (0.22), residues: 1456 helix: 1.13 (0.22), residues: 588 sheet: -0.18 (0.32), residues: 254 loop : -0.55 (0.25), residues: 614 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 0.007 0.001 PHE A 255 TYR 0.010 0.001 TYR C 294 ARG 0.002 0.000 ARG B 95 *********************** 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 173 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 139 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 72 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7456 (mt-10) REVERT: B 104 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8145 (tp) REVERT: C 11 ASP cc_start: 0.8033 (t0) cc_final: 0.7779 (t70) REVERT: C 64 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8386 (pp) outliers start: 34 outliers final: 24 residues processed: 167 average time/residue: 0.2171 time to fit residues: 54.6436 Evaluate side-chains 163 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 136 time to evaluate : 1.432 ------------------------------------------------------------------------------- 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 153 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 139 VAL 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 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 201 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 0.6980 chunk 56 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 95 optimal weight: 0.3980 chunk 69 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 128 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 87 HIS ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11911 Z= 0.163 Angle : 0.516 6.277 16170 Z= 0.253 Chirality : 0.044 0.153 1793 Planarity : 0.004 0.039 2063 Dihedral : 6.321 86.366 1682 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.88 % Favored : 97.05 % Rotamer: Outliers : 2.65 % Allowed : 20.82 % Favored : 76.53 % 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: 1.22 (0.22), residues: 588 sheet: -0.06 (0.33), residues: 247 loop : -0.45 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 340 HIS 0.011 0.001 HIS D 87 PHE 0.007 0.001 PHE A 255 TYR 0.008 0.001 TYR C 294 ARG 0.002 0.000 ARG B 95 *********************** 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 176 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 143 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 72 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7482 (mt-10) REVERT: B 104 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8132 (tp) REVERT: B 180 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8688 (tp) REVERT: C 11 ASP cc_start: 0.7997 (t0) cc_final: 0.7775 (t70) REVERT: C 64 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8384 (pp) REVERT: C 222 ASP cc_start: 0.7075 (OUTLIER) cc_final: 0.6634 (p0) outliers start: 33 outliers final: 26 residues processed: 167 average time/residue: 0.2074 time to fit residues: 51.9809 Evaluate side-chains 172 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 141 time to evaluate : 2.056 ------------------------------------------------------------------------------- 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 153 LEU Chi-restraints excluded: chain B residue 180 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 288 ASP Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 139 VAL 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 323 SER Chi-restraints excluded: chain C residue 324 THR 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 201 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 131 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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** D 87 HIS ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11911 Z= 0.293 Angle : 0.576 6.533 16170 Z= 0.286 Chirality : 0.047 0.191 1793 Planarity : 0.004 0.041 2063 Dihedral : 6.600 91.852 1682 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.71 % Favored : 96.22 % Rotamer: Outliers : 3.54 % Allowed : 19.94 % Favored : 76.53 % 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: 0.05 (0.22), residues: 1456 helix: 0.95 (0.22), residues: 590 sheet: -0.23 (0.32), residues: 254 loop : -0.67 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 340 HIS 0.011 0.001 HIS D 87 PHE 0.012 0.001 PHE B 352 TYR 0.009 0.001 TYR A 143 ARG 0.002 0.000 ARG D 335 *********************** 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 184 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 140 time to evaluate : 1.299 Fit side-chains revert: symmetry clash REVERT: B 72 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7526 (mt-10) REVERT: B 104 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8087 (tp) REVERT: B 180 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8791 (tp) REVERT: C 11 ASP cc_start: 0.8046 (t0) cc_final: 0.7826 (t70) REVERT: C 64 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8440 (pp) outliers start: 44 outliers final: 36 residues processed: 175 average time/residue: 0.2165 time to fit residues: 56.0115 Evaluate side-chains 179 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 139 time to evaluate : 1.182 ------------------------------------------------------------------------------- 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 180 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 B residue 351 THR Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain C residue 6 THR 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 139 VAL 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 51 ASP Chi-restraints excluded: chain D residue 57 GLU 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 138 optimal weight: 10.0000 chunk 84 optimal weight: 0.0980 chunk 65 optimal weight: 0.8980 chunk 96 optimal weight: 0.0970 chunk 145 optimal weight: 10.0000 chunk 133 optimal weight: 0.0010 chunk 115 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 overall best weight: 0.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 87 HIS D 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1678 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= 0.120 Angle : 0.499 6.228 16170 Z= 0.244 Chirality : 0.043 0.171 1793 Planarity : 0.004 0.038 2063 Dihedral : 6.059 73.834 1682 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.82 % Favored : 97.12 % Rotamer: Outliers : 1.93 % Allowed : 21.38 % Favored : 76.69 % 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: 0.58 (0.22), residues: 1456 helix: 1.38 (0.22), residues: 587 sheet: 0.09 (0.33), residues: 245 loop : -0.37 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 356 HIS 0.011 0.001 HIS D 87 PHE 0.008 0.001 PHE A 255 TYR 0.010 0.001 TYR B 218 ARG 0.002 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 171 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 147 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 72 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: B 104 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8100 (tp) REVERT: C 11 ASP cc_start: 0.7941 (t0) cc_final: 0.7737 (t70) REVERT: C 64 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8373 (pp) REVERT: D 184 ASP cc_start: 0.7011 (m-30) cc_final: 0.6801 (m-30) outliers start: 24 outliers final: 20 residues processed: 165 average time/residue: 0.2083 time to fit residues: 51.6797 Evaluate side-chains 166 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 143 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 GLU 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 288 ASP Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain C residue 6 THR 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 139 VAL 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 201 VAL 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: 0.9990 chunk 106 optimal weight: 0.4980 chunk 17 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.136765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.112499 restraints weight = 14910.806| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.08 r_work: 0.3209 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11911 Z= 0.232 Angle : 0.539 6.556 16170 Z= 0.265 Chirality : 0.045 0.168 1793 Planarity : 0.004 0.039 2063 Dihedral : 6.237 81.043 1682 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.30 % Favored : 96.63 % Rotamer: Outliers : 2.09 % Allowed : 21.22 % Favored : 76.69 % 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: 0.40 (0.22), residues: 1456 helix: 1.26 (0.22), residues: 589 sheet: -0.06 (0.32), residues: 251 loop : -0.49 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 340 HIS 0.004 0.001 HIS C 161 PHE 0.008 0.001 PHE B 352 TYR 0.008 0.001 TYR A 143 ARG 0.002 0.000 ARG B 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2500.03 seconds wall clock time: 47 minutes 9.11 seconds (2829.11 seconds total)