Starting phenix.real_space_refine on Sat Mar 16 15:54:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q8c_13864/03_2024/7q8c_13864_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q8c_13864/03_2024/7q8c_13864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q8c_13864/03_2024/7q8c_13864.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q8c_13864/03_2024/7q8c_13864.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q8c_13864/03_2024/7q8c_13864_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q8c_13864/03_2024/7q8c_13864_updated.pdb" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 10 5.49 5 Mg 5 5.21 5 S 115 5.16 5 C 9195 2.51 5 N 2470 2.21 5 O 3180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14975 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2895 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 21, 'TRANS': 348} Chain: "B" Number of atoms: 2895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2895 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 21, 'TRANS': 348} Chain: "C" Number of atoms: 2895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2895 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 21, 'TRANS': 348} Chain: "D" Number of atoms: 2895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2895 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 21, 'TRANS': 348} Chain: "E" Number of atoms: 2895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2895 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 21, 'TRANS': 348} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "B" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 76 Classifications: {'water': 76} Link IDs: {None: 75} Chain: "C" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 74 Classifications: {'water': 74} Link IDs: {None: 73} Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "E" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Time building chain proxies: 8.08, per 1000 atoms: 0.54 Number of scatterers: 14975 At special positions: 0 Unit cell: (87.0317, 100.819, 198.191, 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 115 16.00 P 10 15.00 Mg 5 11.99 O 3180 8.00 N 2470 7.00 C 9195 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: 5.88 Conformation dependent library (CDL) restraints added in 2.9 seconds 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 25 sheets defined 43.2% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.30 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.568A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 196 removed outlier: 4.100A pdb=" N MET 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) removed outlier: 4.739A pdb=" N THR A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 removed outlier: 3.539A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 233 removed outlier: 3.632A pdb=" N LYS A 232 " --> pdb=" O THR A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.578A pdb=" N PHE A 254 " --> pdb=" O ASN A 251 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 255 " --> pdb=" O GLN A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 255' Processing helix chain 'A' and resid 257 through 260 Processing helix chain 'A' and resid 263 through 266 Processing helix chain 'A' and resid 274 through 284 removed outlier: 3.699A pdb=" N LYS A 284 " --> pdb=" O GLN A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 309 through 318 Processing helix chain 'A' and resid 335 through 348 removed outlier: 3.531A pdb=" N SER A 338 " --> pdb=" O ARG A 335 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY A 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 346 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 removed outlier: 3.577A pdb=" N GLN A 353 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 350 through 354' Processing helix chain 'A' and resid 359 through 365 removed outlier: 3.537A pdb=" N GLU A 364 " --> pdb=" O SER A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.510A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.568A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) 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: 4.100A pdb=" N MET B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N THR B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.538A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 233 removed outlier: 3.632A pdb=" N LYS B 232 " --> pdb=" O THR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 255 removed outlier: 3.578A pdb=" N PHE B 254 " --> pdb=" O ASN B 251 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG B 255 " --> pdb=" O GLN B 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 251 through 255' Processing helix chain 'B' and resid 257 through 260 Processing helix chain 'B' and resid 263 through 266 Processing helix chain 'B' and resid 274 through 284 removed outlier: 3.699A pdb=" N LYS B 284 " --> pdb=" O GLN B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 309 through 318 Processing helix chain 'B' and resid 335 through 348 removed outlier: 3.531A pdb=" N SER B 338 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY B 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 346 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 354 removed outlier: 3.577A pdb=" N GLN B 353 " --> pdb=" O THR B 350 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 350 through 354' Processing helix chain 'B' and resid 359 through 365 removed outlier: 3.537A pdb=" N GLU B 364 " --> pdb=" O SER B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 372 removed outlier: 3.510A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.568A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) 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: 4.100A pdb=" N MET C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N THR C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.538A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 233 removed outlier: 3.632A pdb=" N LYS C 232 " --> pdb=" O THR C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 255 removed outlier: 3.577A pdb=" N PHE C 254 " --> pdb=" O ASN C 251 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG C 255 " --> pdb=" O GLN C 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 251 through 255' Processing helix chain 'C' and resid 257 through 260 Processing helix chain 'C' and resid 263 through 266 Processing helix chain 'C' and resid 274 through 284 removed outlier: 3.699A pdb=" N LYS C 284 " --> pdb=" O GLN C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 294 Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 309 through 318 Processing helix chain 'C' and resid 335 through 348 removed outlier: 3.532A pdb=" N SER C 338 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 346 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 354 removed outlier: 3.577A pdb=" N GLN C 353 " --> pdb=" O THR C 350 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 350 through 354' Processing helix chain 'C' and resid 359 through 365 removed outlier: 3.537A pdb=" N GLU C 364 " --> pdb=" O SER C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.509A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.568A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 196 removed outlier: 4.101A pdb=" N MET D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N THR D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 removed outlier: 3.539A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 233 removed outlier: 3.632A pdb=" N LYS D 232 " --> pdb=" O THR D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 255 removed outlier: 3.578A pdb=" N PHE D 254 " --> pdb=" O ASN D 251 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG D 255 " --> pdb=" O GLN D 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 251 through 255' Processing helix chain 'D' and resid 257 through 260 Processing helix chain 'D' and resid 263 through 266 Processing helix chain 'D' and resid 274 through 284 removed outlier: 3.699A pdb=" N LYS D 284 " --> pdb=" O GLN D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 294 Processing helix chain 'D' and resid 302 through 304 No H-bonds generated for 'chain 'D' and resid 302 through 304' Processing helix chain 'D' and resid 309 through 318 Processing helix chain 'D' and resid 335 through 348 removed outlier: 3.531A pdb=" N SER D 338 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY D 342 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU D 346 " --> pdb=" O GLY D 343 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 354 removed outlier: 3.577A pdb=" N GLN D 353 " --> pdb=" O THR D 350 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 350 through 354' Processing helix chain 'D' and resid 359 through 365 removed outlier: 3.536A pdb=" N GLU D 364 " --> pdb=" O SER D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 372 removed outlier: 3.510A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 79 through 91 Processing helix chain 'E' and resid 113 through 125 Processing helix chain 'E' and resid 137 through 145 removed outlier: 3.568A pdb=" N LEU E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR E 143 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER E 144 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 182 through 196 removed outlier: 4.100A pdb=" N MET E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N THR E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 removed outlier: 3.539A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 233 removed outlier: 3.632A pdb=" N LYS E 232 " --> pdb=" O THR E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 255 removed outlier: 3.578A pdb=" N PHE E 254 " --> pdb=" O ASN E 251 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG E 255 " --> pdb=" O GLN E 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 251 through 255' Processing helix chain 'E' and resid 257 through 260 Processing helix chain 'E' and resid 263 through 266 Processing helix chain 'E' and resid 274 through 284 removed outlier: 3.699A pdb=" N LYS E 284 " --> pdb=" O GLN E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 294 Processing helix chain 'E' and resid 302 through 304 No H-bonds generated for 'chain 'E' and resid 302 through 304' Processing helix chain 'E' and resid 309 through 318 Processing helix chain 'E' and resid 335 through 348 removed outlier: 3.531A pdb=" N SER E 338 " --> pdb=" O ARG E 335 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY E 342 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU E 346 " --> pdb=" O GLY E 343 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER E 347 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 354 removed outlier: 3.576A pdb=" N GLN E 353 " --> pdb=" O THR E 350 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 350 through 354' Processing helix chain 'E' and resid 359 through 365 removed outlier: 3.537A pdb=" N GLU E 364 " --> pdb=" O SER E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 372 removed outlier: 3.510A pdb=" N VAL E 370 " --> pdb=" O PRO E 367 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 8 through 12 removed outlier: 3.545A pdb=" N HIS A 29 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 35 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 103 through 107 Processing sheet with id= D, first strand: chain 'A' and resid 160 through 165 Processing sheet with id= E, first strand: chain 'A' and resid 237 through 240 Processing sheet with id= F, first strand: chain 'B' and resid 8 through 12 removed outlier: 3.545A pdb=" N HIS B 29 " --> pdb=" O ALA B 19 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 35 through 38 Processing sheet with id= H, first strand: chain 'B' and resid 103 through 107 Processing sheet with id= I, first strand: chain 'B' and resid 160 through 165 Processing sheet with id= J, first strand: chain 'B' and resid 237 through 240 Processing sheet with id= K, first strand: chain 'C' and resid 8 through 12 removed outlier: 3.545A pdb=" N HIS C 29 " --> pdb=" O ALA C 19 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= M, first strand: chain 'C' and resid 103 through 107 Processing sheet with id= N, first strand: chain 'C' and resid 160 through 165 Processing sheet with id= O, first strand: chain 'C' and resid 237 through 240 Processing sheet with id= P, first strand: chain 'D' and resid 8 through 12 removed outlier: 3.545A pdb=" N HIS D 29 " --> pdb=" O ALA D 19 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 35 through 38 Processing sheet with id= R, first strand: chain 'D' and resid 103 through 107 Processing sheet with id= S, first strand: chain 'D' and resid 160 through 165 Processing sheet with id= T, first strand: chain 'D' and resid 237 through 240 Processing sheet with id= U, first strand: chain 'E' and resid 8 through 12 removed outlier: 3.545A pdb=" N HIS E 29 " --> pdb=" O ALA E 19 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 35 through 38 Processing sheet with id= W, first strand: chain 'E' and resid 103 through 107 Processing sheet with id= X, first strand: chain 'E' and resid 160 through 165 Processing sheet with id= Y, first strand: chain 'E' and resid 237 through 240 480 hydrogen bonds defined for protein. 1245 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: 4.07 Time building geometry restraints manager: 6.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4780 1.34 - 1.46: 2264 1.46 - 1.57: 7671 1.57 - 1.69: 15 1.69 - 1.80: 205 Bond restraints: 14935 Sorted by residual: bond pdb=" C4 ADP A 600 " pdb=" C5 ADP A 600 " ideal model delta sigma weight residual 1.490 1.462 0.028 2.00e-02 2.50e+03 1.91e+00 bond pdb=" C4 ADP C 600 " pdb=" C5 ADP C 600 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.86e+00 bond pdb=" C4 ADP E 600 " pdb=" C5 ADP E 600 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.83e+00 bond pdb=" C4 ADP B 600 " pdb=" C5 ADP B 600 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.79e+00 bond pdb=" C4 ADP D 600 " pdb=" C5 ADP D 600 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.79e+00 ... (remaining 14930 not shown) Histogram of bond angle deviations from ideal: 100.21 - 107.41: 705 107.41 - 114.61: 8696 114.61 - 121.81: 7563 121.81 - 129.01: 3181 129.01 - 136.21: 105 Bond angle restraints: 20250 Sorted by residual: angle pdb=" C1' ADP D 600 " pdb=" C2' ADP D 600 " pdb=" C3' ADP D 600 " ideal model delta sigma weight residual 111.00 103.56 7.44 3.00e+00 1.11e-01 6.14e+00 angle pdb=" C1' ADP A 600 " pdb=" C2' ADP A 600 " pdb=" C3' ADP A 600 " ideal model delta sigma weight residual 111.00 103.57 7.43 3.00e+00 1.11e-01 6.13e+00 angle pdb=" C1' ADP C 600 " pdb=" C2' ADP C 600 " pdb=" C3' ADP C 600 " ideal model delta sigma weight residual 111.00 103.59 7.41 3.00e+00 1.11e-01 6.10e+00 angle pdb=" C1' ADP B 600 " pdb=" C2' ADP B 600 " pdb=" C3' ADP B 600 " ideal model delta sigma weight residual 111.00 103.59 7.41 3.00e+00 1.11e-01 6.10e+00 angle pdb=" C1' ADP E 600 " pdb=" C2' ADP E 600 " pdb=" C3' ADP E 600 " ideal model delta sigma weight residual 111.00 103.59 7.41 3.00e+00 1.11e-01 6.10e+00 ... (remaining 20245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.68: 8870 26.68 - 53.35: 155 53.35 - 80.03: 10 80.03 - 106.70: 0 106.70 - 133.38: 5 Dihedral angle restraints: 9040 sinusoidal: 3700 harmonic: 5340 Sorted by residual: dihedral pdb=" O1B ADP A 600 " pdb=" O3A ADP A 600 " pdb=" PB ADP A 600 " pdb=" PA ADP A 600 " ideal model delta sinusoidal sigma weight residual 300.00 166.62 133.38 1 2.00e+01 2.50e-03 4.05e+01 dihedral pdb=" O1B ADP E 600 " pdb=" O3A ADP E 600 " pdb=" PB ADP E 600 " pdb=" PA ADP E 600 " ideal model delta sinusoidal sigma weight residual 300.00 166.63 133.36 1 2.00e+01 2.50e-03 4.05e+01 dihedral pdb=" O1B ADP B 600 " pdb=" O3A ADP B 600 " pdb=" PB ADP B 600 " pdb=" PA ADP B 600 " ideal model delta sinusoidal sigma weight residual 300.00 166.64 133.36 1 2.00e+01 2.50e-03 4.05e+01 ... (remaining 9037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1062 0.031 - 0.062: 762 0.062 - 0.093: 208 0.093 - 0.124: 186 0.124 - 0.155: 17 Chirality restraints: 2235 Sorted by residual: chirality pdb=" C3' ADP B 600 " pdb=" C2' ADP B 600 " pdb=" C4' ADP B 600 " pdb=" O3' ADP B 600 " both_signs ideal model delta sigma weight residual False -2.51 -2.67 0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" C3' ADP E 600 " pdb=" C2' ADP E 600 " pdb=" C4' ADP E 600 " pdb=" O3' ADP E 600 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" C3' ADP D 600 " pdb=" C2' ADP D 600 " pdb=" C4' ADP D 600 " pdb=" O3' ADP D 600 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.15 2.00e-01 2.50e+01 5.83e-01 ... (remaining 2232 not shown) Planarity restraints: 2605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 163 " -0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO B 164 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 164 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 164 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 163 " -0.025 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO E 164 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO E 164 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 164 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 163 " 0.025 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO D 164 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO D 164 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 164 " 0.021 5.00e-02 4.00e+02 ... (remaining 2602 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 130 2.54 - 3.13: 10972 3.13 - 3.72: 21661 3.72 - 4.31: 34718 4.31 - 4.90: 55149 Nonbonded interactions: 122630 Sorted by model distance: nonbonded pdb="MG MG E 601 " pdb=" O HOH E 765 " model vdw 1.953 2.170 nonbonded pdb="MG MG D 601 " pdb=" O HOH D 767 " model vdw 1.956 2.170 nonbonded pdb="MG MG B 601 " pdb=" O HOH B 771 " model vdw 1.957 2.170 nonbonded pdb="MG MG A 601 " pdb=" O HOH A 769 " model vdw 1.957 2.170 nonbonded pdb="MG MG C 601 " pdb=" O HOH C 770 " model vdw 1.957 2.170 ... (remaining 122625 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 1.320 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: 5.820 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 41.970 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 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 : 0.005 0.040 14935 Z= 0.304 Angle : 0.618 7.435 20250 Z= 0.300 Chirality : 0.050 0.155 2235 Planarity : 0.005 0.039 2605 Dihedral : 10.883 133.379 5610 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % 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: 0.25 (0.20), residues: 1840 helix: -0.61 (0.18), residues: 675 sheet: 0.75 (0.27), residues: 365 loop : 0.87 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 79 HIS 0.004 0.001 HIS E 161 PHE 0.010 0.001 PHE C 254 TYR 0.011 0.001 TYR E 294 ARG 0.003 0.001 ARG B 255 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.773 Fit side-chains REVERT: A 132 LEU cc_start: 0.8791 (tp) cc_final: 0.8507 (tp) REVERT: B 82 MET cc_start: 0.8965 (tpt) cc_final: 0.8260 (tpt) REVERT: C 25 ASP cc_start: 0.7262 (p0) cc_final: 0.7034 (p0) REVERT: C 42 GLN cc_start: 0.8469 (tp40) cc_final: 0.8139 (mm-40) REVERT: C 82 MET cc_start: 0.8929 (tpt) cc_final: 0.8475 (tpt) REVERT: C 227 MET cc_start: 0.8252 (mmm) cc_final: 0.7985 (tpt) REVERT: C 248 MET cc_start: 0.8077 (mmt) cc_final: 0.7862 (mmp) REVERT: D 190 MET cc_start: 0.8201 (ttp) cc_final: 0.7979 (ttp) REVERT: E 227 MET cc_start: 0.8310 (mmm) cc_final: 0.8027 (tpt) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 1.8723 time to fit residues: 368.3692 Evaluate side-chains 128 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 77 optimal weight: 0.3980 chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 74 optimal weight: 20.0000 chunk 145 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 GLN B 353 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN D 353 GLN E 353 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14935 Z= 0.232 Angle : 0.641 7.333 20250 Z= 0.316 Chirality : 0.049 0.161 2235 Planarity : 0.005 0.042 2605 Dihedral : 8.866 125.030 2045 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.04 % Allowed : 7.53 % Favored : 90.43 % 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: 0.66 (0.19), residues: 1840 helix: 0.10 (0.19), residues: 660 sheet: 0.98 (0.27), residues: 360 loop : 0.70 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 79 HIS 0.006 0.001 HIS D 161 PHE 0.010 0.001 PHE A 254 TYR 0.012 0.001 TYR C 294 ARG 0.004 0.001 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 136 time to evaluate : 1.784 Fit side-chains REVERT: A 240 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7338 (tt0) REVERT: B 227 MET cc_start: 0.8584 (tpt) cc_final: 0.8363 (tpt) REVERT: C 25 ASP cc_start: 0.7263 (p0) cc_final: 0.7029 (p0) REVERT: C 42 GLN cc_start: 0.8438 (tp40) cc_final: 0.8230 (mm-40) REVERT: C 227 MET cc_start: 0.8231 (mmm) cc_final: 0.7957 (tpt) REVERT: D 45 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.7110 (mtt) REVERT: D 190 MET cc_start: 0.8173 (ttp) cc_final: 0.7936 (ttp) REVERT: D 227 MET cc_start: 0.8508 (tpt) cc_final: 0.8275 (tpt) REVERT: E 227 MET cc_start: 0.8315 (mmm) cc_final: 0.8093 (tpt) outliers start: 33 outliers final: 8 residues processed: 158 average time/residue: 1.6904 time to fit residues: 288.1805 Evaluate side-chains 143 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 133 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 262 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 181 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 166 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 135 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 GLN E 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 14935 Z= 0.438 Angle : 0.770 8.570 20250 Z= 0.384 Chirality : 0.055 0.174 2235 Planarity : 0.006 0.045 2605 Dihedral : 9.714 131.024 2045 Min Nonbonded Distance : 1.655 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.79 % Allowed : 9.51 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.19), residues: 1840 helix: 0.12 (0.19), residues: 660 sheet: 0.68 (0.27), residues: 370 loop : 0.42 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP D 340 HIS 0.009 0.002 HIS D 161 PHE 0.013 0.002 PHE B 254 TYR 0.014 0.002 TYR A 294 ARG 0.005 0.001 ARG E 255 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 131 time to evaluate : 1.831 Fit side-chains REVERT: B 227 MET cc_start: 0.8637 (tpt) cc_final: 0.8261 (tpt) REVERT: C 227 MET cc_start: 0.8298 (mmm) cc_final: 0.7986 (tpt) REVERT: D 45 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.7114 (mtt) REVERT: E 227 MET cc_start: 0.8364 (mmm) cc_final: 0.8131 (tpt) outliers start: 29 outliers final: 14 residues processed: 154 average time/residue: 1.7097 time to fit residues: 283.7607 Evaluate side-chains 147 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 262 LYS Chi-restraints excluded: chain E residue 375 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 168 optimal weight: 0.5980 chunk 178 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 160 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN D 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14935 Z= 0.182 Angle : 0.605 7.026 20250 Z= 0.294 Chirality : 0.047 0.147 2235 Planarity : 0.005 0.043 2605 Dihedral : 8.724 122.114 2045 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.60 % Allowed : 10.12 % Favored : 88.27 % 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: 0.56 (0.19), residues: 1840 helix: 0.25 (0.19), residues: 670 sheet: 0.90 (0.28), residues: 360 loop : 0.44 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 79 HIS 0.004 0.001 HIS B 161 PHE 0.009 0.001 PHE A 254 TYR 0.012 0.001 TYR A 279 ARG 0.001 0.000 ARG E 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 127 time to evaluate : 1.894 Fit side-chains REVERT: A 240 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7433 (tt0) REVERT: B 82 MET cc_start: 0.8982 (tpt) cc_final: 0.8766 (tpp) REVERT: B 227 MET cc_start: 0.8619 (tpt) cc_final: 0.8242 (tpt) REVERT: C 227 MET cc_start: 0.8268 (mmm) cc_final: 0.7903 (tpt) REVERT: D 305 MET cc_start: 0.8574 (mmm) cc_final: 0.8160 (mmt) REVERT: E 227 MET cc_start: 0.8321 (mmm) cc_final: 0.8035 (tpt) outliers start: 26 outliers final: 10 residues processed: 147 average time/residue: 1.7135 time to fit residues: 271.4581 Evaluate side-chains 135 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 262 LYS Chi-restraints excluded: chain E residue 375 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 20.0000 chunk 101 optimal weight: 4.9990 chunk 2 optimal weight: 0.3980 chunk 133 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 152 optimal weight: 0.9980 chunk 123 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14935 Z= 0.239 Angle : 0.634 7.359 20250 Z= 0.309 Chirality : 0.049 0.156 2235 Planarity : 0.005 0.041 2605 Dihedral : 8.980 124.050 2045 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.85 % Allowed : 10.37 % Favored : 87.78 % 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: 0.24 (0.19), residues: 1840 helix: 0.09 (0.19), residues: 700 sheet: 0.75 (0.27), residues: 365 loop : 0.15 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 79 HIS 0.006 0.001 HIS D 161 PHE 0.011 0.001 PHE B 254 TYR 0.012 0.001 TYR A 279 ARG 0.002 0.000 ARG E 255 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 127 time to evaluate : 1.939 Fit side-chains REVERT: A 176 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7620 (mtp180) REVERT: A 240 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7501 (tt0) REVERT: B 227 MET cc_start: 0.8624 (tpt) cc_final: 0.8178 (tpt) REVERT: C 176 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7694 (mtp180) REVERT: C 227 MET cc_start: 0.8286 (mmm) cc_final: 0.7927 (tpt) REVERT: D 114 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7378 (mp-120) outliers start: 30 outliers final: 16 residues processed: 148 average time/residue: 1.7210 time to fit residues: 275.4517 Evaluate side-chains 146 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain C residue 176 ARG Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain D residue 114 GLN Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 262 LYS Chi-restraints excluded: chain E residue 375 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 9.9990 chunk 161 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 178 optimal weight: 6.9990 chunk 148 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 93 optimal weight: 0.4980 overall best weight: 5.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 GLN D 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 14935 Z= 0.426 Angle : 0.756 8.753 20250 Z= 0.376 Chirality : 0.054 0.171 2235 Planarity : 0.006 0.043 2605 Dihedral : 9.698 131.413 2045 Min Nonbonded Distance : 1.652 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.41 % Allowed : 10.37 % Favored : 87.22 % 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: 0.35 (0.19), residues: 1840 helix: 0.16 (0.19), residues: 665 sheet: 0.52 (0.27), residues: 375 loop : 0.37 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP D 340 HIS 0.007 0.002 HIS D 161 PHE 0.014 0.002 PHE B 254 TYR 0.011 0.002 TYR D 69 ARG 0.005 0.001 ARG E 255 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 129 time to evaluate : 2.057 Fit side-chains REVERT: A 176 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7589 (mtp180) REVERT: A 240 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7605 (tt0) REVERT: B 227 MET cc_start: 0.8658 (tpt) cc_final: 0.8203 (tpt) REVERT: C 227 MET cc_start: 0.8323 (mmm) cc_final: 0.8051 (tpt) REVERT: D 114 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7432 (mp-120) REVERT: E 269 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7697 (m-30) outliers start: 39 outliers final: 16 residues processed: 158 average time/residue: 1.6445 time to fit residues: 280.9757 Evaluate side-chains 150 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain D residue 114 GLN Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 269 ASP Chi-restraints excluded: chain E residue 375 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 178 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 GLN D 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14935 Z= 0.273 Angle : 0.665 7.692 20250 Z= 0.327 Chirality : 0.050 0.153 2235 Planarity : 0.005 0.043 2605 Dihedral : 9.322 131.355 2045 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.98 % Allowed : 10.68 % Favored : 87.35 % 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: 0.01 (0.19), residues: 1840 helix: -0.08 (0.19), residues: 700 sheet: 0.63 (0.27), residues: 365 loop : -0.01 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 79 HIS 0.006 0.001 HIS D 161 PHE 0.012 0.001 PHE A 254 TYR 0.011 0.002 TYR A 279 ARG 0.003 0.001 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 128 time to evaluate : 1.935 Fit side-chains REVERT: A 176 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7639 (mtp180) REVERT: A 240 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7550 (tt0) REVERT: B 82 MET cc_start: 0.9025 (tpt) cc_final: 0.8791 (tpp) REVERT: B 227 MET cc_start: 0.8675 (tpt) cc_final: 0.8219 (tpt) REVERT: C 227 MET cc_start: 0.8325 (mmm) cc_final: 0.7981 (tpt) REVERT: D 82 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8537 (tpt) REVERT: D 114 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7393 (mp-120) REVERT: E 269 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7674 (m-30) outliers start: 32 outliers final: 20 residues processed: 154 average time/residue: 1.6710 time to fit residues: 278.1660 Evaluate side-chains 151 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 126 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 114 GLN Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain E residue 131 SER Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 269 ASP Chi-restraints excluded: chain E residue 375 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 6.9990 chunk 106 optimal weight: 0.0670 chunk 53 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 34 optimal weight: 0.0970 chunk 113 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 140 optimal weight: 8.9990 chunk 162 optimal weight: 10.0000 overall best weight: 2.4120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14935 Z= 0.219 Angle : 0.628 7.275 20250 Z= 0.306 Chirality : 0.048 0.153 2235 Planarity : 0.005 0.042 2605 Dihedral : 8.985 125.917 2045 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.79 % Allowed : 10.93 % Favored : 87.28 % 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: 0.11 (0.19), residues: 1840 helix: 0.01 (0.19), residues: 700 sheet: 0.66 (0.27), residues: 365 loop : 0.04 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 79 HIS 0.004 0.001 HIS C 161 PHE 0.011 0.001 PHE A 254 TYR 0.011 0.001 TYR A 279 ARG 0.003 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 127 time to evaluate : 1.901 Fit side-chains REVERT: A 176 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7623 (mtp180) REVERT: A 240 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7512 (tt0) REVERT: B 227 MET cc_start: 0.8684 (tpt) cc_final: 0.8225 (tpt) REVERT: C 227 MET cc_start: 0.8298 (mmm) cc_final: 0.7946 (tpt) REVERT: D 82 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8572 (tpt) REVERT: D 114 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7357 (mp-120) REVERT: D 305 MET cc_start: 0.8548 (mmm) cc_final: 0.8140 (mmt) REVERT: E 269 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7660 (m-30) outliers start: 29 outliers final: 18 residues processed: 149 average time/residue: 1.7222 time to fit residues: 279.7594 Evaluate side-chains 148 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 125 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 114 GLN Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain E residue 131 SER Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 269 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 9.9990 chunk 155 optimal weight: 0.7980 chunk 166 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 72 optimal weight: 0.3980 chunk 130 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 chunk 157 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 109 optimal weight: 9.9990 overall best weight: 3.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14935 Z= 0.272 Angle : 0.660 7.599 20250 Z= 0.324 Chirality : 0.050 0.156 2235 Planarity : 0.005 0.042 2605 Dihedral : 9.229 128.820 2045 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.04 % Allowed : 10.80 % Favored : 87.16 % 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: 0.07 (0.19), residues: 1840 helix: -0.03 (0.19), residues: 705 sheet: 0.63 (0.27), residues: 365 loop : 0.04 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 340 HIS 0.005 0.001 HIS D 161 PHE 0.012 0.001 PHE A 254 TYR 0.011 0.002 TYR A 279 ARG 0.002 0.001 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 126 time to evaluate : 1.864 Fit side-chains REVERT: A 176 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7628 (mtp180) REVERT: A 240 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7548 (tt0) REVERT: B 227 MET cc_start: 0.8691 (tpt) cc_final: 0.8194 (tpt) REVERT: C 227 MET cc_start: 0.8323 (mmm) cc_final: 0.7975 (tpt) REVERT: D 114 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7377 (mp-120) REVERT: E 269 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7676 (m-30) outliers start: 33 outliers final: 20 residues processed: 152 average time/residue: 1.6074 time to fit residues: 264.7274 Evaluate side-chains 150 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 126 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 114 GLN Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain E residue 131 SER Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 269 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 0.9990 chunk 107 optimal weight: 0.3980 chunk 83 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 184 optimal weight: 2.9990 chunk 169 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14935 Z= 0.263 Angle : 0.657 7.570 20250 Z= 0.322 Chirality : 0.050 0.154 2235 Planarity : 0.005 0.042 2605 Dihedral : 9.188 128.371 2045 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.67 % Allowed : 11.11 % Favored : 87.22 % 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: 0.08 (0.19), residues: 1840 helix: -0.03 (0.19), residues: 705 sheet: 0.62 (0.27), residues: 365 loop : 0.05 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 79 HIS 0.005 0.001 HIS D 161 PHE 0.012 0.001 PHE A 254 TYR 0.011 0.002 TYR A 279 ARG 0.002 0.001 ARG C 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 126 time to evaluate : 1.860 Fit side-chains REVERT: A 176 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7629 (mtp180) REVERT: A 240 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7540 (tt0) REVERT: B 227 MET cc_start: 0.8676 (tpt) cc_final: 0.8169 (tpt) REVERT: C 180 MET cc_start: 0.8229 (ttp) cc_final: 0.7979 (ttp) REVERT: C 227 MET cc_start: 0.8318 (mmm) cc_final: 0.7974 (tpt) REVERT: D 114 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7376 (mp-120) REVERT: E 269 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7684 (m-30) outliers start: 27 outliers final: 21 residues processed: 149 average time/residue: 1.6694 time to fit residues: 269.2581 Evaluate side-chains 151 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 126 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 114 GLN Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain E residue 131 SER Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 269 ASP Chi-restraints excluded: chain E residue 375 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 135 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 150 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN D 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.093918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.078579 restraints weight = 20725.602| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.18 r_work: 0.2816 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14935 Z= 0.202 Angle : 0.615 7.168 20250 Z= 0.299 Chirality : 0.048 0.151 2235 Planarity : 0.005 0.041 2605 Dihedral : 8.823 123.051 2045 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.60 % Allowed : 11.17 % Favored : 87.22 % 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 (0.19), residues: 1840 helix: 0.13 (0.20), residues: 695 sheet: 0.57 (0.27), residues: 370 loop : 0.09 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 79 HIS 0.004 0.001 HIS D 161 PHE 0.010 0.001 PHE A 254 TYR 0.012 0.001 TYR A 279 ARG 0.003 0.000 ARG C 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4957.19 seconds wall clock time: 88 minutes 28.65 seconds (5308.65 seconds total)