Starting phenix.real_space_refine (version: dev) on Fri Mar 17 14:26:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q8s_13865/03_2023/7q8s_13865_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q8s_13865/03_2023/7q8s_13865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q8s_13865/03_2023/7q8s_13865.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q8s_13865/03_2023/7q8s_13865.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q8s_13865/03_2023/7q8s_13865_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q8s_13865/03_2023/7q8s_13865_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 19665 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2815 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 21, 'TRANS': 337} Chain breaks: 1 Chain: "B" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1090 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "C" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2815 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 21, 'TRANS': 337} Chain breaks: 1 Chain: "G" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1090 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "D" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2815 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 21, 'TRANS': 337} Chain breaks: 1 Chain: "H" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1090 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "E" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2815 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 21, 'TRANS': 337} Chain breaks: 1 Chain: "I" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1090 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "F" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2815 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 21, 'TRANS': 337} Chain breaks: 1 Chain: "J" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1090 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} 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: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.37, per 1000 atoms: 0.58 Number of scatterers: 19665 At special positions: 0 Unit cell: (103.404, 114.606, 205.946, 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 135 16.00 P 10 15.00 Mg 5 11.99 O 3810 8.00 N 3350 7.00 C 12355 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: 7.73 Conformation dependent library (CDL) restraints added in 3.1 seconds 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4620 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 130 helices and 30 sheets defined 43.3% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 55 through 60 removed outlier: 3.731A pdb=" N SER A 60 " --> pdb=" O GLU A 57 " (cutoff:3.500A) 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 removed outlier: 4.144A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 125 removed outlier: 3.553A pdb=" N MET A 123 " --> pdb=" O MET A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.770A 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: 3.579A pdb=" N GLU A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N MET A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N THR A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.627A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 233 removed outlier: 3.841A pdb=" N ALA A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS A 232 " --> pdb=" O THR A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 261 removed outlier: 3.594A pdb=" N PHE A 254 " --> pdb=" O ASN A 251 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG A 255 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N CYS A 256 " --> pdb=" O ARG A 253 " (cutoff:3.500A) Proline residue: A 257 - end of helix Processing helix chain 'A' and resid 263 through 266 removed outlier: 3.630A pdb=" N ILE A 266 " --> pdb=" O PRO A 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 263 through 266' Processing helix chain 'A' and resid 274 through 284 removed outlier: 3.728A pdb=" N LYS A 284 " --> pdb=" O GLN A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 294 removed outlier: 4.702A pdb=" N ARG A 291 " --> pdb=" O ASP A 288 " (cutoff:3.500A) 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 320 removed outlier: 3.538A pdb=" N LYS A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 348 removed outlier: 3.723A pdb=" N SER A 338 " --> pdb=" O ARG A 335 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A 341 " --> pdb=" O SER A 338 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY A 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 345 " --> pdb=" O GLY A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 removed outlier: 3.911A pdb=" N GLN A 353 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 3.766A 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 Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.598A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 20 removed outlier: 4.098A pdb=" N GLY B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 56 removed outlier: 3.759A pdb=" N GLU B 55 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 101 Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.674A pdb=" N SER B 108 " --> pdb=" O ALA B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 124 Processing helix chain 'B' and resid 126 through 135 Processing helix chain 'C' and resid 55 through 60 removed outlier: 3.731A pdb=" N SER C 60 " --> pdb=" O GLU C 57 " (cutoff:3.500A) 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 removed outlier: 4.144A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 removed outlier: 3.553A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.770A 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: 3.578A pdb=" N GLU C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N MET C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N THR C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 213 removed outlier: 3.626A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 233 removed outlier: 3.841A pdb=" N ALA C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS C 232 " --> pdb=" O THR C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 261 removed outlier: 3.594A pdb=" N PHE C 254 " --> pdb=" O ASN C 251 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG C 255 " --> pdb=" O GLN C 252 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N CYS C 256 " --> pdb=" O ARG C 253 " (cutoff:3.500A) Proline residue: C 257 - end of helix Processing helix chain 'C' and resid 263 through 266 removed outlier: 3.630A pdb=" N ILE C 266 " --> pdb=" O PRO C 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 263 through 266' Processing helix chain 'C' and resid 274 through 284 removed outlier: 3.728A pdb=" N LYS C 284 " --> pdb=" O GLN C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 294 removed outlier: 4.701A pdb=" N ARG C 291 " --> pdb=" O ASP C 288 " (cutoff:3.500A) 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 320 removed outlier: 3.538A pdb=" N LYS C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 348 removed outlier: 3.723A pdb=" N SER C 338 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE C 341 " --> pdb=" O SER C 338 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE C 345 " --> pdb=" O GLY C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 354 removed outlier: 3.911A pdb=" N GLN C 353 " --> pdb=" O THR C 350 " (cutoff:3.500A) removed outlier: 3.765A 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 Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.598A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 20 removed outlier: 4.098A pdb=" N GLY G 14 " --> pdb=" O GLU G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 56 removed outlier: 3.759A pdb=" N GLU G 55 " --> pdb=" O THR G 51 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS G 56 " --> pdb=" O ASP G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 101 Processing helix chain 'G' and resid 103 through 108 removed outlier: 3.674A pdb=" N SER G 108 " --> pdb=" O ALA G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 124 Processing helix chain 'G' and resid 126 through 135 Processing helix chain 'D' and resid 55 through 60 removed outlier: 3.731A pdb=" N SER D 60 " --> pdb=" O GLU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 79 through 91 removed outlier: 4.144A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 125 removed outlier: 3.553A pdb=" N MET D 123 " --> pdb=" O MET D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.769A 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: 3.579A pdb=" N GLU D 187 " --> pdb=" O ARG D 183 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N MET D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N THR D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 213 removed outlier: 3.626A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 233 removed outlier: 3.841A pdb=" N ALA D 231 " --> pdb=" O MET D 227 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS D 232 " --> pdb=" O THR D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 261 removed outlier: 3.594A pdb=" N PHE D 254 " --> pdb=" O ASN D 251 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG D 255 " --> pdb=" O GLN D 252 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N CYS D 256 " --> pdb=" O ARG D 253 " (cutoff:3.500A) Proline residue: D 257 - end of helix Processing helix chain 'D' and resid 263 through 266 removed outlier: 3.630A pdb=" N ILE D 266 " --> pdb=" O PRO D 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 263 through 266' Processing helix chain 'D' and resid 274 through 284 removed outlier: 3.728A pdb=" N LYS D 284 " --> pdb=" O GLN D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 294 removed outlier: 4.701A pdb=" N ARG D 291 " --> pdb=" O ASP D 288 " (cutoff:3.500A) 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 320 removed outlier: 3.538A pdb=" N LYS D 315 " --> pdb=" O GLU D 311 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 348 removed outlier: 3.723A pdb=" N SER D 338 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE D 341 " --> pdb=" O SER D 338 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY D 342 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE D 345 " --> pdb=" O GLY D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 354 removed outlier: 3.910A pdb=" N GLN D 353 " --> pdb=" O THR D 350 " (cutoff:3.500A) removed outlier: 3.765A 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 Processing helix chain 'D' and resid 367 through 372 removed outlier: 3.597A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 20 removed outlier: 4.098A pdb=" N GLY H 14 " --> pdb=" O GLU H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 56 removed outlier: 3.759A pdb=" N GLU H 55 " --> pdb=" O THR H 51 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS H 56 " --> pdb=" O ASP H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 101 Processing helix chain 'H' and resid 103 through 108 removed outlier: 3.674A pdb=" N SER H 108 " --> pdb=" O ALA H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 124 Processing helix chain 'H' and resid 126 through 135 Processing helix chain 'E' and resid 55 through 60 removed outlier: 3.731A pdb=" N SER E 60 " --> pdb=" O GLU E 57 " (cutoff:3.500A) 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 removed outlier: 4.143A pdb=" N LYS E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE E 85 " --> pdb=" O ASP E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 113 through 125 removed outlier: 3.552A pdb=" N MET E 123 " --> pdb=" O MET E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 removed outlier: 3.770A 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: 3.578A pdb=" N GLU E 187 " --> pdb=" O ARG E 183 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N MET E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N THR E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 213 removed outlier: 3.626A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 233 removed outlier: 3.841A pdb=" N ALA E 231 " --> pdb=" O MET E 227 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS E 232 " --> pdb=" O THR E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 261 removed outlier: 3.594A pdb=" N PHE E 254 " --> pdb=" O ASN E 251 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG E 255 " --> pdb=" O GLN E 252 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N CYS E 256 " --> pdb=" O ARG E 253 " (cutoff:3.500A) Proline residue: E 257 - end of helix Processing helix chain 'E' and resid 263 through 266 removed outlier: 3.630A pdb=" N ILE E 266 " --> pdb=" O PRO E 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 263 through 266' Processing helix chain 'E' and resid 274 through 284 removed outlier: 3.729A pdb=" N LYS E 284 " --> pdb=" O GLN E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 294 removed outlier: 4.702A pdb=" N ARG E 291 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 304 No H-bonds generated for 'chain 'E' and resid 302 through 304' Processing helix chain 'E' and resid 309 through 320 removed outlier: 3.539A pdb=" N LYS E 315 " --> pdb=" O GLU E 311 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU E 320 " --> pdb=" O GLU E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 348 removed outlier: 3.723A pdb=" N SER E 338 " --> pdb=" O ARG E 335 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE E 341 " --> pdb=" O SER E 338 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY E 342 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE E 345 " --> pdb=" O GLY E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 354 removed outlier: 3.910A pdb=" N GLN E 353 " --> pdb=" O THR E 350 " (cutoff:3.500A) removed outlier: 3.765A 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 Processing helix chain 'E' and resid 367 through 372 removed outlier: 3.597A pdb=" N VAL E 370 " --> pdb=" O PRO E 367 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 20 removed outlier: 4.098A pdb=" N GLY I 14 " --> pdb=" O GLU I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 56 removed outlier: 3.758A pdb=" N GLU I 55 " --> pdb=" O THR I 51 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS I 56 " --> pdb=" O ASP I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 101 Processing helix chain 'I' and resid 103 through 108 removed outlier: 3.674A pdb=" N SER I 108 " --> pdb=" O ALA I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 124 Processing helix chain 'I' and resid 126 through 135 Processing helix chain 'F' and resid 55 through 60 removed outlier: 3.731A pdb=" N SER F 60 " --> pdb=" O GLU F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 79 through 91 removed outlier: 4.143A pdb=" N LYS F 84 " --> pdb=" O ASP F 80 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE F 85 " --> pdb=" O ASP F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 100 No H-bonds generated for 'chain 'F' and resid 98 through 100' Processing helix chain 'F' and resid 113 through 125 removed outlier: 3.553A pdb=" N MET F 123 " --> pdb=" O MET F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 removed outlier: 3.770A pdb=" N SER F 145 " --> pdb=" O SER F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 174 No H-bonds generated for 'chain 'F' and resid 172 through 174' Processing helix chain 'F' and resid 182 through 196 removed outlier: 3.578A pdb=" N GLU F 187 " --> pdb=" O ARG F 183 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N MET F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLU F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N THR F 196 " --> pdb=" O ILE F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 213 removed outlier: 3.627A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 233 removed outlier: 3.841A pdb=" N ALA F 231 " --> pdb=" O MET F 227 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS F 232 " --> pdb=" O THR F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 261 removed outlier: 3.594A pdb=" N PHE F 254 " --> pdb=" O ASN F 251 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG F 255 " --> pdb=" O GLN F 252 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N CYS F 256 " --> pdb=" O ARG F 253 " (cutoff:3.500A) Proline residue: F 257 - end of helix Processing helix chain 'F' and resid 263 through 266 removed outlier: 3.630A pdb=" N ILE F 266 " --> pdb=" O PRO F 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 263 through 266' Processing helix chain 'F' and resid 274 through 284 removed outlier: 3.729A pdb=" N LYS F 284 " --> pdb=" O GLN F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 294 removed outlier: 4.702A pdb=" N ARG F 291 " --> pdb=" O ASP F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 304 No H-bonds generated for 'chain 'F' and resid 302 through 304' Processing helix chain 'F' and resid 309 through 320 removed outlier: 3.539A pdb=" N LYS F 315 " --> pdb=" O GLU F 311 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU F 320 " --> pdb=" O GLU F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 348 removed outlier: 3.722A pdb=" N SER F 338 " --> pdb=" O ARG F 335 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VAL F 339 " --> pdb=" O LYS F 336 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE F 341 " --> pdb=" O SER F 338 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY F 342 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE F 345 " --> pdb=" O GLY F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 354 removed outlier: 3.910A pdb=" N GLN F 353 " --> pdb=" O THR F 350 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 350 through 354' Processing helix chain 'F' and resid 359 through 365 Processing helix chain 'F' and resid 367 through 372 removed outlier: 3.597A pdb=" N VAL F 370 " --> pdb=" O PRO F 367 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 20 removed outlier: 4.098A pdb=" N GLY J 14 " --> pdb=" O GLU J 10 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 56 removed outlier: 3.759A pdb=" N GLU J 55 " --> pdb=" O THR J 51 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS J 56 " --> pdb=" O ASP J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 101 Processing helix chain 'J' and resid 103 through 108 removed outlier: 3.674A pdb=" N SER J 108 " --> pdb=" O ALA J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 124 Processing helix chain 'J' and resid 126 through 135 Processing sheet with id= A, first strand: chain 'A' and resid 8 through 11 Processing sheet with id= B, first strand: chain 'A' and resid 52 through 54 Processing sheet with id= C, first strand: chain 'A' and resid 102 through 107 removed outlier: 6.635A pdb=" N SER A 131 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N LEU A 105 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TYR A 133 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N GLU A 107 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLY A 135 " --> pdb=" O GLU A 107 " (cutoff:3.500A) No H-bonds generated for sheet with id= C 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 114 through 118 removed outlier: 3.745A pdb=" N TYR B 26 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU B 42 " --> pdb=" O MET B 28 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N CYS B 30 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N VAL B 40 " --> pdb=" O CYS B 30 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 8 through 11 Processing sheet with id= H, first strand: chain 'C' and resid 52 through 54 Processing sheet with id= I, first strand: chain 'C' and resid 102 through 107 removed outlier: 6.635A pdb=" N SER C 131 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LEU C 105 " --> pdb=" O SER C 131 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N TYR C 133 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N GLU C 107 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLY C 135 " --> pdb=" O GLU C 107 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'C' and resid 160 through 165 Processing sheet with id= K, first strand: chain 'C' and resid 237 through 240 Processing sheet with id= L, first strand: chain 'G' and resid 114 through 118 removed outlier: 3.745A pdb=" N TYR G 26 " --> pdb=" O GLY G 44 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU G 42 " --> pdb=" O MET G 28 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N CYS G 30 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N VAL G 40 " --> pdb=" O CYS G 30 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 8 through 11 Processing sheet with id= N, first strand: chain 'D' and resid 52 through 54 Processing sheet with id= O, first strand: chain 'D' and resid 102 through 107 removed outlier: 6.635A pdb=" N SER D 131 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LEU D 105 " --> pdb=" O SER D 131 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TYR D 133 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N GLU D 107 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLY D 135 " --> pdb=" O GLU D 107 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'D' and resid 160 through 165 Processing sheet with id= Q, first strand: chain 'D' and resid 237 through 240 Processing sheet with id= R, first strand: chain 'H' and resid 114 through 118 removed outlier: 3.745A pdb=" N TYR H 26 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU H 42 " --> pdb=" O MET H 28 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N CYS H 30 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N VAL H 40 " --> pdb=" O CYS H 30 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 8 through 11 Processing sheet with id= T, first strand: chain 'E' and resid 52 through 54 Processing sheet with id= U, first strand: chain 'E' and resid 102 through 107 removed outlier: 6.635A pdb=" N SER E 131 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LEU E 105 " --> pdb=" O SER E 131 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TYR E 133 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N GLU E 107 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLY E 135 " --> pdb=" O GLU E 107 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'E' and resid 160 through 165 Processing sheet with id= W, first strand: chain 'E' and resid 237 through 240 Processing sheet with id= X, first strand: chain 'I' and resid 114 through 118 removed outlier: 3.744A pdb=" N TYR I 26 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU I 42 " --> pdb=" O MET I 28 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N CYS I 30 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N VAL I 40 " --> pdb=" O CYS I 30 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 8 through 11 Processing sheet with id= Z, first strand: chain 'F' and resid 52 through 54 Processing sheet with id= AA, first strand: chain 'F' and resid 102 through 107 removed outlier: 6.635A pdb=" N SER F 131 " --> pdb=" O VAL F 103 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LEU F 105 " --> pdb=" O SER F 131 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N TYR F 133 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N GLU F 107 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLY F 135 " --> pdb=" O GLU F 107 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'F' and resid 160 through 165 Processing sheet with id= AC, first strand: chain 'F' and resid 237 through 240 Processing sheet with id= AD, first strand: chain 'J' and resid 114 through 118 removed outlier: 3.745A pdb=" N TYR J 26 " --> pdb=" O GLY J 44 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU J 42 " --> pdb=" O MET J 28 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N CYS J 30 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N VAL J 40 " --> pdb=" O CYS J 30 " (cutoff:3.500A) 675 hydrogen bonds defined for protein. 1650 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.43 Time building geometry restraints manager: 8.34 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: 6468 1.34 - 1.46: 4007 1.46 - 1.58: 9325 1.58 - 1.69: 15 1.69 - 1.81: 235 Bond restraints: 20050 Sorted by residual: bond pdb=" C4 ADP C 600 " pdb=" C5 ADP C 600 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.15e+00 bond pdb=" C4 ADP D 600 " pdb=" C5 ADP D 600 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.12e+00 bond pdb=" C4 ADP F 600 " pdb=" C5 ADP F 600 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.11e+00 bond pdb=" C4 ADP E 600 " pdb=" C5 ADP E 600 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.07e+00 bond pdb=" C4 ADP A 600 " pdb=" C5 ADP A 600 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.07e+00 ... (remaining 20045 not shown) Histogram of bond angle deviations from ideal: 100.67 - 107.76: 873 107.76 - 114.84: 11955 114.84 - 121.93: 10063 121.93 - 129.02: 4099 129.02 - 136.11: 120 Bond angle restraints: 27110 Sorted by residual: angle pdb=" O1B ADP C 600 " pdb=" PB ADP C 600 " pdb=" O2B ADP C 600 " ideal model delta sigma weight residual 119.90 113.89 6.01 3.00e+00 1.11e-01 4.01e+00 angle pdb=" O1B ADP D 600 " pdb=" PB ADP D 600 " pdb=" O2B ADP D 600 " ideal model delta sigma weight residual 119.90 113.92 5.98 3.00e+00 1.11e-01 3.98e+00 angle pdb=" O1B ADP E 600 " pdb=" PB ADP E 600 " pdb=" O2B ADP E 600 " ideal model delta sigma weight residual 119.90 113.93 5.97 3.00e+00 1.11e-01 3.95e+00 angle pdb=" O1B ADP F 600 " pdb=" PB ADP F 600 " pdb=" O2B ADP F 600 " ideal model delta sigma weight residual 119.90 113.94 5.96 3.00e+00 1.11e-01 3.95e+00 angle pdb=" O1B ADP A 600 " pdb=" PB ADP A 600 " pdb=" O2B ADP A 600 " ideal model delta sigma weight residual 119.90 113.98 5.92 3.00e+00 1.11e-01 3.89e+00 ... (remaining 27105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.26: 12061 23.26 - 46.51: 144 46.51 - 69.77: 15 69.77 - 93.02: 5 93.02 - 116.28: 5 Dihedral angle restraints: 12230 sinusoidal: 5045 harmonic: 7185 Sorted by residual: dihedral pdb=" O1B ADP C 600 " pdb=" O3A ADP C 600 " pdb=" PB ADP C 600 " pdb=" PA ADP C 600 " ideal model delta sinusoidal sigma weight residual -60.00 -176.28 116.28 1 2.00e+01 2.50e-03 3.46e+01 dihedral pdb=" O1B ADP F 600 " pdb=" O3A ADP F 600 " pdb=" PB ADP F 600 " pdb=" PA ADP F 600 " ideal model delta sinusoidal sigma weight residual -60.00 -176.28 116.28 1 2.00e+01 2.50e-03 3.46e+01 dihedral pdb=" O1B ADP D 600 " pdb=" O3A ADP D 600 " pdb=" PB ADP D 600 " pdb=" PA ADP D 600 " ideal model delta sinusoidal sigma weight residual -60.00 -176.27 116.26 1 2.00e+01 2.50e-03 3.46e+01 ... (remaining 12227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1599 0.025 - 0.051: 778 0.051 - 0.076: 313 0.076 - 0.101: 183 0.101 - 0.126: 122 Chirality restraints: 2995 Sorted by residual: chirality pdb=" CA ILE H 38 " pdb=" N ILE H 38 " pdb=" C ILE H 38 " pdb=" CB ILE H 38 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA ILE I 38 " pdb=" N ILE I 38 " pdb=" C ILE I 38 " pdb=" CB ILE I 38 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA ILE J 38 " pdb=" N ILE J 38 " pdb=" C ILE J 38 " pdb=" CB ILE J 38 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 2992 not shown) Planarity restraints: 3485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 108 " 0.018 5.00e-02 4.00e+02 2.67e-02 1.14e+00 pdb=" N PRO C 109 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO C 109 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 109 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 108 " -0.018 5.00e-02 4.00e+02 2.65e-02 1.13e+00 pdb=" N PRO D 109 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO D 109 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 109 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 108 " 0.017 5.00e-02 4.00e+02 2.64e-02 1.12e+00 pdb=" N PRO A 109 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 109 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 109 " 0.015 5.00e-02 4.00e+02 ... (remaining 3482 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2775 2.76 - 3.29: 18092 3.29 - 3.83: 29289 3.83 - 4.36: 36495 4.36 - 4.90: 64730 Nonbonded interactions: 151381 Sorted by model distance: nonbonded pdb=" OD1 ASP G 120 " pdb=" OG SER G 122 " model vdw 2.222 2.440 nonbonded pdb=" OD1 ASP H 120 " pdb=" OG SER H 122 " model vdw 2.222 2.440 nonbonded pdb=" OD1 ASP J 120 " pdb=" OG SER J 122 " model vdw 2.223 2.440 nonbonded pdb=" OD1 ASP B 120 " pdb=" OG SER B 122 " model vdw 2.223 2.440 nonbonded pdb=" OD1 ASP I 120 " pdb=" OG SER I 122 " model vdw 2.223 2.440 ... (remaining 151376 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 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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 135 5.16 5 C 12355 2.51 5 N 3350 2.21 5 O 3810 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.810 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: 0.030 Extract box with map and model: 7.210 Check model and map are aligned: 0.290 Process input model: 51.290 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.180 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 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 0.021 20050 Z= 0.102 Angle : 0.442 6.006 27110 Z= 0.212 Chirality : 0.043 0.126 2995 Planarity : 0.003 0.027 3485 Dihedral : 8.150 116.277 7610 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.17), residues: 2455 helix: 0.75 (0.18), residues: 805 sheet: 1.28 (0.22), residues: 520 loop : 0.97 (0.20), residues: 1130 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 355 time to evaluate : 2.411 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 360 average time/residue: 0.4002 time to fit residues: 205.8110 Evaluate side-chains 210 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 207 time to evaluate : 1.805 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1317 time to fit residues: 3.1333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 8.9990 chunk 181 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 62 optimal weight: 0.5980 chunk 122 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 188 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 114 optimal weight: 0.1980 chunk 140 optimal weight: 10.0000 chunk 217 optimal weight: 8.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: