Starting phenix.real_space_refine on Mon Mar 18 03:20:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q8s_13865/03_2024/7q8s_13865_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q8s_13865/03_2024/7q8s_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_2024/7q8s_13865.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q8s_13865/03_2024/7q8s_13865.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q8s_13865/03_2024/7q8s_13865_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q8s_13865/03_2024/7q8s_13865_updated.pdb" } resolution = 3.4 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 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. 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 10.03, per 1000 atoms: 0.51 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: 6.73 Conformation dependent library (CDL) restraints added in 3.8 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: 3.91 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: 5.58 Time building geometry restraints manager: 7.31 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 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: 1.180 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: 0.020 Extract box with map and model: 6.000 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 50.710 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 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 % Allowed : 1.38 % Favored : 98.39 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 86 HIS 0.002 0.000 HIS D 161 PHE 0.005 0.001 PHE D 254 TYR 0.006 0.001 TYR B 71 ARG 0.001 0.000 ARG J 103 *********************** 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 : 2.114 Fit side-chains REVERT: A 82 MET cc_start: 0.9145 (tpt) cc_final: 0.8821 (tpt) REVERT: A 193 MET cc_start: 0.8516 (tpp) cc_final: 0.8228 (tpt) REVERT: B 120 ASP cc_start: 0.7807 (p0) cc_final: 0.7577 (p0) REVERT: C 193 MET cc_start: 0.8628 (tpp) cc_final: 0.8289 (tpt) REVERT: C 247 MET cc_start: 0.7697 (ttp) cc_final: 0.7453 (ttm) REVERT: G 120 ASP cc_start: 0.7855 (p0) cc_final: 0.7558 (p0) REVERT: E 82 MET cc_start: 0.9028 (tpt) cc_final: 0.8604 (tpt) REVERT: I 125 ASP cc_start: 0.7800 (t0) cc_final: 0.6793 (t70) REVERT: F 82 MET cc_start: 0.9233 (tpt) cc_final: 0.8763 (tpt) REVERT: F 248 MET cc_start: 0.8724 (mmt) cc_final: 0.8364 (mmt) outliers start: 5 outliers final: 3 residues processed: 360 average time/residue: 0.3776 time to fit residues: 194.2927 Evaluate side-chains 210 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 207 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain I residue 27 VAL 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: 5.9990 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: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN D 121 GLN F 215 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 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 : 0.004 0.029 20050 Z= 0.237 Angle : 0.550 6.734 27110 Z= 0.272 Chirality : 0.047 0.183 2995 Planarity : 0.004 0.028 3485 Dihedral : 6.965 111.203 2758 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.15 % Allowed : 4.61 % Favored : 94.24 % 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: 1.19 (0.17), residues: 2455 helix: 1.05 (0.18), residues: 840 sheet: 0.94 (0.22), residues: 525 loop : 0.70 (0.20), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 356 HIS 0.005 0.001 HIS A 87 PHE 0.011 0.001 PHE A 31 TYR 0.015 0.001 TYR H 71 ARG 0.005 0.001 ARG J 92 *********************** REFINEMENT MACRO_CYCLE 2 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 243 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 218 time to evaluate : 2.336 Fit side-chains REVERT: A 187 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6677 (mp0) REVERT: B 120 ASP cc_start: 0.7925 (p0) cc_final: 0.7679 (p0) REVERT: C 193 MET cc_start: 0.8754 (tpp) cc_final: 0.8380 (tpt) REVERT: C 247 MET cc_start: 0.7924 (ttp) cc_final: 0.7471 (ttm) REVERT: G 120 ASP cc_start: 0.7894 (p0) cc_final: 0.7628 (p0) REVERT: F 187 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6730 (mp0) REVERT: J 42 GLU cc_start: 0.7427 (tt0) cc_final: 0.7225 (tt0) outliers start: 25 outliers final: 18 residues processed: 240 average time/residue: 0.2848 time to fit residues: 108.3987 Evaluate side-chains 226 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 206 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain J residue 27 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 181 optimal weight: 0.9980 chunk 148 optimal weight: 9.9990 chunk 60 optimal weight: 0.6980 chunk 218 optimal weight: 0.8980 chunk 235 optimal weight: 6.9990 chunk 194 optimal weight: 0.9990 chunk 216 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN B 85 GLN D 121 GLN I 85 GLN J 136 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 20050 Z= 0.110 Angle : 0.474 6.608 27110 Z= 0.226 Chirality : 0.044 0.124 2995 Planarity : 0.003 0.030 3485 Dihedral : 6.544 104.941 2758 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.97 % Allowed : 5.53 % Favored : 93.50 % 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: 1.33 (0.18), residues: 2455 helix: 1.27 (0.18), residues: 845 sheet: 0.80 (0.22), residues: 530 loop : 0.81 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 356 HIS 0.003 0.001 HIS J 136 PHE 0.006 0.001 PHE B 67 TYR 0.007 0.001 TYR H 71 ARG 0.004 0.000 ARG G 131 *********************** REFINEMENT MACRO_CYCLE 3 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 250 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 229 time to evaluate : 2.335 Fit side-chains REVERT: B 120 ASP cc_start: 0.7797 (p0) cc_final: 0.7571 (p0) REVERT: C 187 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: C 193 MET cc_start: 0.8700 (tpp) cc_final: 0.8311 (tpt) REVERT: G 120 ASP cc_start: 0.7782 (p0) cc_final: 0.7527 (p0) REVERT: D 187 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6701 (mp0) REVERT: E 187 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6645 (mp0) outliers start: 21 outliers final: 12 residues processed: 243 average time/residue: 0.2894 time to fit residues: 110.6245 Evaluate side-chains 221 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 206 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 27 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 9.9990 chunk 164 optimal weight: 9.9990 chunk 113 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 104 optimal weight: 9.9990 chunk 146 optimal weight: 0.2980 chunk 219 optimal weight: 0.6980 chunk 231 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN D 121 GLN D 215 GLN I 85 GLN J 136 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20050 Z= 0.197 Angle : 0.504 6.670 27110 Z= 0.243 Chirality : 0.045 0.128 2995 Planarity : 0.004 0.035 3485 Dihedral : 6.700 106.167 2758 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.43 % Allowed : 5.71 % Favored : 92.86 % 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: 1.20 (0.17), residues: 2455 helix: 1.29 (0.18), residues: 840 sheet: 0.71 (0.22), residues: 525 loop : 0.64 (0.20), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 79 HIS 0.003 0.001 HIS A 161 PHE 0.010 0.001 PHE C 223 TYR 0.012 0.001 TYR H 71 ARG 0.004 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 4 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 240 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 209 time to evaluate : 2.296 Fit side-chains REVERT: A 187 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6831 (mp0) REVERT: B 120 ASP cc_start: 0.7861 (p0) cc_final: 0.7601 (p0) REVERT: C 187 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6793 (mp0) REVERT: C 193 MET cc_start: 0.8702 (tpp) cc_final: 0.8306 (tpt) REVERT: G 120 ASP cc_start: 0.7845 (p0) cc_final: 0.7562 (p0) REVERT: D 187 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6738 (mp0) REVERT: D 305 MET cc_start: 0.8711 (mmm) cc_final: 0.8455 (mmt) REVERT: E 187 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6668 (mp0) REVERT: F 187 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.6818 (mp0) outliers start: 31 outliers final: 23 residues processed: 235 average time/residue: 0.2758 time to fit residues: 103.7094 Evaluate side-chains 232 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 204 time to evaluate : 2.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 247 MET Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 109 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 8.9990 chunk 131 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 172 optimal weight: 0.5980 chunk 95 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 160 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 208 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 GLN J 136 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 20050 Z= 0.314 Angle : 0.566 6.643 27110 Z= 0.279 Chirality : 0.048 0.139 2995 Planarity : 0.004 0.039 3485 Dihedral : 7.391 117.239 2758 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.61 % Allowed : 6.04 % Favored : 92.35 % 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: 0.95 (0.17), residues: 2455 helix: 1.16 (0.19), residues: 830 sheet: 0.51 (0.22), residues: 525 loop : 0.45 (0.20), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 79 HIS 0.005 0.001 HIS A 161 PHE 0.011 0.002 PHE C 223 TYR 0.018 0.002 TYR H 71 ARG 0.003 0.001 ARG C 116 *********************** REFINEMENT MACRO_CYCLE 5 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 243 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 208 time to evaluate : 2.570 Fit side-chains REVERT: A 187 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6885 (mp0) REVERT: C 187 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6661 (mp0) REVERT: C 193 MET cc_start: 0.8721 (tpp) cc_final: 0.8362 (tpt) REVERT: G 120 ASP cc_start: 0.7937 (p0) cc_final: 0.7648 (p0) REVERT: D 187 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6879 (mp0) REVERT: D 305 MET cc_start: 0.8720 (mmm) cc_final: 0.8467 (mmt) REVERT: E 187 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6651 (mp0) REVERT: F 187 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.6790 (mp0) outliers start: 35 outliers final: 24 residues processed: 238 average time/residue: 0.2620 time to fit residues: 101.6063 Evaluate side-chains 231 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 202 time to evaluate : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 247 MET Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 109 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 7.9990 chunk 208 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 136 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 232 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 121 optimal weight: 0.5980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20050 Z= 0.230 Angle : 0.526 6.693 27110 Z= 0.256 Chirality : 0.046 0.127 2995 Planarity : 0.004 0.036 3485 Dihedral : 7.228 116.704 2758 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.75 % Allowed : 7.14 % Favored : 91.11 % 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: 0.95 (0.17), residues: 2455 helix: 1.16 (0.19), residues: 835 sheet: 0.45 (0.22), residues: 525 loop : 0.48 (0.20), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 79 HIS 0.005 0.001 HIS A 161 PHE 0.009 0.001 PHE A 31 TYR 0.013 0.001 TYR G 71 ARG 0.003 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 6 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 242 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 204 time to evaluate : 2.438 Fit side-chains REVERT: A 187 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6897 (mp0) REVERT: C 187 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6749 (mp0) REVERT: C 193 MET cc_start: 0.8724 (tpp) cc_final: 0.8359 (tpt) REVERT: G 120 ASP cc_start: 0.7852 (p0) cc_final: 0.7576 (p0) REVERT: D 187 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6841 (mp0) REVERT: E 187 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.6654 (mp0) REVERT: F 187 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.6782 (mp0) outliers start: 38 outliers final: 28 residues processed: 237 average time/residue: 0.2682 time to fit residues: 103.1113 Evaluate side-chains 234 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 201 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 247 MET Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 109 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 169 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 195 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 231 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 20050 Z= 0.374 Angle : 0.593 6.814 27110 Z= 0.293 Chirality : 0.049 0.146 2995 Planarity : 0.004 0.040 3485 Dihedral : 7.686 123.081 2758 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.94 % Allowed : 7.65 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.17), residues: 2455 helix: 0.98 (0.18), residues: 835 sheet: 0.31 (0.22), residues: 525 loop : 0.27 (0.20), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 79 HIS 0.006 0.001 HIS A 161 PHE 0.012 0.002 PHE G 69 TYR 0.018 0.002 TYR B 71 ARG 0.004 0.001 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 7 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 249 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 207 time to evaluate : 2.345 Fit side-chains REVERT: A 187 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.6953 (mp0) REVERT: C 16 MET cc_start: 0.8061 (mmt) cc_final: 0.7831 (mmt) REVERT: C 187 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.6697 (mp0) REVERT: C 193 MET cc_start: 0.8750 (tpp) cc_final: 0.8367 (tpt) REVERT: G 120 ASP cc_start: 0.7961 (p0) cc_final: 0.7657 (p0) REVERT: D 187 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6891 (mp0) REVERT: D 305 MET cc_start: 0.8726 (mmm) cc_final: 0.8508 (mmt) REVERT: E 160 THR cc_start: 0.8967 (OUTLIER) cc_final: 0.8707 (p) REVERT: E 187 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6634 (mp0) REVERT: F 187 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6841 (mp0) outliers start: 42 outliers final: 35 residues processed: 244 average time/residue: 0.2693 time to fit residues: 107.0874 Evaluate side-chains 245 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 204 time to evaluate : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 247 MET Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 139 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 138 optimal weight: 0.0870 chunk 69 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 181 optimal weight: 3.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20050 Z= 0.266 Angle : 0.545 6.775 27110 Z= 0.267 Chirality : 0.047 0.167 2995 Planarity : 0.004 0.036 3485 Dihedral : 7.494 121.470 2758 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.07 % Allowed : 7.74 % Favored : 90.18 % 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: 0.71 (0.17), residues: 2455 helix: 1.01 (0.18), residues: 840 sheet: 0.30 (0.22), residues: 525 loop : 0.30 (0.20), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 79 HIS 0.005 0.001 HIS A 161 PHE 0.010 0.001 PHE D 31 TYR 0.013 0.001 TYR G 71 ARG 0.002 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 8 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 251 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 206 time to evaluate : 2.351 Fit side-chains REVERT: A 187 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6964 (mp0) REVERT: C 16 MET cc_start: 0.8070 (mmt) cc_final: 0.7845 (mmt) REVERT: C 187 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.6705 (mp0) REVERT: C 193 MET cc_start: 0.8730 (tpp) cc_final: 0.8355 (tpt) REVERT: G 120 ASP cc_start: 0.7901 (p0) cc_final: 0.7615 (p0) REVERT: D 187 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6896 (mp0) REVERT: E 187 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6659 (mp0) REVERT: F 187 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.6841 (mp0) outliers start: 45 outliers final: 38 residues processed: 246 average time/residue: 0.2742 time to fit residues: 110.0085 Evaluate side-chains 243 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 200 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 247 MET Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 139 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 4.9990 chunk 221 optimal weight: 2.9990 chunk 202 optimal weight: 9.9990 chunk 215 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 chunk 66 optimal weight: 20.0000 chunk 194 optimal weight: 0.9990 chunk 203 optimal weight: 3.9990 chunk 214 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20050 Z= 0.207 Angle : 0.522 7.121 27110 Z= 0.252 Chirality : 0.046 0.126 2995 Planarity : 0.004 0.035 3485 Dihedral : 7.199 117.095 2758 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.07 % Allowed : 7.83 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.17), residues: 2455 helix: 1.09 (0.19), residues: 840 sheet: 0.30 (0.22), residues: 525 loop : 0.40 (0.20), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 79 HIS 0.004 0.001 HIS D 161 PHE 0.009 0.001 PHE A 31 TYR 0.011 0.001 TYR G 71 ARG 0.002 0.000 ARG J 92 *********************** REFINEMENT MACRO_CYCLE 9 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 248 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 203 time to evaluate : 2.385 Fit side-chains REVERT: A 187 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6940 (mp0) REVERT: A 227 MET cc_start: 0.6694 (mmm) cc_final: 0.6487 (mmt) REVERT: C 16 MET cc_start: 0.8013 (mmt) cc_final: 0.7790 (mmt) REVERT: C 187 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.6717 (mp0) REVERT: C 193 MET cc_start: 0.8705 (tpp) cc_final: 0.8347 (tpt) REVERT: G 120 ASP cc_start: 0.7833 (p0) cc_final: 0.7581 (p0) REVERT: D 187 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6866 (mp0) REVERT: E 187 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6678 (mp0) REVERT: F 187 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.6802 (mp0) outliers start: 45 outliers final: 38 residues processed: 244 average time/residue: 0.2566 time to fit residues: 102.3200 Evaluate side-chains 243 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 200 time to evaluate : 2.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 247 MET Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 139 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.9980 chunk 227 optimal weight: 9.9990 chunk 139 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 239 optimal weight: 8.9990 chunk 220 optimal weight: 1.9990 chunk 190 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20050 Z= 0.133 Angle : 0.496 6.550 27110 Z= 0.236 Chirality : 0.044 0.124 2995 Planarity : 0.003 0.032 3485 Dihedral : 6.630 106.798 2758 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.52 % Allowed : 8.43 % Favored : 90.05 % 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: 1.04 (0.18), residues: 2455 helix: 1.22 (0.19), residues: 835 sheet: 0.34 (0.22), residues: 525 loop : 0.66 (0.20), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 356 HIS 0.002 0.001 HIS D 161 PHE 0.009 0.001 PHE D 31 TYR 0.008 0.001 TYR G 71 ARG 0.007 0.000 ARG B 137 ********************** REFINEMENT MACRO_CYCLE 10 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 239 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 206 time to evaluate : 2.395 Fit side-chains REVERT: A 187 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6900 (mp0) REVERT: C 16 MET cc_start: 0.7999 (mmt) cc_final: 0.7780 (mmt) REVERT: C 187 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6796 (mp0) REVERT: C 193 MET cc_start: 0.8651 (tpp) cc_final: 0.8291 (tpt) REVERT: G 120 ASP cc_start: 0.7705 (p0) cc_final: 0.7457 (p0) REVERT: D 187 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.6833 (mp0) REVERT: E 187 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6688 (mp0) REVERT: F 187 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6834 (mp0) outliers start: 33 outliers final: 28 residues processed: 234 average time/residue: 0.2785 time to fit residues: 104.4599 Evaluate side-chains 234 residues out of total 2170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 201 time to evaluate : 3.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 247 MET Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 9.9990 chunk 202 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 175 optimal weight: 0.0570 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 190 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 195 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.0570 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.103500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.085996 restraints weight = 34742.035| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.68 r_work: 0.2906 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 20050 Z= 0.112 Angle : 0.486 7.467 27110 Z= 0.229 Chirality : 0.044 0.126 2995 Planarity : 0.003 0.032 3485 Dihedral : 6.138 95.309 2758 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.29 % Allowed : 8.71 % Favored : 90.00 % 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: 1.11 (0.18), residues: 2455 helix: 1.20 (0.18), residues: 870 sheet: 0.35 (0.22), residues: 525 loop : 0.76 (0.21), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 79 HIS 0.002 0.000 HIS E 87 PHE 0.008 0.001 PHE F 223 TYR 0.006 0.001 TYR G 71 ARG 0.007 0.000 ARG B 137 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3766.49 seconds wall clock time: 69 minutes 17.32 seconds (4157.32 seconds total)