Starting phenix.real_space_refine on Wed Mar 20 01:16:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ztd_14958/03_2024/7ztd_14958_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ztd_14958/03_2024/7ztd_14958.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ztd_14958/03_2024/7ztd_14958.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ztd_14958/03_2024/7ztd_14958.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ztd_14958/03_2024/7ztd_14958_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ztd_14958/03_2024/7ztd_14958_updated.pdb" } resolution = 4.6 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= 0.004 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: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 168 5.16 5 C 16148 2.51 5 N 4428 2.21 5 O 4980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25740 Number of models: 1 Model: "" Number of chains: 20 Chain: "E" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2853 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain: "A" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2853 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain: "B" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2853 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain: "C" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2853 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain: "D" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2853 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain: "F" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2853 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain: "G" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2853 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain: "H" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2853 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain: "P" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "Q" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "R" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "S" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.79, per 1000 atoms: 0.50 Number of scatterers: 25740 At special positions: 0 Unit cell: (100.88, 101.85, 281.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 168 16.00 P 16 15.00 O 4980 8.00 N 4428 7.00 C 16148 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: 9.43 Conformation dependent library (CDL) restraints added in 3.8 seconds 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6488 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 148 helices and 32 sheets defined 59.3% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.60 Creating SS restraints... Processing helix chain 'E' and resid 55 through 58 No H-bonds generated for 'chain 'E' and resid 55 through 58' Processing helix chain 'E' and resid 79 through 91 Processing helix chain 'E' and resid 114 through 125 Processing helix chain 'E' and resid 137 through 145 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 195 removed outlier: 4.412A pdb=" N ASP E 187 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS E 191 " --> pdb=" O TYR E 188 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR E 194 " --> pdb=" O LYS E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 215 removed outlier: 3.567A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL E 209 " --> pdb=" O GLU E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 231 Processing helix chain 'E' and resid 256 through 261 removed outlier: 3.901A pdb=" N ALA E 260 " --> pdb=" O ARG E 256 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU E 261 " --> pdb=" O CYS E 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 256 through 261' Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 274 through 284 removed outlier: 3.578A pdb=" N ILE E 282 " --> pdb=" O THR E 278 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS E 284 " --> pdb=" O ASN E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 293 removed outlier: 4.482A pdb=" N LYS E 291 " --> pdb=" O VAL E 287 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ASP E 292 " --> 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 Processing helix chain 'E' and resid 335 through 348 removed outlier: 4.684A pdb=" N VAL E 339 " --> pdb=" O ARG E 335 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N TRP E 340 " --> pdb=" O LYS E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 354 removed outlier: 3.800A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 367 through 371 Processing helix chain 'A' and resid 55 through 58 No H-bonds generated for 'chain 'A' and resid 55 through 58' Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 195 removed outlier: 4.318A pdb=" N ASP A 187 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS A 191 " --> pdb=" O TYR A 188 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR A 194 " --> pdb=" O LYS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 215 removed outlier: 3.665A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 231 Processing helix chain 'A' and resid 256 through 261 removed outlier: 4.038A pdb=" N ALA A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU A 261 " --> pdb=" O CYS A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 256 through 261' Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 284 removed outlier: 3.637A pdb=" N LYS A 284 " --> pdb=" O ASN A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 293 removed outlier: 4.443A pdb=" N LYS A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ASP A 292 " --> 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 Processing helix chain 'A' and resid 335 through 348 removed outlier: 4.714A pdb=" N VAL A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TRP A 340 " --> pdb=" O LYS A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 removed outlier: 3.704A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'B' and resid 55 through 58 No H-bonds generated for 'chain 'B' and resid 55 through 58' Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.555A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 195 removed outlier: 4.253A pdb=" N ASP B 187 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS B 191 " --> pdb=" O TYR B 188 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR B 194 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 215 removed outlier: 4.089A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 231 Processing helix chain 'B' and resid 256 through 261 removed outlier: 3.978A pdb=" N ALA B 260 " --> pdb=" O ARG B 256 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU B 261 " --> pdb=" O CYS B 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 256 through 261' Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 284 removed outlier: 3.503A pdb=" N ILE B 282 " --> pdb=" O THR B 278 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS B 284 " --> pdb=" O ASN B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 293 removed outlier: 4.559A pdb=" N LYS B 291 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 335 through 348 removed outlier: 4.792A pdb=" N VAL B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N TRP B 340 " --> pdb=" O LYS B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 354 removed outlier: 3.906A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'C' and resid 55 through 58 No H-bonds generated for 'chain 'C' and resid 55 through 58' Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.507A pdb=" N ALA C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.669A 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 195 removed outlier: 4.298A pdb=" N ASP C 187 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS C 191 " --> pdb=" O TYR C 188 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR C 194 " --> pdb=" O LYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 215 removed outlier: 3.592A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 231 Processing helix chain 'C' and resid 258 through 261 Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 284 removed outlier: 3.692A pdb=" N ILE C 282 " --> pdb=" O THR C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 293 removed outlier: 4.480A pdb=" N LYS C 291 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ASP C 292 " --> 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 Processing helix chain 'C' and resid 335 through 348 removed outlier: 4.651A pdb=" N VAL C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N TRP C 340 " --> pdb=" O LYS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 354 removed outlier: 3.847A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'D' and resid 55 through 58 No H-bonds generated for 'chain 'D' and resid 55 through 58' Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.554A 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 195 removed outlier: 4.413A pdb=" N ASP D 187 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS D 191 " --> pdb=" O TYR D 188 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D 193 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR D 194 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 215 removed outlier: 3.715A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 231 Processing helix chain 'D' and resid 256 through 261 removed outlier: 4.092A pdb=" N ALA D 260 " --> pdb=" O ARG D 256 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU D 261 " --> pdb=" O CYS D 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 256 through 261' Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 274 through 284 removed outlier: 3.504A pdb=" N ILE D 282 " --> pdb=" O THR D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 293 removed outlier: 4.624A pdb=" N LYS D 291 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ASP D 292 " --> 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 Processing helix chain 'D' and resid 335 through 348 removed outlier: 4.557A pdb=" N VAL D 339 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N TRP D 340 " --> pdb=" O LYS D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 354 removed outlier: 3.846A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'F' and resid 55 through 58 No H-bonds generated for 'chain 'F' and resid 55 through 58' Processing helix chain 'F' and resid 79 through 91 Processing helix chain 'F' and resid 113 through 125 removed outlier: 3.674A pdb=" N GLU F 125 " --> pdb=" O ILE F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 removed outlier: 3.504A 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 195 removed outlier: 4.250A pdb=" N ASP F 187 " --> pdb=" O ASP F 184 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS F 191 " --> pdb=" O TYR F 188 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU F 193 " --> pdb=" O MET F 190 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR F 194 " --> pdb=" O LYS F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 215 removed outlier: 3.538A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL F 209 " --> pdb=" O GLU F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 231 Processing helix chain 'F' and resid 256 through 261 removed outlier: 4.037A pdb=" N ALA F 260 " --> pdb=" O ARG F 256 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU F 261 " --> pdb=" O CYS F 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 256 through 261' Processing helix chain 'F' and resid 264 through 267 Processing helix chain 'F' and resid 274 through 284 removed outlier: 3.671A pdb=" N ILE F 282 " --> pdb=" O THR F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 293 removed outlier: 4.525A pdb=" N LYS F 291 " --> pdb=" O VAL F 287 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASP F 292 " --> 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 Processing helix chain 'F' and resid 335 through 348 removed outlier: 4.754A pdb=" N VAL F 339 " --> pdb=" O ARG F 335 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N TRP F 340 " --> pdb=" O LYS F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 354 removed outlier: 3.953A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 365 Processing helix chain 'F' and resid 367 through 371 Processing helix chain 'G' and resid 55 through 58 No H-bonds generated for 'chain 'G' and resid 55 through 58' Processing helix chain 'G' and resid 79 through 91 removed outlier: 3.543A pdb=" N LYS G 84 " --> pdb=" O ASP G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 125 removed outlier: 3.580A pdb=" N LYS G 118 " --> pdb=" O ASN G 115 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU G 125 " --> pdb=" O ILE G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 145 removed outlier: 3.559A pdb=" N SER G 145 " --> pdb=" O SER G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 174 No H-bonds generated for 'chain 'G' and resid 172 through 174' Processing helix chain 'G' and resid 182 through 195 removed outlier: 4.362A pdb=" N ASP G 187 " --> pdb=" O ASP G 184 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS G 191 " --> pdb=" O TYR G 188 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR G 194 " --> pdb=" O LYS G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 215 removed outlier: 3.553A pdb=" N GLU G 207 " --> pdb=" O THR G 203 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE G 208 " --> pdb=" O ALA G 204 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL G 209 " --> pdb=" O GLU G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 231 Processing helix chain 'G' and resid 258 through 261 Processing helix chain 'G' and resid 264 through 267 Processing helix chain 'G' and resid 274 through 284 removed outlier: 3.543A pdb=" N ILE G 282 " --> pdb=" O THR G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 293 removed outlier: 4.553A pdb=" N LYS G 291 " --> pdb=" O VAL G 287 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ASP G 292 " --> pdb=" O ASP G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 304 No H-bonds generated for 'chain 'G' and resid 302 through 304' Processing helix chain 'G' and resid 309 through 320 Processing helix chain 'G' and resid 335 through 348 removed outlier: 5.595A pdb=" N VAL G 339 " --> pdb=" O LYS G 336 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA G 347 " --> pdb=" O SER G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 354 removed outlier: 3.950A pdb=" N GLN G 354 " --> pdb=" O THR G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 365 Processing helix chain 'G' and resid 367 through 371 Processing helix chain 'H' and resid 55 through 58 No H-bonds generated for 'chain 'H' and resid 55 through 58' Processing helix chain 'H' and resid 79 through 91 Processing helix chain 'H' and resid 113 through 125 removed outlier: 3.552A pdb=" N LYS H 118 " --> pdb=" O ASN H 115 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE H 124 " --> pdb=" O GLN H 121 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU H 125 " --> pdb=" O ILE H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 145 removed outlier: 3.502A pdb=" N SER H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 174 No H-bonds generated for 'chain 'H' and resid 172 through 174' Processing helix chain 'H' and resid 182 through 196 removed outlier: 4.345A pdb=" N ASP H 187 " --> pdb=" O ASP H 184 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS H 191 " --> pdb=" O TYR H 188 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU H 193 " --> pdb=" O MET H 190 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR H 194 " --> pdb=" O LYS H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 215 removed outlier: 3.526A pdb=" N GLU H 207 " --> pdb=" O THR H 203 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE H 208 " --> pdb=" O ALA H 204 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL H 209 " --> pdb=" O GLU H 205 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 231 Processing helix chain 'H' and resid 256 through 261 removed outlier: 4.109A pdb=" N ALA H 260 " --> pdb=" O ARG H 256 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU H 261 " --> pdb=" O CYS H 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 256 through 261' Processing helix chain 'H' and resid 264 through 267 Processing helix chain 'H' and resid 274 through 284 Processing helix chain 'H' and resid 287 through 293 removed outlier: 4.575A pdb=" N LYS H 291 " --> pdb=" O VAL H 287 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASP H 292 " --> pdb=" O ASP H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 302 through 304 No H-bonds generated for 'chain 'H' and resid 302 through 304' Processing helix chain 'H' and resid 309 through 320 Processing helix chain 'H' and resid 335 through 348 removed outlier: 4.768A pdb=" N VAL H 339 " --> pdb=" O ARG H 335 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N TRP H 340 " --> pdb=" O LYS H 336 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 354 removed outlier: 3.913A pdb=" N GLN H 354 " --> pdb=" O THR H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 365 Processing helix chain 'H' and resid 367 through 371 Processing helix chain 'P' and resid 3 through 134 Processing helix chain 'Q' and resid 2 through 130 Processing helix chain 'R' and resid 3 through 133 Processing helix chain 'S' and resid 3 through 134 removed outlier: 3.712A pdb=" N UNK S 134 " --> pdb=" O UNK S 130 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'E' and resid 132 through 136 removed outlier: 7.189A pdb=" N VAL E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N ALA E 135 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N VAL E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE E 31 " --> pdb=" O CYS E 17 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 35 through 38 removed outlier: 3.560A pdb=" N ARG E 37 " --> pdb=" O THR E 66 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 159 through 165 Processing sheet with id= D, first strand: chain 'E' and resid 238 through 241 removed outlier: 3.633A pdb=" N LYS E 238 " --> pdb=" O ILE E 250 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.700A pdb=" N VAL A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ALA A 135 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N VAL A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 31 " --> pdb=" O CYS A 17 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 29 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 35 through 38 removed outlier: 3.546A pdb=" N VAL A 35 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 159 through 165 Processing sheet with id= H, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= I, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.970A pdb=" N VAL B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N ALA B 135 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N VAL B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 29 " --> pdb=" O ALA B 19 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 35 through 38 removed outlier: 3.518A pdb=" N VAL B 35 " --> pdb=" O LYS B 68 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR B 66 " --> pdb=" O ARG B 37 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.603A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N MET B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 176 " --> pdb=" O THR B 162 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= M, first strand: chain 'C' and resid 132 through 136 removed outlier: 7.141A pdb=" N VAL C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N ALA C 135 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N VAL C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE C 31 " --> pdb=" O CYS C 17 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 19 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA C 29 " --> pdb=" O ALA C 19 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= O, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.472A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N MET C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU C 176 " --> pdb=" O THR C 162 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 238 through 241 removed outlier: 3.626A pdb=" N LYS C 238 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE C 250 " --> pdb=" O LYS C 238 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 132 through 136 removed outlier: 6.924A pdb=" N VAL D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ALA D 135 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N VAL D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 35 through 38 Processing sheet with id= S, first strand: chain 'D' and resid 159 through 165 Processing sheet with id= T, first strand: chain 'D' and resid 238 through 241 Processing sheet with id= U, first strand: chain 'F' and resid 132 through 136 removed outlier: 6.794A pdb=" N VAL F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ALA F 135 " --> pdb=" O VAL F 103 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N VAL F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA F 29 " --> pdb=" O ALA F 19 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 34 through 38 Processing sheet with id= W, first strand: chain 'F' and resid 159 through 165 Processing sheet with id= X, first strand: chain 'F' and resid 238 through 241 Processing sheet with id= Y, first strand: chain 'G' and resid 132 through 136 removed outlier: 7.071A pdb=" N VAL G 103 " --> pdb=" O TYR G 133 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N ALA G 135 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU G 105 " --> pdb=" O ALA G 135 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU G 8 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N THR G 106 " --> pdb=" O LEU G 8 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N VAL G 10 " --> pdb=" O THR G 106 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE G 31 " --> pdb=" O CYS G 17 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 65 through 69 Processing sheet with id= AA, first strand: chain 'G' and resid 297 through 300 removed outlier: 6.494A pdb=" N ILE G 151 " --> pdb=" O VAL G 298 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N SER G 300 " --> pdb=" O ILE G 151 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N MET G 153 " --> pdb=" O SER G 300 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU G 176 " --> pdb=" O THR G 162 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 238 through 241 Processing sheet with id= AC, first strand: chain 'H' and resid 132 through 136 removed outlier: 6.895A pdb=" N VAL H 103 " --> pdb=" O TYR H 133 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ALA H 135 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU H 105 " --> pdb=" O ALA H 135 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU H 8 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N THR H 106 " --> pdb=" O LEU H 8 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N VAL H 10 " --> pdb=" O THR H 106 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 35 through 38 Processing sheet with id= AE, first strand: chain 'H' and resid 159 through 165 Processing sheet with id= AF, first strand: chain 'H' and resid 238 through 241 1277 hydrogen bonds defined for protein. 3330 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: 8.27 Time building geometry restraints manager: 10.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 8424 1.33 - 1.45: 3595 1.45 - 1.57: 13909 1.57 - 1.69: 24 1.69 - 1.81: 296 Bond restraints: 26248 Sorted by residual: bond pdb=" CB ASN H 78 " pdb=" CG ASN H 78 " ideal model delta sigma weight residual 1.516 1.475 0.041 2.50e-02 1.60e+03 2.68e+00 bond pdb=" CB TRP A 79 " pdb=" CG TRP A 79 " ideal model delta sigma weight residual 1.498 1.448 0.050 3.10e-02 1.04e+03 2.65e+00 bond pdb=" CG1 ILE A 64 " pdb=" CD1 ILE A 64 " ideal model delta sigma weight residual 1.513 1.450 0.063 3.90e-02 6.57e+02 2.64e+00 bond pdb=" CG GLU D 270 " pdb=" CD GLU D 270 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.49e+00 bond pdb=" CD1 TYR F 169 " pdb=" CE1 TYR F 169 " ideal model delta sigma weight residual 1.382 1.336 0.046 3.00e-02 1.11e+03 2.34e+00 ... (remaining 26243 not shown) Histogram of bond angle deviations from ideal: 97.13 - 104.92: 637 104.92 - 112.72: 13733 112.72 - 120.52: 11401 120.52 - 128.31: 9769 128.31 - 136.11: 180 Bond angle restraints: 35720 Sorted by residual: angle pdb=" CA TYR C 169 " pdb=" CB TYR C 169 " pdb=" CG TYR C 169 " ideal model delta sigma weight residual 113.90 106.63 7.27 1.80e+00 3.09e-01 1.63e+01 angle pdb=" N ALA C 181 " pdb=" CA ALA C 181 " pdb=" C ALA C 181 " ideal model delta sigma weight residual 110.35 115.24 -4.89 1.38e+00 5.25e-01 1.26e+01 angle pdb=" N MET B 16 " pdb=" CA MET B 16 " pdb=" C MET B 16 " ideal model delta sigma weight residual 108.32 114.00 -5.68 1.64e+00 3.72e-01 1.20e+01 angle pdb=" N PHE A 255 " pdb=" CA PHE A 255 " pdb=" C PHE A 255 " ideal model delta sigma weight residual 113.88 118.09 -4.21 1.23e+00 6.61e-01 1.17e+01 angle pdb=" N ALA B 181 " pdb=" CA ALA B 181 " pdb=" C ALA B 181 " ideal model delta sigma weight residual 110.35 114.95 -4.60 1.38e+00 5.25e-01 1.11e+01 ... (remaining 35715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.21: 15348 30.21 - 60.41: 340 60.41 - 90.62: 72 90.62 - 120.82: 16 120.82 - 151.03: 16 Dihedral angle restraints: 15792 sinusoidal: 5728 harmonic: 10064 Sorted by residual: dihedral pdb=" C5' ADP G 401 " pdb=" O5' ADP G 401 " pdb=" PA ADP G 401 " pdb=" O2A ADP G 401 " ideal model delta sinusoidal sigma weight residual -60.00 91.03 -151.03 1 2.00e+01 2.50e-03 4.50e+01 dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 89.06 -149.06 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" C5' ADP H 401 " pdb=" O5' ADP H 401 " pdb=" PA ADP H 401 " pdb=" O2A ADP H 401 " ideal model delta sinusoidal sigma weight residual -60.00 88.97 -148.97 1 2.00e+01 2.50e-03 4.46e+01 ... (remaining 15789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2244 0.042 - 0.083: 1154 0.083 - 0.125: 509 0.125 - 0.166: 145 0.166 - 0.208: 40 Chirality restraints: 4092 Sorted by residual: chirality pdb=" CA GLU B 270 " pdb=" N GLU B 270 " pdb=" C GLU B 270 " pdb=" CB GLU B 270 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA PHE B 255 " pdb=" N PHE B 255 " pdb=" C PHE B 255 " pdb=" CB PHE B 255 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA GLU G 270 " pdb=" N GLU G 270 " pdb=" C GLU G 270 " pdb=" CB GLU G 270 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 4089 not shown) Planarity restraints: 4616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 169 " 0.030 2.00e-02 2.50e+03 2.80e-02 1.57e+01 pdb=" CG TYR C 169 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TYR C 169 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR C 169 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR C 169 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR C 169 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR C 169 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR C 169 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 169 " 0.027 2.00e-02 2.50e+03 2.74e-02 1.50e+01 pdb=" CG TYR F 169 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TYR F 169 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR F 169 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR F 169 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR F 169 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR F 169 " 0.014 2.00e-02 2.50e+03 pdb=" OH TYR F 169 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 169 " 0.028 2.00e-02 2.50e+03 2.61e-02 1.36e+01 pdb=" CG TYR B 169 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR B 169 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR B 169 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 169 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR B 169 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR B 169 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR B 169 " -0.010 2.00e-02 2.50e+03 ... (remaining 4613 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 400 2.66 - 3.22: 26848 3.22 - 3.78: 38814 3.78 - 4.34: 51203 4.34 - 4.90: 80970 Nonbonded interactions: 198235 Sorted by model distance: nonbonded pdb=" OG1 THR H 160 " pdb=" O LEU H 178 " model vdw 2.097 2.440 nonbonded pdb=" O GLY A 48 " pdb=" OH TYR A 53 " model vdw 2.111 2.440 nonbonded pdb=" OG1 THR E 160 " pdb=" O LEU E 178 " model vdw 2.127 2.440 nonbonded pdb=" OE1 GLN F 49 " pdb=" OH TYR F 53 " model vdw 2.140 2.440 nonbonded pdb=" OD2 ASP E 244 " pdb=" NH1 ARG B 290 " model vdw 2.160 2.520 ... (remaining 198230 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } pdb_interpretation.ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } Set refine NCS operators NCS operators will be refined. 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 group one per residue 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: 3.190 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: 14.790 Check model and map are aligned: 0.300 Set scattering table: 0.200 Process input model: 64.440 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 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 : 0.007 0.063 26248 Z= 0.468 Angle : 1.045 9.702 35720 Z= 0.560 Chirality : 0.060 0.208 4092 Planarity : 0.010 0.117 4616 Dihedral : 15.694 151.030 9304 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -2.32 (0.14), residues: 2912 helix: -2.74 (0.11), residues: 1168 sheet: -0.37 (0.21), residues: 488 loop : -0.53 (0.18), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.005 TRP H 79 HIS 0.013 0.003 HIS A 88 PHE 0.027 0.003 PHE D 90 TYR 0.069 0.006 TYR C 169 ARG 0.030 0.005 ARG H 312 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8042 (mtp85) cc_final: 0.7704 (ttm110) REVERT: A 115 ASN cc_start: 0.8870 (t0) cc_final: 0.8363 (t0) REVERT: A 119 MET cc_start: 0.8510 (ttm) cc_final: 0.8185 (ttm) REVERT: A 167 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7490 (tm-30) REVERT: A 238 LYS cc_start: 0.8386 (mttm) cc_final: 0.8111 (mmtt) REVERT: A 242 LEU cc_start: 0.8799 (mt) cc_final: 0.8343 (mm) REVERT: A 356 TRP cc_start: 0.8104 (m-90) cc_final: 0.7804 (m-90) REVERT: A 357 ILE cc_start: 0.9084 (mp) cc_final: 0.8483 (tp) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1593 time to fit residues: 15.9867 Evaluate side-chains 43 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.346 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.029 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0420 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 287 optimal weight: 10.0000 chunk 257 optimal weight: 0.9990 chunk 142 optimal weight: 8.9990 chunk 88 optimal weight: 0.0370 chunk 173 optimal weight: 0.4980 chunk 137 optimal weight: 6.9990 chunk 266 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 162 optimal weight: 5.9990 chunk 198 optimal weight: 4.9990 chunk 308 optimal weight: 8.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS A 88 HIS ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 HIS A 252 ASN Total number of N/Q/H flips: 4 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.7916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.371 26248 Z= 0.496 Angle : 1.262 34.990 35720 Z= 0.601 Chirality : 0.064 1.061 4092 Planarity : 0.006 0.061 4616 Dihedral : 12.439 153.129 3808 Min Nonbonded Distance : 1.267 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.49 % 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: -0.59 (0.16), residues: 2912 helix: -0.95 (0.14), residues: 1200 sheet: -0.18 (0.22), residues: 496 loop : 0.42 (0.20), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 356 HIS 0.006 0.002 HIS C 88 PHE 0.006 0.001 PHE D 262 TYR 0.029 0.001 TYR H 169 ARG 0.004 0.001 ARG F 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.7760 (mtp85) cc_final: 0.7187 (ttm110) REVERT: A 105 LEU cc_start: 0.8622 (pp) cc_final: 0.8216 (pp) REVERT: A 157 ASP cc_start: 0.7898 (t0) cc_final: 0.7307 (t70) REVERT: A 179 ASP cc_start: 0.7483 (p0) cc_final: 0.7081 (p0) REVERT: A 180 LEU cc_start: 0.8785 (tp) cc_final: 0.8462 (tt) REVERT: A 293 LEU cc_start: 0.9467 (mt) cc_final: 0.9145 (mt) REVERT: A 314 GLN cc_start: 0.8492 (tt0) cc_final: 0.7757 (tm-30) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1742 time to fit residues: 12.9093 Evaluate side-chains 42 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.334 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.026 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0379 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 171 optimal weight: 0.0870 chunk 95 optimal weight: 0.0670 chunk 256 optimal weight: 10.0000 chunk 210 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 309 optimal weight: 20.0000 chunk 334 optimal weight: 7.9990 chunk 275 optimal weight: 1.9990 chunk 306 optimal weight: 9.9990 chunk 105 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 overall best weight: 1.2100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.8448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.349 26248 Z= 0.405 Angle : 0.861 15.635 35720 Z= 0.417 Chirality : 0.044 0.261 4092 Planarity : 0.005 0.040 4616 Dihedral : 11.238 142.945 3808 Min Nonbonded Distance : 1.367 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.16), residues: 2912 helix: -0.11 (0.15), residues: 1200 sheet: -0.04 (0.22), residues: 496 loop : 0.56 (0.20), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 79 HIS 0.006 0.002 HIS C 73 PHE 0.007 0.001 PHE E 124 TYR 0.011 0.001 TYR C 362 ARG 0.005 0.001 ARG H 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.304 Fit side-chains REVERT: A 105 LEU cc_start: 0.8723 (pp) cc_final: 0.8494 (pp) REVERT: A 111 ASN cc_start: 0.8684 (t0) cc_final: 0.8414 (t0) REVERT: A 155 SER cc_start: 0.8536 (m) cc_final: 0.8189 (p) REVERT: A 157 ASP cc_start: 0.7850 (t0) cc_final: 0.7271 (t0) REVERT: A 179 ASP cc_start: 0.7671 (p0) cc_final: 0.7248 (p0) REVERT: A 180 LEU cc_start: 0.8822 (tp) cc_final: 0.8493 (tt) REVERT: A 293 LEU cc_start: 0.9457 (mt) cc_final: 0.9163 (mt) REVERT: A 314 GLN cc_start: 0.8490 (tt0) cc_final: 0.7805 (tm-30) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1641 time to fit residues: 10.0754 Evaluate side-chains 40 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.307 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.031 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0455 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 305 optimal weight: 20.0000 chunk 232 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 147 optimal weight: 0.0010 chunk 207 optimal weight: 4.9990 chunk 310 optimal weight: 20.0000 chunk 328 optimal weight: 20.0000 chunk 162 optimal weight: 6.9990 chunk 294 optimal weight: 0.0470 chunk 88 optimal weight: 7.9990 overall best weight: 3.0090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.8595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 26248 Z= 0.300 Angle : 0.839 20.822 35720 Z= 0.400 Chirality : 0.049 0.660 4092 Planarity : 0.004 0.035 4616 Dihedral : 10.720 124.925 3808 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.16), residues: 2912 helix: 0.24 (0.16), residues: 1200 sheet: 0.04 (0.23), residues: 496 loop : 0.58 (0.20), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 79 HIS 0.006 0.002 HIS D 371 PHE 0.005 0.001 PHE D 21 TYR 0.021 0.002 TYR C 169 ARG 0.003 0.000 ARG E 196 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.381 Fit side-chains REVERT: A 44 MET cc_start: 0.7957 (pmm) cc_final: 0.6266 (ttt) REVERT: A 111 ASN cc_start: 0.8894 (t0) cc_final: 0.8564 (t0) REVERT: A 155 SER cc_start: 0.8757 (m) cc_final: 0.8469 (p) REVERT: A 157 ASP cc_start: 0.7948 (t0) cc_final: 0.7496 (t0) REVERT: A 179 ASP cc_start: 0.7474 (p0) cc_final: 0.7262 (p0) REVERT: A 293 LEU cc_start: 0.9471 (mt) cc_final: 0.9142 (mt) REVERT: A 314 GLN cc_start: 0.8509 (tt0) cc_final: 0.7897 (tm-30) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1401 time to fit residues: 9.9909 Evaluate side-chains 36 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.400 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.038 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0465 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 273 optimal weight: 0.5980 chunk 186 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 135 optimal weight: 0.5980 chunk 280 optimal weight: 0.1980 chunk 227 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 167 optimal weight: 0.0870 chunk 294 optimal weight: 5.9990 chunk 82 optimal weight: 0.0050 overall best weight: 0.2972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 275 HIS Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.9130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 26248 Z= 0.230 Angle : 0.731 8.520 35720 Z= 0.348 Chirality : 0.043 0.259 4092 Planarity : 0.004 0.051 4616 Dihedral : 9.724 118.702 3808 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % 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: 0.54 (0.16), residues: 2912 helix: 0.50 (0.16), residues: 1192 sheet: 0.18 (0.23), residues: 496 loop : 0.55 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 79 HIS 0.004 0.001 HIS H 87 PHE 0.008 0.001 PHE D 31 TYR 0.012 0.001 TYR B 169 ARG 0.004 0.000 ARG E 196 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.336 Fit side-chains REVERT: A 44 MET cc_start: 0.8128 (pmm) cc_final: 0.6060 (ttt) REVERT: A 59 GLN cc_start: 0.8865 (tp40) cc_final: 0.8293 (tm-30) REVERT: A 111 ASN cc_start: 0.8650 (t0) cc_final: 0.8345 (t0) REVERT: A 155 SER cc_start: 0.8842 (m) cc_final: 0.8517 (p) REVERT: A 157 ASP cc_start: 0.7920 (t0) cc_final: 0.7272 (t70) REVERT: A 179 ASP cc_start: 0.7415 (p0) cc_final: 0.7070 (p0) REVERT: A 180 LEU cc_start: 0.8781 (tp) cc_final: 0.8394 (tt) REVERT: A 293 LEU cc_start: 0.9445 (mt) cc_final: 0.9124 (mt) REVERT: A 314 GLN cc_start: 0.8439 (tt0) cc_final: 0.7819 (tm-30) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1065 time to fit residues: 8.4015 Evaluate side-chains 46 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.327 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.029 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0378 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 110 optimal weight: 8.9990 chunk 295 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 192 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 328 optimal weight: 30.0000 chunk 273 optimal weight: 0.0770 chunk 152 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 172 optimal weight: 8.9990 overall best weight: 1.3540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.9225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26248 Z= 0.211 Angle : 0.636 5.785 35720 Z= 0.305 Chirality : 0.041 0.125 4092 Planarity : 0.004 0.050 4616 Dihedral : 8.701 109.522 3808 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 0.63 (0.17), residues: 2912 helix: 0.54 (0.16), residues: 1200 sheet: 0.40 (0.23), residues: 496 loop : 0.53 (0.19), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 79 HIS 0.003 0.001 HIS H 87 PHE 0.006 0.001 PHE H 200 TYR 0.018 0.001 TYR G 169 ARG 0.002 0.000 ARG H 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.342 Fit side-chains REVERT: A 44 MET cc_start: 0.7987 (pmm) cc_final: 0.5660 (ttt) REVERT: A 59 GLN cc_start: 0.8770 (tp40) cc_final: 0.8217 (tm-30) REVERT: A 111 ASN cc_start: 0.8737 (t0) cc_final: 0.8387 (t0) REVERT: A 132 MET cc_start: 0.8075 (ppp) cc_final: 0.7779 (ppp) REVERT: A 155 SER cc_start: 0.8891 (m) cc_final: 0.8568 (p) REVERT: A 157 ASP cc_start: 0.7762 (t0) cc_final: 0.7355 (t70) REVERT: A 179 ASP cc_start: 0.7392 (p0) cc_final: 0.7169 (p0) REVERT: A 180 LEU cc_start: 0.8803 (tp) cc_final: 0.8452 (tt) REVERT: A 293 LEU cc_start: 0.9419 (mt) cc_final: 0.9105 (mt) REVERT: A 314 GLN cc_start: 0.8471 (tt0) cc_final: 0.7823 (tm-30) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1176 time to fit residues: 8.2041 Evaluate side-chains 42 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.302 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.025 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0367 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 317 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 187 optimal weight: 0.0370 chunk 240 optimal weight: 0.0020 chunk 186 optimal weight: 7.9990 chunk 276 optimal weight: 0.0020 chunk 183 optimal weight: 0.7980 chunk 327 optimal weight: 20.0000 chunk 205 optimal weight: 0.0010 chunk 199 optimal weight: 0.0570 chunk 151 optimal weight: 0.0030 overall best weight: 0.0090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.9600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26248 Z= 0.193 Angle : 0.616 5.715 35720 Z= 0.292 Chirality : 0.040 0.131 4092 Planarity : 0.004 0.045 4616 Dihedral : 7.764 97.587 3808 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % 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: 0.63 (0.17), residues: 2912 helix: 0.50 (0.16), residues: 1184 sheet: 0.35 (0.23), residues: 496 loop : 0.62 (0.20), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 356 HIS 0.004 0.001 HIS H 40 PHE 0.007 0.001 PHE C 31 TYR 0.013 0.001 TYR B 169 ARG 0.006 0.000 ARG H 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.8372 (pmm) cc_final: 0.8006 (pmm) REVERT: A 59 GLN cc_start: 0.8708 (tp40) cc_final: 0.8441 (tm-30) REVERT: A 82 MET cc_start: 0.9127 (tpp) cc_final: 0.8518 (tmm) REVERT: A 111 ASN cc_start: 0.8685 (t0) cc_final: 0.8336 (t0) REVERT: A 132 MET cc_start: 0.7921 (ppp) cc_final: 0.7635 (ppp) REVERT: A 155 SER cc_start: 0.8877 (m) cc_final: 0.8560 (p) REVERT: A 157 ASP cc_start: 0.7796 (t0) cc_final: 0.7286 (t70) REVERT: A 179 ASP cc_start: 0.7328 (p0) cc_final: 0.7085 (p0) REVERT: A 180 LEU cc_start: 0.8763 (tp) cc_final: 0.8403 (tt) REVERT: A 293 LEU cc_start: 0.9411 (mt) cc_final: 0.9095 (mt) REVERT: A 314 GLN cc_start: 0.8372 (tt0) cc_final: 0.7801 (tm-30) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1222 time to fit residues: 8.7266 Evaluate side-chains 41 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.307 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.026 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0369 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 202 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 195 optimal weight: 0.0870 chunk 98 optimal weight: 0.0970 chunk 64 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 208 optimal weight: 0.0060 chunk 223 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 257 optimal weight: 7.9990 overall best weight: 1.0374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.9697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26248 Z= 0.191 Angle : 0.601 5.857 35720 Z= 0.288 Chirality : 0.040 0.124 4092 Planarity : 0.004 0.045 4616 Dihedral : 7.372 97.255 3808 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.62 (0.17), residues: 2912 helix: 0.45 (0.16), residues: 1192 sheet: 0.27 (0.23), residues: 496 loop : 0.70 (0.20), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 356 HIS 0.004 0.001 HIS A 40 PHE 0.005 0.001 PHE H 200 TYR 0.025 0.002 TYR A 169 ARG 0.004 0.000 ARG G 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8837 (tp40) cc_final: 0.8359 (tm-30) REVERT: A 82 MET cc_start: 0.9094 (tpp) cc_final: 0.8558 (mmm) REVERT: A 111 ASN cc_start: 0.8757 (t0) cc_final: 0.8485 (t0) REVERT: A 132 MET cc_start: 0.7842 (ppp) cc_final: 0.7589 (ppp) REVERT: A 155 SER cc_start: 0.8923 (m) cc_final: 0.8664 (p) REVERT: A 157 ASP cc_start: 0.7785 (t0) cc_final: 0.7295 (t70) REVERT: A 179 ASP cc_start: 0.7290 (p0) cc_final: 0.7066 (p0) REVERT: A 180 LEU cc_start: 0.8776 (tp) cc_final: 0.8388 (tt) REVERT: A 283 MET cc_start: 0.8744 (tpp) cc_final: 0.8506 (tpp) REVERT: A 293 LEU cc_start: 0.9430 (mt) cc_final: 0.9099 (mt) REVERT: A 314 GLN cc_start: 0.8389 (tt0) cc_final: 0.7817 (tm-30) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1010 time to fit residues: 6.7066 Evaluate side-chains 42 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.335 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.027 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0387 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 298 optimal weight: 6.9990 chunk 313 optimal weight: 7.9990 chunk 286 optimal weight: 7.9990 chunk 305 optimal weight: 20.0000 chunk 183 optimal weight: 0.0270 chunk 133 optimal weight: 4.9990 chunk 239 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 275 optimal weight: 0.8980 chunk 288 optimal weight: 10.0000 chunk 304 optimal weight: 7.9990 overall best weight: 2.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.9445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 26248 Z= 0.232 Angle : 0.612 5.941 35720 Z= 0.298 Chirality : 0.041 0.126 4092 Planarity : 0.004 0.044 4616 Dihedral : 6.690 89.866 3808 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 0.32 (0.16), residues: 2912 helix: 0.33 (0.16), residues: 1200 sheet: 0.12 (0.23), residues: 496 loop : 0.38 (0.19), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 79 HIS 0.005 0.001 HIS H 40 PHE 0.006 0.001 PHE G 262 TYR 0.008 0.001 TYR D 53 ARG 0.005 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.8618 (pmm) cc_final: 0.8137 (pmm) REVERT: A 57 GLU cc_start: 0.8264 (tp30) cc_final: 0.7988 (tp30) REVERT: A 111 ASN cc_start: 0.8875 (t0) cc_final: 0.8599 (t0) REVERT: A 132 MET cc_start: 0.7810 (ppp) cc_final: 0.7571 (ppp) REVERT: A 151 ILE cc_start: 0.9051 (tt) cc_final: 0.8835 (mp) REVERT: A 155 SER cc_start: 0.8833 (m) cc_final: 0.8547 (p) REVERT: A 157 ASP cc_start: 0.8002 (t0) cc_final: 0.7391 (t0) REVERT: A 283 MET cc_start: 0.8966 (tpp) cc_final: 0.8552 (tpp) REVERT: A 314 GLN cc_start: 0.8441 (tt0) cc_final: 0.8109 (tm-30) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0877 time to fit residues: 5.8119 Evaluate side-chains 37 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.348 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.028 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0401 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 200 optimal weight: 0.0040 chunk 322 optimal weight: 0.0470 chunk 197 optimal weight: 7.9990 chunk 153 optimal weight: 6.9990 chunk 224 optimal weight: 5.9990 chunk 338 optimal weight: 20.0000 chunk 311 optimal weight: 20.0000 chunk 269 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 208 optimal weight: 4.9990 chunk 165 optimal weight: 0.0050 overall best weight: 2.2108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 HIS Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.9625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26248 Z= 0.205 Angle : 0.609 5.773 35720 Z= 0.295 Chirality : 0.041 0.126 4092 Planarity : 0.004 0.044 4616 Dihedral : 6.234 79.149 3808 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.16), residues: 2912 helix: 0.40 (0.16), residues: 1200 sheet: 0.14 (0.22), residues: 536 loop : 0.32 (0.20), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 79 HIS 0.003 0.001 HIS E 40 PHE 0.005 0.001 PHE H 124 TYR 0.024 0.002 TYR H 198 ARG 0.004 0.000 ARG E 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8236 (tp30) cc_final: 0.7951 (tp30) REVERT: A 111 ASN cc_start: 0.8846 (t0) cc_final: 0.8563 (t0) REVERT: A 132 MET cc_start: 0.7825 (ppp) cc_final: 0.7517 (ppp) REVERT: A 151 ILE cc_start: 0.9018 (tt) cc_final: 0.8817 (mp) REVERT: A 155 SER cc_start: 0.8866 (m) cc_final: 0.8492 (p) REVERT: A 157 ASP cc_start: 0.7999 (t0) cc_final: 0.7369 (t0) REVERT: A 184 ASP cc_start: 0.8526 (m-30) cc_final: 0.7454 (t0) REVERT: A 269 MET cc_start: 0.8484 (mmt) cc_final: 0.8280 (tpp) REVERT: A 283 MET cc_start: 0.8940 (tpp) cc_final: 0.8470 (tpp) REVERT: A 314 GLN cc_start: 0.8439 (tt0) cc_final: 0.7917 (tm-30) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.0973 time to fit residues: 6.7274 Evaluate side-chains 41 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.258 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.029 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0399 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 214 optimal weight: 0.7980 chunk 287 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 248 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 74 optimal weight: 5.9990 chunk 270 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 277 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 49 optimal weight: 10.0000 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.068637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.059821 restraints weight = 10412.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.061643 restraints weight = 6198.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.062946 restraints weight = 4107.597| |-----------------------------------------------------------------------------| r_work (final): 0.2870 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.068978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.060977 restraints weight = 10278.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.061148 restraints weight = 9499.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.061249 restraints weight = 8894.474| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.9753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26248 Z= 0.182 Angle : 0.592 5.811 35720 Z= 0.286 Chirality : 0.040 0.128 4092 Planarity : 0.004 0.045 4616 Dihedral : 5.659 65.065 3808 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: 0.39 (0.17), residues: 2912 helix: 0.46 (0.16), residues: 1192 sheet: 0.10 (0.22), residues: 536 loop : 0.37 (0.20), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 356 HIS 0.003 0.001 HIS H 87 PHE 0.006 0.001 PHE F 31 TYR 0.030 0.002 TYR G 198 ARG 0.005 0.000 ARG G 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3054.89 seconds wall clock time: 57 minutes 37.46 seconds (3457.46 seconds total)