Starting phenix.real_space_refine on Sat Jul 4 16:51:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8bq2_16170/07_2026/8bq2_16170.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bq2_16170/07_2026/8bq2_16170.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8bq2_16170/07_2026/8bq2_16170.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bq2_16170/07_2026/8bq2_16170.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8bq2_16170/07_2026/8bq2_16170.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8bq2_16170/07_2026/8bq2_16170.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bq2_16170/07_2026/8bq2_16170.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bq2_16170/07_2026/8bq2_16170.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 18 9.91 5 P 57 5.49 5 S 117 5.16 5 C 13791 2.51 5 N 3975 2.21 5 O 4373 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22331 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2376 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Chain: "B" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2376 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Chain: "C" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2376 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Chain: "D" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2376 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Chain: "E" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2376 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Chain: "F" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2376 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Chain: "G" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2376 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Chain: "H" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2376 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Chain: "I" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2376 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Chain: "W" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 650 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CA': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.93, per 1000 atoms: 0.22 Number of scatterers: 22331 At special positions: 0 Unit cell: (114.4, 117.26, 217.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 18 19.99 S 117 16.00 P 57 15.00 O 4373 8.00 N 3975 7.00 C 13791 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 - 3.00 Amino acid : True - 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: 1.88 Conformation dependent library (CDL) restraints added in 1.1 seconds 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5094 Finding SS restraints... Secondary structure from input PDB file: 153 helices and 18 sheets defined 54.2% alpha, 16.4% beta 0 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 3.39 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 removed outlier: 3.511A pdb=" N GLY A 32 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 44 removed outlier: 3.782A pdb=" N VAL A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS A 39 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 44 " --> pdb=" O LYS A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 54 Processing helix chain 'A' and resid 56 through 63 removed outlier: 3.921A pdb=" N LEU A 60 " --> pdb=" O PRO A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 82 removed outlier: 3.731A pdb=" N LYS A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 97 Processing helix chain 'A' and resid 106 through 113 Processing helix chain 'A' and resid 132 through 144 removed outlier: 3.600A pdb=" N ILE A 136 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N CYS A 137 " --> pdb=" O LYS A 133 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 146 No H-bonds generated for 'chain 'A' and resid 145 through 146' Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 167 through 179 removed outlier: 3.895A pdb=" N LEU A 171 " --> pdb=" O ARG A 167 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 186 Processing helix chain 'A' and resid 196 through 214 removed outlier: 4.008A pdb=" N LEU A 204 " --> pdb=" O GLN A 200 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR A 205 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN A 206 " --> pdb=" O GLN A 202 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A 214 " --> pdb=" O MET A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 232 removed outlier: 3.961A pdb=" N TYR A 232 " --> pdb=" O TYR A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 237 through 260 removed outlier: 3.664A pdb=" N MET A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS A 244 " --> pdb=" O ALA A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 296 removed outlier: 4.177A pdb=" N ILE A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 32 removed outlier: 3.512A pdb=" N GLY B 32 " --> pdb=" O GLU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 44 removed outlier: 3.782A pdb=" N VAL B 38 " --> pdb=" O ASN B 34 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B 39 " --> pdb=" O ALA B 35 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA B 44 " --> pdb=" O LYS B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 54 Processing helix chain 'B' and resid 56 through 63 removed outlier: 3.921A pdb=" N LEU B 60 " --> pdb=" O PRO B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 82 removed outlier: 3.731A pdb=" N LYS B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 97 Processing helix chain 'B' and resid 106 through 113 Processing helix chain 'B' and resid 132 through 144 removed outlier: 3.600A pdb=" N ILE B 136 " --> pdb=" O GLY B 132 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N CYS B 137 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL B 142 " --> pdb=" O HIS B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 146 No H-bonds generated for 'chain 'B' and resid 145 through 146' Processing helix chain 'B' and resid 147 through 151 Processing helix chain 'B' and resid 167 through 179 removed outlier: 3.895A pdb=" N LEU B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR B 178 " --> pdb=" O VAL B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 186 Processing helix chain 'B' and resid 196 through 214 removed outlier: 4.008A pdb=" N LEU B 204 " --> pdb=" O GLN B 200 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TYR B 205 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN B 206 " --> pdb=" O GLN B 202 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 214 " --> pdb=" O MET B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.961A pdb=" N TYR B 232 " --> pdb=" O TYR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 237 through 260 removed outlier: 3.663A pdb=" N MET B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS B 244 " --> pdb=" O ALA B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 296 removed outlier: 4.178A pdb=" N ILE B 292 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA B 293 " --> pdb=" O GLY B 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 32 removed outlier: 3.512A pdb=" N GLY C 32 " --> pdb=" O GLU C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 44 removed outlier: 3.782A pdb=" N VAL C 38 " --> pdb=" O ASN C 34 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS C 39 " --> pdb=" O ALA C 35 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA C 44 " --> pdb=" O LYS C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 54 Processing helix chain 'C' and resid 56 through 63 removed outlier: 3.920A pdb=" N LEU C 60 " --> pdb=" O PRO C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 82 removed outlier: 3.731A pdb=" N LYS C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU C 81 " --> pdb=" O GLU C 77 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 97 Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 132 through 144 removed outlier: 3.599A pdb=" N ILE C 136 " --> pdb=" O GLY C 132 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N CYS C 137 " --> pdb=" O LYS C 133 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL C 142 " --> pdb=" O HIS C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 146 No H-bonds generated for 'chain 'C' and resid 145 through 146' Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 167 through 179 removed outlier: 3.895A pdb=" N LEU C 171 " --> pdb=" O ARG C 167 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG C 177 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR C 178 " --> pdb=" O VAL C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 186 Processing helix chain 'C' and resid 196 through 214 removed outlier: 4.008A pdb=" N LEU C 204 " --> pdb=" O GLN C 200 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TYR C 205 " --> pdb=" O THR C 201 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN C 206 " --> pdb=" O GLN C 202 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER C 214 " --> pdb=" O MET C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 232 removed outlier: 3.961A pdb=" N TYR C 232 " --> pdb=" O TYR C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 237 through 260 removed outlier: 3.663A pdb=" N MET C 243 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS C 244 " --> pdb=" O ALA C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 296 removed outlier: 4.178A pdb=" N ILE C 292 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA C 293 " --> pdb=" O GLY C 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 32 removed outlier: 3.512A pdb=" N GLY D 32 " --> pdb=" O GLU D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 44 removed outlier: 3.782A pdb=" N VAL D 38 " --> pdb=" O ASN D 34 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 54 Processing helix chain 'D' and resid 56 through 63 removed outlier: 3.920A pdb=" N LEU D 60 " --> pdb=" O PRO D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 removed outlier: 3.731A pdb=" N LYS D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 97 Processing helix chain 'D' and resid 106 through 113 Processing helix chain 'D' and resid 132 through 144 removed outlier: 3.599A pdb=" N ILE D 136 " --> pdb=" O GLY D 132 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N CYS D 137 " --> pdb=" O LYS D 133 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL D 142 " --> pdb=" O HIS D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 146 No H-bonds generated for 'chain 'D' and resid 145 through 146' Processing helix chain 'D' and resid 147 through 151 Processing helix chain 'D' and resid 167 through 179 removed outlier: 3.895A pdb=" N LEU D 171 " --> pdb=" O ARG D 167 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG D 177 " --> pdb=" O ALA D 173 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR D 178 " --> pdb=" O VAL D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 186 Processing helix chain 'D' and resid 196 through 214 removed outlier: 4.008A pdb=" N LEU D 204 " --> pdb=" O GLN D 200 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR D 205 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN D 206 " --> pdb=" O GLN D 202 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU D 213 " --> pdb=" O ALA D 209 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER D 214 " --> pdb=" O MET D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 232 removed outlier: 3.961A pdb=" N TYR D 232 " --> pdb=" O TYR D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 237 through 260 removed outlier: 3.663A pdb=" N MET D 243 " --> pdb=" O SER D 239 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N HIS D 244 " --> pdb=" O ALA D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 296 removed outlier: 4.178A pdb=" N ILE D 292 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA D 293 " --> pdb=" O GLY D 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 32 removed outlier: 3.512A pdb=" N GLY E 32 " --> pdb=" O GLU E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 44 removed outlier: 3.782A pdb=" N VAL E 38 " --> pdb=" O ASN E 34 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS E 39 " --> pdb=" O ALA E 35 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA E 44 " --> pdb=" O LYS E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 54 Processing helix chain 'E' and resid 56 through 63 removed outlier: 3.921A pdb=" N LEU E 60 " --> pdb=" O PRO E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 82 removed outlier: 3.731A pdb=" N LYS E 80 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU E 81 " --> pdb=" O GLU E 77 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 97 Processing helix chain 'E' and resid 106 through 113 Processing helix chain 'E' and resid 132 through 144 removed outlier: 3.599A pdb=" N ILE E 136 " --> pdb=" O GLY E 132 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N CYS E 137 " --> pdb=" O LYS E 133 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL E 142 " --> pdb=" O HIS E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 146 No H-bonds generated for 'chain 'E' and resid 145 through 146' Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 167 through 179 removed outlier: 3.895A pdb=" N LEU E 171 " --> pdb=" O ARG E 167 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR E 178 " --> pdb=" O VAL E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 186 Processing helix chain 'E' and resid 196 through 214 removed outlier: 4.008A pdb=" N LEU E 204 " --> pdb=" O GLN E 200 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR E 205 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN E 206 " --> pdb=" O GLN E 202 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER E 214 " --> pdb=" O MET E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 232 removed outlier: 3.961A pdb=" N TYR E 232 " --> pdb=" O TYR E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 236 No H-bonds generated for 'chain 'E' and resid 234 through 236' Processing helix chain 'E' and resid 237 through 260 removed outlier: 3.663A pdb=" N MET E 243 " --> pdb=" O SER E 239 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS E 244 " --> pdb=" O ALA E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 296 removed outlier: 4.177A pdb=" N ILE E 292 " --> pdb=" O GLY E 288 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA E 293 " --> pdb=" O GLY E 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 32 removed outlier: 3.512A pdb=" N GLY F 32 " --> pdb=" O GLU F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 44 removed outlier: 3.782A pdb=" N VAL F 38 " --> pdb=" O ASN F 34 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS F 39 " --> pdb=" O ALA F 35 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA F 44 " --> pdb=" O LYS F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 54 Processing helix chain 'F' and resid 56 through 63 removed outlier: 3.921A pdb=" N LEU F 60 " --> pdb=" O PRO F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 82 removed outlier: 3.730A pdb=" N LYS F 80 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU F 81 " --> pdb=" O GLU F 77 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL F 82 " --> pdb=" O ALA F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 97 Processing helix chain 'F' and resid 106 through 113 Processing helix chain 'F' and resid 132 through 144 removed outlier: 3.599A pdb=" N ILE F 136 " --> pdb=" O GLY F 132 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N CYS F 137 " --> pdb=" O LYS F 133 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL F 142 " --> pdb=" O HIS F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 146 No H-bonds generated for 'chain 'F' and resid 145 through 146' Processing helix chain 'F' and resid 147 through 151 Processing helix chain 'F' and resid 167 through 179 removed outlier: 3.896A pdb=" N LEU F 171 " --> pdb=" O ARG F 167 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG F 177 " --> pdb=" O ALA F 173 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR F 178 " --> pdb=" O VAL F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 186 Processing helix chain 'F' and resid 196 through 214 removed outlier: 4.009A pdb=" N LEU F 204 " --> pdb=" O GLN F 200 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR F 205 " --> pdb=" O THR F 201 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN F 206 " --> pdb=" O GLN F 202 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU F 213 " --> pdb=" O ALA F 209 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER F 214 " --> pdb=" O MET F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 232 removed outlier: 3.961A pdb=" N TYR F 232 " --> pdb=" O TYR F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 236 No H-bonds generated for 'chain 'F' and resid 234 through 236' Processing helix chain 'F' and resid 237 through 260 removed outlier: 3.664A pdb=" N MET F 243 " --> pdb=" O SER F 239 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS F 244 " --> pdb=" O ALA F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 296 removed outlier: 4.177A pdb=" N ILE F 292 " --> pdb=" O GLY F 288 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA F 293 " --> pdb=" O GLY F 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 32 removed outlier: 3.512A pdb=" N GLY G 32 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 44 removed outlier: 3.781A pdb=" N VAL G 38 " --> pdb=" O ASN G 34 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS G 39 " --> pdb=" O ALA G 35 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA G 44 " --> pdb=" O LYS G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 54 Processing helix chain 'G' and resid 56 through 63 removed outlier: 3.920A pdb=" N LEU G 60 " --> pdb=" O PRO G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 82 removed outlier: 3.731A pdb=" N LYS G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU G 81 " --> pdb=" O GLU G 77 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL G 82 " --> pdb=" O ALA G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 97 Processing helix chain 'G' and resid 106 through 113 Processing helix chain 'G' and resid 132 through 144 removed outlier: 3.599A pdb=" N ILE G 136 " --> pdb=" O GLY G 132 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N CYS G 137 " --> pdb=" O LYS G 133 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL G 142 " --> pdb=" O HIS G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 146 No H-bonds generated for 'chain 'G' and resid 145 through 146' Processing helix chain 'G' and resid 147 through 151 Processing helix chain 'G' and resid 167 through 179 removed outlier: 3.895A pdb=" N LEU G 171 " --> pdb=" O ARG G 167 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG G 177 " --> pdb=" O ALA G 173 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR G 178 " --> pdb=" O VAL G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 186 Processing helix chain 'G' and resid 196 through 214 removed outlier: 4.009A pdb=" N LEU G 204 " --> pdb=" O GLN G 200 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR G 205 " --> pdb=" O THR G 201 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN G 206 " --> pdb=" O GLN G 202 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU G 213 " --> pdb=" O ALA G 209 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER G 214 " --> pdb=" O MET G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 232 removed outlier: 3.961A pdb=" N TYR G 232 " --> pdb=" O TYR G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 236 No H-bonds generated for 'chain 'G' and resid 234 through 236' Processing helix chain 'G' and resid 237 through 260 removed outlier: 3.662A pdb=" N MET G 243 " --> pdb=" O SER G 239 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS G 244 " --> pdb=" O ALA G 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 296 removed outlier: 4.177A pdb=" N ILE G 292 " --> pdb=" O GLY G 288 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA G 293 " --> pdb=" O GLY G 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 32 removed outlier: 3.512A pdb=" N GLY H 32 " --> pdb=" O GLU H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 44 removed outlier: 3.782A pdb=" N VAL H 38 " --> pdb=" O ASN H 34 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 54 Processing helix chain 'H' and resid 56 through 63 removed outlier: 3.921A pdb=" N LEU H 60 " --> pdb=" O PRO H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 82 removed outlier: 3.731A pdb=" N LYS H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU H 81 " --> pdb=" O GLU H 77 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL H 82 " --> pdb=" O ALA H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 97 Processing helix chain 'H' and resid 106 through 113 Processing helix chain 'H' and resid 132 through 144 removed outlier: 3.600A pdb=" N ILE H 136 " --> pdb=" O GLY H 132 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N CYS H 137 " --> pdb=" O LYS H 133 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL H 142 " --> pdb=" O HIS H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 146 No H-bonds generated for 'chain 'H' and resid 145 through 146' Processing helix chain 'H' and resid 147 through 151 Processing helix chain 'H' and resid 167 through 179 removed outlier: 3.895A pdb=" N LEU H 171 " --> pdb=" O ARG H 167 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG H 177 " --> pdb=" O ALA H 173 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR H 178 " --> pdb=" O VAL H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 186 Processing helix chain 'H' and resid 196 through 214 removed outlier: 4.008A pdb=" N LEU H 204 " --> pdb=" O GLN H 200 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR H 205 " --> pdb=" O THR H 201 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN H 206 " --> pdb=" O GLN H 202 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL H 212 " --> pdb=" O SER H 208 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU H 213 " --> pdb=" O ALA H 209 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER H 214 " --> pdb=" O MET H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 232 removed outlier: 3.961A pdb=" N TYR H 232 " --> pdb=" O TYR H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 234 through 236 No H-bonds generated for 'chain 'H' and resid 234 through 236' Processing helix chain 'H' and resid 237 through 260 removed outlier: 3.663A pdb=" N MET H 243 " --> pdb=" O SER H 239 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N HIS H 244 " --> pdb=" O ALA H 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 288 through 296 removed outlier: 4.177A pdb=" N ILE H 292 " --> pdb=" O GLY H 288 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA H 293 " --> pdb=" O GLY H 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 32 removed outlier: 3.513A pdb=" N GLY I 32 " --> pdb=" O GLU I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 44 removed outlier: 3.782A pdb=" N VAL I 38 " --> pdb=" O ASN I 34 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS I 39 " --> pdb=" O ALA I 35 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA I 44 " --> pdb=" O LYS I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 54 Processing helix chain 'I' and resid 56 through 63 removed outlier: 3.920A pdb=" N LEU I 60 " --> pdb=" O PRO I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 82 removed outlier: 3.731A pdb=" N LYS I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU I 81 " --> pdb=" O GLU I 77 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL I 82 " --> pdb=" O ALA I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 97 Processing helix chain 'I' and resid 106 through 113 Processing helix chain 'I' and resid 132 through 144 removed outlier: 3.600A pdb=" N ILE I 136 " --> pdb=" O GLY I 132 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N CYS I 137 " --> pdb=" O LYS I 133 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL I 142 " --> pdb=" O HIS I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 146 No H-bonds generated for 'chain 'I' and resid 145 through 146' Processing helix chain 'I' and resid 147 through 151 Processing helix chain 'I' and resid 167 through 179 removed outlier: 3.895A pdb=" N LEU I 171 " --> pdb=" O ARG I 167 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG I 177 " --> pdb=" O ALA I 173 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR I 178 " --> pdb=" O VAL I 174 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 186 Processing helix chain 'I' and resid 196 through 214 removed outlier: 4.008A pdb=" N LEU I 204 " --> pdb=" O GLN I 200 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR I 205 " --> pdb=" O THR I 201 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN I 206 " --> pdb=" O GLN I 202 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL I 212 " --> pdb=" O SER I 208 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU I 213 " --> pdb=" O ALA I 209 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER I 214 " --> pdb=" O MET I 210 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 232 removed outlier: 3.961A pdb=" N TYR I 232 " --> pdb=" O TYR I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 234 through 236 No H-bonds generated for 'chain 'I' and resid 234 through 236' Processing helix chain 'I' and resid 237 through 260 removed outlier: 3.663A pdb=" N MET I 243 " --> pdb=" O SER I 239 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N HIS I 244 " --> pdb=" O ALA I 240 " (cutoff:3.500A) Processing helix chain 'I' and resid 288 through 296 removed outlier: 4.178A pdb=" N ILE I 292 " --> pdb=" O GLY I 288 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA I 293 " --> pdb=" O GLY I 289 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88 removed outlier: 5.574A pdb=" N LYS B 156 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU B 218 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B 262 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR B 123 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ASN B 267 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET B 125 " --> pdb=" O ASN B 267 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE B 122 " --> pdb=" O THR B 298 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N LEU B 300 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLU B 124 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU B 302 " --> pdb=" O GLU B 124 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE B 126 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N LYS B 304 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG B 299 " --> pdb=" O TYR B 315 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 189 through 193 removed outlier: 5.574A pdb=" N LYS A 156 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 218 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA A 262 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR A 123 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ASN A 267 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET A 125 " --> pdb=" O ASN A 267 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE A 122 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N LEU A 300 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLU A 124 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU A 302 " --> pdb=" O GLU A 124 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE A 126 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N LYS A 304 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG A 299 " --> pdb=" O TYR A 315 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 271 Processing sheet with id=AA4, first strand: chain 'B' and resid 87 through 88 removed outlier: 5.573A pdb=" N LYS C 156 " --> pdb=" O TYR C 216 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU C 218 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA C 262 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR C 123 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ASN C 267 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET C 125 " --> pdb=" O ASN C 267 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE C 122 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N LEU C 300 " --> pdb=" O ILE C 122 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLU C 124 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU C 302 " --> pdb=" O GLU C 124 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE C 126 " --> pdb=" O LEU C 302 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N LYS C 304 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG C 299 " --> pdb=" O TYR C 315 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 269 through 271 Processing sheet with id=AA6, first strand: chain 'C' and resid 87 through 88 removed outlier: 5.574A pdb=" N LYS D 156 " --> pdb=" O TYR D 216 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU D 218 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA D 262 " --> pdb=" O ALA D 217 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N THR D 123 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ASN D 267 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET D 125 " --> pdb=" O ASN D 267 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE D 122 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N LEU D 300 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLU D 124 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU D 302 " --> pdb=" O GLU D 124 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE D 126 " --> pdb=" O LEU D 302 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N LYS D 304 " --> pdb=" O PHE D 126 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG D 299 " --> pdb=" O TYR D 315 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 269 through 271 Processing sheet with id=AA8, first strand: chain 'D' and resid 87 through 88 removed outlier: 5.573A pdb=" N LYS E 156 " --> pdb=" O TYR E 216 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU E 218 " --> pdb=" O LYS E 156 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA E 262 " --> pdb=" O ALA E 217 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N THR E 123 " --> pdb=" O ILE E 265 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ASN E 267 " --> pdb=" O THR E 123 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET E 125 " --> pdb=" O ASN E 267 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE E 122 " --> pdb=" O THR E 298 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N LEU E 300 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLU E 124 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU E 302 " --> pdb=" O GLU E 124 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE E 126 " --> pdb=" O LEU E 302 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N LYS E 304 " --> pdb=" O PHE E 126 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ARG E 299 " --> pdb=" O TYR E 315 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 269 through 271 Processing sheet with id=AB1, first strand: chain 'E' and resid 87 through 88 removed outlier: 5.573A pdb=" N LYS F 156 " --> pdb=" O TYR F 216 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU F 218 " --> pdb=" O LYS F 156 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA F 262 " --> pdb=" O ALA F 217 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR F 123 " --> pdb=" O ILE F 265 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ASN F 267 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET F 125 " --> pdb=" O ASN F 267 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE F 122 " --> pdb=" O THR F 298 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N LEU F 300 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLU F 124 " --> pdb=" O LEU F 300 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU F 302 " --> pdb=" O GLU F 124 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE F 126 " --> pdb=" O LEU F 302 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N LYS F 304 " --> pdb=" O PHE F 126 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ARG F 299 " --> pdb=" O TYR F 315 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 269 through 271 Processing sheet with id=AB3, first strand: chain 'F' and resid 87 through 88 removed outlier: 5.573A pdb=" N LYS G 156 " --> pdb=" O TYR G 216 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU G 218 " --> pdb=" O LYS G 156 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA G 262 " --> pdb=" O ALA G 217 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR G 123 " --> pdb=" O ILE G 265 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ASN G 267 " --> pdb=" O THR G 123 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N MET G 125 " --> pdb=" O ASN G 267 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE G 122 " --> pdb=" O THR G 298 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N LEU G 300 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLU G 124 " --> pdb=" O LEU G 300 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU G 302 " --> pdb=" O GLU G 124 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE G 126 " --> pdb=" O LEU G 302 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N LYS G 304 " --> pdb=" O PHE G 126 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG G 299 " --> pdb=" O TYR G 315 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 269 through 271 Processing sheet with id=AB5, first strand: chain 'G' and resid 87 through 88 removed outlier: 5.573A pdb=" N LYS H 156 " --> pdb=" O TYR H 216 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU H 218 " --> pdb=" O LYS H 156 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA H 262 " --> pdb=" O ALA H 217 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR H 123 " --> pdb=" O ILE H 265 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ASN H 267 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET H 125 " --> pdb=" O ASN H 267 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE H 122 " --> pdb=" O THR H 298 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N LEU H 300 " --> pdb=" O ILE H 122 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLU H 124 " --> pdb=" O LEU H 300 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU H 302 " --> pdb=" O GLU H 124 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE H 126 " --> pdb=" O LEU H 302 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N LYS H 304 " --> pdb=" O PHE H 126 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG H 299 " --> pdb=" O TYR H 315 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 269 through 271 Processing sheet with id=AB7, first strand: chain 'H' and resid 87 through 88 removed outlier: 5.574A pdb=" N LYS I 156 " --> pdb=" O TYR I 216 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU I 218 " --> pdb=" O LYS I 156 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA I 262 " --> pdb=" O ALA I 217 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR I 123 " --> pdb=" O ILE I 265 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ASN I 267 " --> pdb=" O THR I 123 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET I 125 " --> pdb=" O ASN I 267 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE I 122 " --> pdb=" O THR I 298 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N LEU I 300 " --> pdb=" O ILE I 122 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLU I 124 " --> pdb=" O LEU I 300 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU I 302 " --> pdb=" O GLU I 124 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE I 126 " --> pdb=" O LEU I 302 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N LYS I 304 " --> pdb=" O PHE I 126 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG I 299 " --> pdb=" O TYR I 315 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 269 through 271 Processing sheet with id=AB9, first strand: chain 'I' and resid 269 through 271 980 hydrogen bonds defined for protein. 2700 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 5.22 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7448 1.34 - 1.46: 4142 1.46 - 1.57: 10843 1.57 - 1.69: 104 1.69 - 1.81: 189 Bond restraints: 22726 Sorted by residual: bond pdb=" C5' DG W 29 " pdb=" C4' DG W 29 " ideal model delta sigma weight residual 1.512 1.551 -0.039 7.00e-03 2.04e+04 3.03e+01 bond pdb=" C3' DG W 20 " pdb=" C2' DG W 20 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.40e+01 bond pdb=" C5' DA W 9 " pdb=" C4' DA W 9 " ideal model delta sigma weight residual 1.512 1.536 -0.024 7.00e-03 2.04e+04 1.18e+01 bond pdb=" C3' DA W 27 " pdb=" C2' DA W 27 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DG W 14 " pdb=" O3' DG W 14 " ideal model delta sigma weight residual 1.435 1.396 0.039 1.30e-02 5.92e+03 9.16e+00 ... (remaining 22721 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 30193 1.61 - 3.21: 547 3.21 - 4.82: 85 4.82 - 6.42: 29 6.42 - 8.03: 1 Bond angle restraints: 30855 Sorted by residual: angle pdb=" O4' DG W 20 " pdb=" C1' DG W 20 " pdb=" N9 DG W 20 " ideal model delta sigma weight residual 108.00 99.97 8.03 7.00e-01 2.04e+00 1.32e+02 angle pdb=" O4' DG W 8 " pdb=" C4' DG W 8 " pdb=" C3' DG W 8 " ideal model delta sigma weight residual 106.00 101.82 4.18 6.00e-01 2.78e+00 4.84e+01 angle pdb=" O5' DG W 5 " pdb=" C5' DG W 5 " pdb=" C4' DG W 5 " ideal model delta sigma weight residual 109.40 114.05 -4.65 8.00e-01 1.56e+00 3.38e+01 angle pdb=" O4' DG W 29 " pdb=" C4' DG W 29 " pdb=" C3' DG W 29 " ideal model delta sigma weight residual 106.00 102.94 3.06 6.00e-01 2.78e+00 2.60e+01 angle pdb=" O5' DA W 9 " pdb=" C5' DA W 9 " pdb=" C4' DA W 9 " ideal model delta sigma weight residual 109.40 113.39 -3.99 8.00e-01 1.56e+00 2.49e+01 ... (remaining 30850 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 12353 16.69 - 33.37: 905 33.37 - 50.06: 220 50.06 - 66.74: 100 66.74 - 83.43: 25 Dihedral angle restraints: 13603 sinusoidal: 5647 harmonic: 7956 Sorted by residual: dihedral pdb=" CA ARG G 95 " pdb=" CB ARG G 95 " pdb=" CG ARG G 95 " pdb=" CD ARG G 95 " ideal model delta sinusoidal sigma weight residual -60.00 -119.32 59.32 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG B 95 " pdb=" CB ARG B 95 " pdb=" CG ARG B 95 " pdb=" CD ARG B 95 " ideal model delta sinusoidal sigma weight residual -60.00 -119.31 59.31 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG E 95 " pdb=" CB ARG E 95 " pdb=" CG ARG E 95 " pdb=" CD ARG E 95 " ideal model delta sinusoidal sigma weight residual -60.00 -119.30 59.30 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 13600 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2899 0.051 - 0.101: 496 0.101 - 0.152: 108 0.152 - 0.203: 0 0.203 - 0.253: 1 Chirality restraints: 3504 Sorted by residual: chirality pdb=" P DA W 6 " pdb=" OP1 DA W 6 " pdb=" OP2 DA W 6 " pdb=" O5' DA W 6 " both_signs ideal model delta sigma weight residual True 2.34 -2.08 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" C1' DG W 20 " pdb=" O4' DG W 20 " pdb=" C2' DG W 20 " pdb=" N9 DG W 20 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 chirality pdb=" C4' DG W 17 " pdb=" C5' DG W 17 " pdb=" O4' DG W 17 " pdb=" C3' DG W 17 " both_signs ideal model delta sigma weight residual False -2.53 -2.41 -0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 3501 not shown) Planarity restraints: 3846 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG W 20 " -0.046 2.00e-02 2.50e+03 4.33e-02 5.63e+01 pdb=" N9 DG W 20 " 0.034 2.00e-02 2.50e+03 pdb=" C8 DG W 20 " -0.062 2.00e-02 2.50e+03 pdb=" N7 DG W 20 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DG W 20 " 0.015 2.00e-02 2.50e+03 pdb=" C6 DG W 20 " -0.008 2.00e-02 2.50e+03 pdb=" O6 DG W 20 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG W 20 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG W 20 " 0.003 2.00e-02 2.50e+03 pdb=" N2 DG W 20 " -0.064 2.00e-02 2.50e+03 pdb=" N3 DG W 20 " 0.058 2.00e-02 2.50e+03 pdb=" C4 DG W 20 " 0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG W 17 " -0.042 2.00e-02 2.50e+03 4.30e-02 5.54e+01 pdb=" N9 DG W 17 " -0.015 2.00e-02 2.50e+03 pdb=" C8 DG W 17 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG W 17 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG W 17 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DG W 17 " -0.002 2.00e-02 2.50e+03 pdb=" O6 DG W 17 " -0.004 2.00e-02 2.50e+03 pdb=" N1 DG W 17 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG W 17 " -0.030 2.00e-02 2.50e+03 pdb=" N2 DG W 17 " -0.045 2.00e-02 2.50e+03 pdb=" N3 DG W 17 " 0.131 2.00e-02 2.50e+03 pdb=" C4 DG W 17 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG W 4 " 0.020 2.00e-02 2.50e+03 4.02e-02 4.85e+01 pdb=" N9 DG W 4 " -0.004 2.00e-02 2.50e+03 pdb=" C8 DG W 4 " 0.000 2.00e-02 2.50e+03 pdb=" N7 DG W 4 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DG W 4 " -0.045 2.00e-02 2.50e+03 pdb=" C6 DG W 4 " 0.064 2.00e-02 2.50e+03 pdb=" O6 DG W 4 " -0.003 2.00e-02 2.50e+03 pdb=" N1 DG W 4 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DG W 4 " -0.005 2.00e-02 2.50e+03 pdb=" N2 DG W 4 " -0.027 2.00e-02 2.50e+03 pdb=" N3 DG W 4 " 0.075 2.00e-02 2.50e+03 pdb=" C4 DG W 4 " -0.079 2.00e-02 2.50e+03 ... (remaining 3843 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3155 2.76 - 3.29: 20542 3.29 - 3.83: 35205 3.83 - 4.36: 42507 4.36 - 4.90: 73823 Nonbonded interactions: 175232 Sorted by model distance: nonbonded pdb=" OG1 THR B 103 " pdb=" OD2 ASP B 110 " model vdw 2.219 3.040 nonbonded pdb=" OG1 THR D 103 " pdb=" OD2 ASP D 110 " model vdw 2.220 3.040 nonbonded pdb=" OG1 THR E 103 " pdb=" OD2 ASP E 110 " model vdw 2.220 3.040 nonbonded pdb=" OG1 THR A 103 " pdb=" OD2 ASP A 110 " model vdw 2.220 3.040 nonbonded pdb=" OG1 THR C 103 " pdb=" OD2 ASP C 110 " model vdw 2.220 3.040 ... (remaining 175227 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 21 through 402) selection = (chain 'B' and resid 21 through 401) selection = (chain 'C' and resid 21 through 401) selection = (chain 'D' and resid 21 through 401) selection = (chain 'E' and resid 21 through 401) selection = (chain 'F' and resid 21 through 401) selection = (chain 'G' and resid 21 through 401) selection = (chain 'H' and resid 21 through 401) selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 24.810 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 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 : 0.003 0.055 22726 Z= 0.187 Angle : 0.555 8.028 30855 Z= 0.366 Chirality : 0.039 0.253 3504 Planarity : 0.006 0.061 3846 Dihedral : 13.732 83.429 8509 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.15), residues: 2754 helix: -0.20 (0.14), residues: 1260 sheet: 2.47 (0.24), residues: 468 loop : -1.59 (0.16), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG G 229 TYR 0.018 0.002 TYR F 228 PHE 0.015 0.002 PHE F 195 HIS 0.014 0.003 HIS F 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.19 (22726) covalent geometry : angle 0.55514 / 0.37 (30855) hydrogen bonds : bond 0.18017 / 12.17 ( 980) hydrogen bonds : angle 7.27245 / 5.05 ( 2700) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8045 (mmm) cc_final: 0.7703 (mtt) REVERT: A 253 LEU cc_start: 0.9290 (tp) cc_final: 0.8935 (tt) REVERT: B 36 ASN cc_start: 0.7169 (t0) cc_final: 0.6969 (t0) REVERT: C 36 ASN cc_start: 0.8119 (t0) cc_final: 0.7893 (t0) REVERT: C 251 MET cc_start: 0.8038 (tpp) cc_final: 0.7749 (tpt) REVERT: E 36 ASN cc_start: 0.7981 (t0) cc_final: 0.7719 (t0) REVERT: E 222 ASP cc_start: 0.8265 (t0) cc_final: 0.7925 (t70) REVERT: E 326 MET cc_start: 0.8111 (ttm) cc_final: 0.7895 (ttt) REVERT: I 34 ASN cc_start: 0.8241 (p0) cc_final: 0.7993 (p0) REVERT: I 62 ASN cc_start: 0.8303 (m-40) cc_final: 0.7775 (m110) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.1800 time to fit residues: 53.3484 Evaluate side-chains 113 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 50.0000 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 244 HIS H 244 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.070729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.053181 restraints weight = 65328.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.054747 restraints weight = 37564.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.055777 restraints weight = 26479.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.056373 restraints weight = 21267.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.056856 restraints weight = 18647.946| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22726 Z= 0.156 Angle : 0.527 8.249 30855 Z= 0.283 Chirality : 0.041 0.167 3504 Planarity : 0.004 0.042 3846 Dihedral : 12.103 81.827 3415 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.54 % Allowed : 8.20 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.15), residues: 2754 helix: 0.05 (0.14), residues: 1278 sheet: 2.51 (0.24), residues: 450 loop : -1.66 (0.16), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 306 TYR 0.010 0.001 TYR D 315 PHE 0.019 0.001 PHE C 259 HIS 0.003 0.001 HIS F 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 (22726) covalent geometry : angle 0.52750 / 0.28 (30855) hydrogen bonds : bond 0.04209 / 2.90 ( 980) hydrogen bonds : angle 5.51568 / 3.83 ( 2700) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8334 (mmm) cc_final: 0.7954 (mtt) REVERT: B 84 MET cc_start: 0.8374 (mmm) cc_final: 0.7876 (mtt) REVERT: C 84 MET cc_start: 0.8675 (mmm) cc_final: 0.8257 (mtt) REVERT: C 251 MET cc_start: 0.8127 (tpp) cc_final: 0.7841 (tpt) REVERT: E 36 ASN cc_start: 0.8228 (t0) cc_final: 0.7852 (t0) REVERT: E 222 ASP cc_start: 0.8314 (t0) cc_final: 0.8068 (t70) REVERT: E 326 MET cc_start: 0.8125 (ttm) cc_final: 0.7881 (ttt) REVERT: I 34 ASN cc_start: 0.8690 (p0) cc_final: 0.8402 (p0) REVERT: I 62 ASN cc_start: 0.8460 (m-40) cc_final: 0.7719 (m-40) outliers start: 12 outliers final: 9 residues processed: 129 average time/residue: 0.1486 time to fit residues: 30.9346 Evaluate side-chains 116 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 38 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 252 optimal weight: 0.6980 chunk 243 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 chunk 232 optimal weight: 9.9990 chunk 140 optimal weight: 2.9990 chunk 277 optimal weight: 7.9990 chunk 101 optimal weight: 0.3980 chunk 262 optimal weight: 9.9990 chunk 257 optimal weight: 8.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 36 ASN D 244 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.070000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.052222 restraints weight = 65527.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.053793 restraints weight = 38026.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.054811 restraints weight = 26889.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.055393 restraints weight = 21727.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.055839 restraints weight = 19133.448| |-----------------------------------------------------------------------------| r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22726 Z= 0.143 Angle : 0.483 6.306 30855 Z= 0.259 Chirality : 0.041 0.144 3504 Planarity : 0.003 0.042 3846 Dihedral : 12.108 80.576 3415 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.99 % Allowed : 8.38 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.16), residues: 2754 helix: 0.30 (0.15), residues: 1278 sheet: 2.75 (0.24), residues: 432 loop : -1.58 (0.16), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 306 TYR 0.013 0.001 TYR D 315 PHE 0.022 0.001 PHE I 259 HIS 0.004 0.001 HIS E 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (22726) covalent geometry : angle 0.48317 / 0.26 (30855) hydrogen bonds : bond 0.03582 / 2.46 ( 980) hydrogen bonds : angle 4.92131 / 3.44 ( 2700) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8600 (mmm) cc_final: 0.8162 (mtt) REVERT: B 84 MET cc_start: 0.8421 (mmm) cc_final: 0.7991 (mtt) REVERT: C 84 MET cc_start: 0.8686 (mmm) cc_final: 0.8352 (mtt) REVERT: C 251 MET cc_start: 0.8154 (tpp) cc_final: 0.7892 (tpp) REVERT: E 36 ASN cc_start: 0.8245 (t0) cc_final: 0.7865 (t0) REVERT: E 222 ASP cc_start: 0.8227 (t0) cc_final: 0.7953 (t70) REVERT: E 326 MET cc_start: 0.8130 (ttm) cc_final: 0.7911 (ttt) REVERT: F 326 MET cc_start: 0.8160 (tpp) cc_final: 0.7914 (ttt) REVERT: I 34 ASN cc_start: 0.8754 (p0) cc_final: 0.8419 (p0) outliers start: 22 outliers final: 13 residues processed: 128 average time/residue: 0.1411 time to fit residues: 29.7192 Evaluate side-chains 120 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 254 optimal weight: 10.0000 chunk 213 optimal weight: 9.9990 chunk 228 optimal weight: 1.9990 chunk 178 optimal weight: 0.9980 chunk 176 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 177 optimal weight: 0.8980 chunk 114 optimal weight: 9.9990 chunk 233 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 36 ASN F 244 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.068944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.051190 restraints weight = 65822.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.052703 restraints weight = 38238.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.053707 restraints weight = 27187.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.054274 restraints weight = 21987.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.054746 restraints weight = 19395.581| |-----------------------------------------------------------------------------| r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22726 Z= 0.170 Angle : 0.507 9.578 30855 Z= 0.269 Chirality : 0.041 0.182 3504 Planarity : 0.003 0.044 3846 Dihedral : 12.171 79.696 3415 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.08 % Allowed : 8.74 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.16), residues: 2754 helix: 0.49 (0.15), residues: 1278 sheet: 2.55 (0.26), residues: 423 loop : -1.43 (0.17), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 310 TYR 0.018 0.001 TYR C 315 PHE 0.026 0.002 PHE I 259 HIS 0.006 0.001 HIS E 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (22726) covalent geometry : angle 0.50737 / 0.27 (30855) hydrogen bonds : bond 0.03457 / 2.35 ( 980) hydrogen bonds : angle 4.71097 / 3.30 ( 2700) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.804 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.8513 (mmm) cc_final: 0.8228 (mtt) REVERT: A 326 MET cc_start: 0.8513 (tpp) cc_final: 0.8261 (mmm) REVERT: C 84 MET cc_start: 0.8700 (mmm) cc_final: 0.8445 (mtt) REVERT: D 27 ARG cc_start: 0.7250 (tpp-160) cc_final: 0.6945 (tpm170) REVERT: E 36 ASN cc_start: 0.8157 (t0) cc_final: 0.7763 (t0) REVERT: E 222 ASP cc_start: 0.8244 (t0) cc_final: 0.7808 (t70) REVERT: E 326 MET cc_start: 0.8123 (ttm) cc_final: 0.7713 (mtp) REVERT: F 72 ASP cc_start: 0.7521 (m-30) cc_final: 0.7272 (m-30) REVERT: F 326 MET cc_start: 0.8160 (tpp) cc_final: 0.7911 (ttt) REVERT: I 34 ASN cc_start: 0.8816 (p0) cc_final: 0.8497 (p0) outliers start: 24 outliers final: 15 residues processed: 130 average time/residue: 0.1420 time to fit residues: 30.0898 Evaluate side-chains 123 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 184 optimal weight: 8.9990 chunk 218 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 243 optimal weight: 8.9990 chunk 237 optimal weight: 5.9990 chunk 239 optimal weight: 0.8980 chunk 274 optimal weight: 9.9990 chunk 134 optimal weight: 9.9990 chunk 178 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 244 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.067785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.050080 restraints weight = 65585.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.051565 restraints weight = 38165.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.052549 restraints weight = 27223.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.053066 restraints weight = 22004.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.053505 restraints weight = 19516.783| |-----------------------------------------------------------------------------| r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 22726 Z= 0.213 Angle : 0.539 7.375 30855 Z= 0.284 Chirality : 0.042 0.165 3504 Planarity : 0.004 0.046 3846 Dihedral : 12.238 80.111 3415 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.99 % Allowed : 9.36 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.16), residues: 2754 helix: 0.58 (0.15), residues: 1278 sheet: 2.36 (0.26), residues: 423 loop : -1.44 (0.17), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 306 TYR 0.023 0.002 TYR D 315 PHE 0.016 0.002 PHE G 248 HIS 0.007 0.001 HIS E 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.21 (22726) covalent geometry : angle 0.53941 / 0.28 (30855) hydrogen bonds : bond 0.03695 / 2.51 ( 980) hydrogen bonds : angle 4.71144 / 3.30 ( 2700) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.756 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.8514 (mmm) cc_final: 0.8194 (mtt) REVERT: D 27 ARG cc_start: 0.7534 (tpp-160) cc_final: 0.7040 (tpm170) REVERT: E 36 ASN cc_start: 0.8108 (t0) cc_final: 0.7676 (t0) REVERT: E 222 ASP cc_start: 0.8276 (t0) cc_final: 0.7868 (t70) REVERT: E 326 MET cc_start: 0.8167 (ttm) cc_final: 0.7800 (mtp) REVERT: F 72 ASP cc_start: 0.7529 (m-30) cc_final: 0.7285 (m-30) REVERT: F 326 MET cc_start: 0.8167 (tpp) cc_final: 0.7926 (ttt) REVERT: I 34 ASN cc_start: 0.8873 (p0) cc_final: 0.8590 (p0) outliers start: 22 outliers final: 19 residues processed: 125 average time/residue: 0.1507 time to fit residues: 30.0744 Evaluate side-chains 126 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 83 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 281 optimal weight: 20.0000 chunk 173 optimal weight: 7.9990 chunk 201 optimal weight: 2.9990 chunk 219 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 248 optimal weight: 40.0000 chunk 270 optimal weight: 3.9990 chunk 220 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 244 HIS C 244 HIS E 199 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.067878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.049976 restraints weight = 66117.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.051487 restraints weight = 38643.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.052474 restraints weight = 27518.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.053086 restraints weight = 22369.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.053426 restraints weight = 19722.501| |-----------------------------------------------------------------------------| r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22726 Z= 0.185 Angle : 0.500 6.713 30855 Z= 0.265 Chirality : 0.041 0.153 3504 Planarity : 0.003 0.032 3846 Dihedral : 12.224 81.187 3415 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.08 % Allowed : 9.32 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.16), residues: 2754 helix: 0.63 (0.15), residues: 1278 sheet: 2.24 (0.26), residues: 423 loop : -1.43 (0.17), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 306 TYR 0.017 0.001 TYR D 315 PHE 0.015 0.001 PHE G 248 HIS 0.005 0.001 HIS C 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (22726) covalent geometry : angle 0.50042 / 0.26 (30855) hydrogen bonds : bond 0.03460 / 2.35 ( 980) hydrogen bonds : angle 4.54887 / 3.18 ( 2700) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.791 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.8556 (mmm) cc_final: 0.8206 (mtt) REVERT: A 158 MET cc_start: 0.8291 (ttm) cc_final: 0.7896 (mtp) REVERT: D 27 ARG cc_start: 0.7583 (tpp-160) cc_final: 0.6963 (tpm170) REVERT: E 36 ASN cc_start: 0.8117 (t0) cc_final: 0.7666 (t0) REVERT: E 326 MET cc_start: 0.8241 (ttm) cc_final: 0.7890 (mtp) REVERT: F 326 MET cc_start: 0.8154 (tpp) cc_final: 0.7923 (ttt) REVERT: I 34 ASN cc_start: 0.8948 (p0) cc_final: 0.8694 (p0) outliers start: 24 outliers final: 20 residues processed: 125 average time/residue: 0.1520 time to fit residues: 30.7970 Evaluate side-chains 125 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 63 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 262 optimal weight: 10.0000 chunk 195 optimal weight: 8.9990 chunk 162 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 125 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 chunk 267 optimal weight: 0.5980 chunk 97 optimal weight: 9.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.067389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.049504 restraints weight = 65671.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.050974 restraints weight = 38624.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.051948 restraints weight = 27753.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.052570 restraints weight = 22569.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.052887 restraints weight = 19842.972| |-----------------------------------------------------------------------------| r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 22726 Z= 0.202 Angle : 0.521 6.911 30855 Z= 0.274 Chirality : 0.042 0.162 3504 Planarity : 0.003 0.045 3846 Dihedral : 12.270 83.026 3415 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.30 % Allowed : 9.36 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.16), residues: 2754 helix: 0.66 (0.15), residues: 1278 sheet: 2.10 (0.26), residues: 423 loop : -1.51 (0.17), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 306 TYR 0.021 0.002 TYR D 315 PHE 0.014 0.002 PHE B 166 HIS 0.006 0.001 HIS E 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 (22726) covalent geometry : angle 0.52118 / 0.27 (30855) hydrogen bonds : bond 0.03623 / 2.45 ( 980) hydrogen bonds : angle 4.53167 / 3.17 ( 2700) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.796 Fit side-chains REVERT: A 84 MET cc_start: 0.8597 (mmm) cc_final: 0.8313 (mtt) REVERT: A 158 MET cc_start: 0.8214 (ttm) cc_final: 0.7861 (mtp) REVERT: D 27 ARG cc_start: 0.7605 (tpp-160) cc_final: 0.7329 (tpm170) REVERT: D 158 MET cc_start: 0.8233 (ttm) cc_final: 0.8030 (ttm) REVERT: D 235 ARG cc_start: 0.7534 (tpt90) cc_final: 0.7323 (tpt90) REVERT: E 36 ASN cc_start: 0.8142 (t0) cc_final: 0.7697 (t0) REVERT: E 326 MET cc_start: 0.8226 (ttm) cc_final: 0.7906 (mtp) REVERT: G 27 ARG cc_start: 0.7775 (tpp-160) cc_final: 0.7198 (tpm170) REVERT: I 34 ASN cc_start: 0.8965 (p0) cc_final: 0.8731 (p0) REVERT: I 158 MET cc_start: 0.8446 (ttm) cc_final: 0.8025 (ttm) outliers start: 29 outliers final: 25 residues processed: 130 average time/residue: 0.1536 time to fit residues: 31.1747 Evaluate side-chains 134 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 57 optimal weight: 5.9990 chunk 245 optimal weight: 10.0000 chunk 281 optimal weight: 20.0000 chunk 64 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 44 optimal weight: 20.0000 chunk 35 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 123 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.068296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.050353 restraints weight = 65487.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.051869 restraints weight = 38533.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.052851 restraints weight = 27555.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.053507 restraints weight = 22376.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.053826 restraints weight = 19599.592| |-----------------------------------------------------------------------------| r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22726 Z= 0.126 Angle : 0.475 13.599 30855 Z= 0.250 Chirality : 0.040 0.141 3504 Planarity : 0.003 0.046 3846 Dihedral : 12.235 83.440 3415 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.90 % Allowed : 9.95 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.16), residues: 2754 helix: 0.97 (0.15), residues: 1215 sheet: 2.17 (0.26), residues: 423 loop : -1.03 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 306 TYR 0.010 0.001 TYR D 315 PHE 0.037 0.001 PHE I 259 HIS 0.002 0.000 HIS F 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (22726) covalent geometry : angle 0.47518 / 0.25 (30855) hydrogen bonds : bond 0.03136 / 2.13 ( 980) hydrogen bonds : angle 4.36456 / 3.05 ( 2700) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.854 Fit side-chains REVERT: A 84 MET cc_start: 0.8594 (mmm) cc_final: 0.8289 (mtt) REVERT: A 158 MET cc_start: 0.8161 (ttm) cc_final: 0.7832 (mtp) REVERT: D 27 ARG cc_start: 0.7676 (tpp-160) cc_final: 0.7376 (tpm170) REVERT: D 158 MET cc_start: 0.8148 (ttm) cc_final: 0.7947 (ttm) REVERT: D 235 ARG cc_start: 0.7575 (tpt90) cc_final: 0.7265 (tpt-90) REVERT: E 36 ASN cc_start: 0.8103 (t0) cc_final: 0.7727 (t0) REVERT: E 326 MET cc_start: 0.8131 (ttm) cc_final: 0.7807 (mtp) REVERT: F 72 ASP cc_start: 0.7754 (m-30) cc_final: 0.7485 (m-30) REVERT: G 27 ARG cc_start: 0.7802 (tpp-160) cc_final: 0.7391 (tpm170) REVERT: I 34 ASN cc_start: 0.8965 (p0) cc_final: 0.8732 (p0) outliers start: 20 outliers final: 19 residues processed: 128 average time/residue: 0.1595 time to fit residues: 31.4012 Evaluate side-chains 129 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 232 optimal weight: 8.9990 chunk 146 optimal weight: 4.9990 chunk 252 optimal weight: 7.9990 chunk 194 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 230 optimal weight: 20.0000 chunk 51 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 36 ASN G 244 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.067302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.049354 restraints weight = 65995.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.050831 restraints weight = 38916.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.051723 restraints weight = 27997.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.052387 restraints weight = 22951.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.052730 restraints weight = 20191.792| |-----------------------------------------------------------------------------| r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 22726 Z= 0.213 Angle : 0.531 15.969 30855 Z= 0.277 Chirality : 0.042 0.260 3504 Planarity : 0.003 0.051 3846 Dihedral : 12.292 85.294 3415 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.94 % Allowed : 10.04 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.16), residues: 2754 helix: 0.98 (0.15), residues: 1215 sheet: 2.09 (0.26), residues: 423 loop : -1.11 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 27 TYR 0.020 0.002 TYR D 315 PHE 0.019 0.002 PHE B 46 HIS 0.006 0.001 HIS D 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 (22726) covalent geometry : angle 0.53144 / 0.28 (30855) hydrogen bonds : bond 0.03585 / 2.43 ( 980) hydrogen bonds : angle 4.47448 / 3.13 ( 2700) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.709 Fit side-chains REVERT: A 84 MET cc_start: 0.8608 (mmm) cc_final: 0.8326 (mtt) REVERT: A 158 MET cc_start: 0.8204 (ttm) cc_final: 0.7881 (mtp) REVERT: D 27 ARG cc_start: 0.7669 (tpp-160) cc_final: 0.7224 (tpm170) REVERT: E 36 ASN cc_start: 0.8153 (t0) cc_final: 0.7757 (t0) REVERT: E 326 MET cc_start: 0.8219 (ttm) cc_final: 0.7893 (mtp) REVERT: F 72 ASP cc_start: 0.7656 (m-30) cc_final: 0.7446 (m-30) REVERT: G 27 ARG cc_start: 0.7809 (tpp-160) cc_final: 0.7425 (tpm170) REVERT: I 34 ASN cc_start: 0.8974 (p0) cc_final: 0.8743 (p0) outliers start: 21 outliers final: 21 residues processed: 120 average time/residue: 0.1443 time to fit residues: 28.3499 Evaluate side-chains 127 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 227 optimal weight: 9.9990 chunk 165 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 264 optimal weight: 0.0870 chunk 42 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 266 optimal weight: 2.9990 chunk 200 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.068722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.050953 restraints weight = 65366.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.052458 restraints weight = 38174.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.053449 restraints weight = 27301.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.054019 restraints weight = 22144.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.054491 restraints weight = 19523.314| |-----------------------------------------------------------------------------| r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22726 Z= 0.101 Angle : 0.465 15.316 30855 Z= 0.246 Chirality : 0.040 0.137 3504 Planarity : 0.003 0.034 3846 Dihedral : 12.227 85.395 3415 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.76 % Allowed : 10.22 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.16), residues: 2754 helix: 1.03 (0.16), residues: 1215 sheet: 2.14 (0.26), residues: 423 loop : -1.07 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 306 TYR 0.008 0.001 TYR D 191 PHE 0.023 0.001 PHE I 259 HIS 0.002 0.001 HIS G 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (22726) covalent geometry : angle 0.46490 / 0.25 (30855) hydrogen bonds : bond 0.02844 / 1.94 ( 980) hydrogen bonds : angle 4.19139 / 2.93 ( 2700) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.816 Fit side-chains REVERT: A 84 MET cc_start: 0.8690 (mmm) cc_final: 0.8316 (mtt) REVERT: A 158 MET cc_start: 0.8153 (ttm) cc_final: 0.7867 (mtp) REVERT: A 326 MET cc_start: 0.8378 (mmm) cc_final: 0.8072 (tpt) REVERT: D 27 ARG cc_start: 0.7629 (tpp-160) cc_final: 0.7237 (tpm170) REVERT: E 36 ASN cc_start: 0.8054 (t0) cc_final: 0.7703 (t0) REVERT: E 222 ASP cc_start: 0.8194 (t0) cc_final: 0.7819 (t70) REVERT: E 326 MET cc_start: 0.8120 (ttm) cc_final: 0.7843 (mtp) REVERT: F 72 ASP cc_start: 0.7654 (m-30) cc_final: 0.7423 (m-30) REVERT: G 27 ARG cc_start: 0.7788 (tpp-160) cc_final: 0.7448 (tpm170) REVERT: G 84 MET cc_start: 0.8580 (mmm) cc_final: 0.8275 (mmm) REVERT: I 34 ASN cc_start: 0.8964 (p0) cc_final: 0.8735 (p0) outliers start: 17 outliers final: 13 residues processed: 121 average time/residue: 0.1578 time to fit residues: 31.1558 Evaluate side-chains 122 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 181 optimal weight: 8.9990 chunk 176 optimal weight: 0.0980 chunk 231 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 236 optimal weight: 10.0000 chunk 276 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.069393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.051905 restraints weight = 64072.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.053469 restraints weight = 36749.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.054497 restraints weight = 25995.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.055160 restraints weight = 20939.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.055565 restraints weight = 18311.041| |-----------------------------------------------------------------------------| r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22726 Z= 0.117 Angle : 0.457 14.565 30855 Z= 0.242 Chirality : 0.040 0.148 3504 Planarity : 0.003 0.033 3846 Dihedral : 12.196 86.653 3415 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.63 % Allowed : 10.30 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.16), residues: 2754 helix: 1.09 (0.16), residues: 1215 sheet: 2.15 (0.26), residues: 423 loop : -1.04 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 306 TYR 0.010 0.001 TYR C 315 PHE 0.018 0.001 PHE I 259 HIS 0.003 0.000 HIS D 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (22726) covalent geometry : angle 0.45745 / 0.24 (30855) hydrogen bonds : bond 0.02877 / 1.96 ( 980) hydrogen bonds : angle 4.15047 / 2.90 ( 2700) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2949.92 seconds wall clock time: 52 minutes 5.74 seconds (3125.74 seconds total)