Starting phenix.real_space_refine on Fri Aug 7 14:26:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8bq2_16170/08_2026/8bq2_16170.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bq2_16170/08_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_16170/08_2026/8bq2_16170.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bq2_16170/08_2026/8bq2_16170.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bq2_16170/08_2026/8bq2_16170.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bq2_16170/08_2026/8bq2_16170.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8bq2_16170/08_2026/8bq2_16170.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8bq2_16170/08_2026/8bq2_16170.cif" } 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-2.2rc3-6140/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: 6.09, per 1000 atoms: 0.27 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 849.8 milliseconds 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: 2.54 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: 4.18 Time building geometry restraints manager: 2.45 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: 30194 1.61 - 3.21: 546 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 23.680 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.720 ------------------------------------------------------------------------------- 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 : 0.556 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 0.55551 / 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 : 0.764 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: 0.7702 (mtt) REVERT: A 253 LEU cc_start: 0.9290 (tp) cc_final: 0.8934 (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: 0.7748 (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: 0.7924 (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: 0.1968 time to fit residues: 58.1643 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 : 0.901 ------------------------------------------------------------------------------- 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 = 0.3135 r_free = 0.3135 target = 0.070743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.053231 restraints weight = 65325.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.054795 restraints weight = 37420.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.055813 restraints weight = 26352.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.056494 restraints weight = 21219.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.056863 restraints weight = 18455.673| |-----------------------------------------------------------------------------| r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22726 Z= 0.151 Angle : 0.527 7.579 30855 Z= 0.282 Chirality : 0.041 0.164 3504 Planarity : 0.004 0.043 3846 Dihedral : 12.112 81.763 3415 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.54 % Allowed : 8.24 % Favored : 91.22 % 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: 2.49 (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 0.023 0.001 PHE C 259 HIS 0.003 0.001 HIS F 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (22726) covalent geometry : angle 0.52733 / 0.28 (30855) hydrogen bonds : bond 0.04133 / 2.85 ( 980) hydrogen bonds : angle 5.51159 / 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 135 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8335 (mmm) cc_final: 0.7960 (mtt) REVERT: B 84 MET cc_start: 0.8373 (mmm) cc_final: 0.7883 (mtt) REVERT: C 84 MET cc_start: 0.8674 (mmm) cc_final: 0.8259 (mtt) REVERT: C 251 MET cc_start: 0.8131 (tpp) cc_final: 0.7846 (tpt) REVERT: E 36 ASN cc_start: 0.8238 (t0) cc_final: 0.7856 (t0) REVERT: E 222 ASP cc_start: 0.8316 (t0) cc_final: 0.8074 (t70) REVERT: E 326 MET cc_start: 0.8127 (ttm) cc_final: 0.7882 (ttt) REVERT: H 211 MET cc_start: 0.8579 (ttm) cc_final: 0.8299 (ttm) REVERT: I 34 ASN cc_start: 0.8695 (p0) cc_final: 0.8407 (p0) REVERT: I 62 ASN cc_start: 0.8455 (m-40) cc_final: 0.7715 (m-40) outliers start: 12 outliers final: 9 residues processed: 130 average time/residue: 0.1602 time to fit residues: 33.8492 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 : 0.894 ------------------------------------------------------------------------------- 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: 2.9990 chunk 178 optimal weight: 2.9990 chunk 252 optimal weight: 0.7980 chunk 243 optimal weight: 0.0970 chunk 153 optimal weight: 2.9990 chunk 232 optimal weight: 9.9990 chunk 140 optimal weight: 7.9990 chunk 277 optimal weight: 8.9990 chunk 101 optimal weight: 0.8980 chunk 262 optimal weight: 10.0000 chunk 257 optimal weight: 6.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- 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 = 0.3134 r_free = 0.3134 target = 0.070766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.053175 restraints weight = 65170.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.054740 restraints weight = 37289.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.055781 restraints weight = 26276.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.056390 restraints weight = 21054.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.056864 restraints weight = 18451.356| |-----------------------------------------------------------------------------| r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22726 Z= 0.111 Angle : 0.461 7.357 30855 Z= 0.248 Chirality : 0.040 0.145 3504 Planarity : 0.003 0.041 3846 Dihedral : 12.107 80.948 3415 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.90 % Allowed : 8.38 % Favored : 90.73 % 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: 0.02 (0.16), residues: 2754 helix: 0.29 (0.15), residues: 1278 sheet: 2.80 (0.24), residues: 432 loop : -1.56 (0.16), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 306 TYR 0.011 0.001 TYR I 216 PHE 0.016 0.001 PHE I 259 HIS 0.002 0.000 HIS F 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (22726) covalent geometry : angle 0.46097 / 0.25 (30855) hydrogen bonds : bond 0.03378 / 2.33 ( 980) hydrogen bonds : angle 4.84121 / 3.39 ( 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: 20 poor density : 117 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8551 (mmm) cc_final: 0.8115 (mtt) REVERT: B 84 MET cc_start: 0.8392 (mmm) cc_final: 0.7943 (mtt) REVERT: C 84 MET cc_start: 0.8648 (mmm) cc_final: 0.8286 (mtt) REVERT: C 251 MET cc_start: 0.8107 (tpp) cc_final: 0.7848 (tpp) REVERT: E 36 ASN cc_start: 0.8198 (t0) cc_final: 0.7844 (t0) REVERT: E 222 ASP cc_start: 0.8184 (t0) cc_final: 0.7920 (t70) REVERT: E 326 MET cc_start: 0.8097 (ttm) cc_final: 0.7878 (ttt) REVERT: F 326 MET cc_start: 0.8142 (tpp) cc_final: 0.7895 (ttt) REVERT: I 34 ASN cc_start: 0.8725 (p0) cc_final: 0.8370 (p0) outliers start: 20 outliers final: 10 residues processed: 128 average time/residue: 0.1385 time to fit residues: 29.3896 Evaluate side-chains 117 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 270 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 254 optimal weight: 9.9990 chunk 213 optimal weight: 4.9990 chunk 228 optimal weight: 6.9990 chunk 178 optimal weight: 0.8980 chunk 176 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 177 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 233 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 36 ASN F 244 HIS ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.069461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.051740 restraints weight = 65837.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.053263 restraints weight = 38278.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.054276 restraints weight = 27233.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.054813 restraints weight = 21978.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.055292 restraints weight = 19460.297| |-----------------------------------------------------------------------------| r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22726 Z= 0.154 Angle : 0.491 7.985 30855 Z= 0.260 Chirality : 0.041 0.203 3504 Planarity : 0.003 0.041 3846 Dihedral : 12.154 81.017 3415 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.12 % Allowed : 8.60 % Favored : 90.28 % 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 (0.16), residues: 2754 helix: 0.51 (0.15), residues: 1278 sheet: 2.80 (0.25), residues: 414 loop : -1.39 (0.16), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 310 TYR 0.016 0.001 TYR C 315 PHE 0.029 0.001 PHE I 259 HIS 0.006 0.001 HIS E 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (22726) covalent geometry : angle 0.49145 / 0.26 (30855) hydrogen bonds : bond 0.03352 / 2.28 ( 980) hydrogen bonds : angle 4.66327 / 3.26 ( 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 140 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.8598 (mmm) cc_final: 0.8167 (mtt) REVERT: B 84 MET cc_start: 0.8391 (mmm) cc_final: 0.8142 (mtt) REVERT: C 84 MET cc_start: 0.8682 (mmm) cc_final: 0.8412 (mtt) REVERT: C 251 MET cc_start: 0.8236 (tpp) cc_final: 0.8024 (tpp) REVERT: E 36 ASN cc_start: 0.8129 (t0) cc_final: 0.7739 (t0) REVERT: E 222 ASP cc_start: 0.8213 (t0) cc_final: 0.7784 (t70) REVERT: E 326 MET cc_start: 0.8123 (ttm) cc_final: 0.7686 (mtp) REVERT: F 326 MET cc_start: 0.8153 (tpp) cc_final: 0.7905 (ttt) REVERT: G 326 MET cc_start: 0.8282 (tpp) cc_final: 0.7856 (tpp) REVERT: I 34 ASN cc_start: 0.8794 (p0) cc_final: 0.8480 (p0) outliers start: 25 outliers final: 18 residues processed: 131 average time/residue: 0.1299 time to fit residues: 27.9194 Evaluate side-chains 127 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 131 THR Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain D residue 84 MET 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 184 optimal weight: 7.9990 chunk 218 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 243 optimal weight: 10.0000 chunk 237 optimal weight: 10.0000 chunk 239 optimal weight: 2.9990 chunk 274 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.3057 r_free = 0.3057 target = 0.067472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.049537 restraints weight = 65935.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.051005 restraints weight = 38822.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.051980 restraints weight = 27973.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.052608 restraints weight = 22742.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.053019 restraints weight = 19990.955| |-----------------------------------------------------------------------------| r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 22726 Z= 0.245 Angle : 0.571 7.577 30855 Z= 0.300 Chirality : 0.043 0.199 3504 Planarity : 0.004 0.048 3846 Dihedral : 12.258 80.289 3415 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.21 % Allowed : 9.23 % Favored : 89.56 % 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: 0.14 (0.16), residues: 2754 helix: 0.57 (0.15), residues: 1278 sheet: 2.09 (0.26), residues: 432 loop : -1.38 (0.17), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 306 TYR 0.027 0.002 TYR C 315 PHE 0.020 0.002 PHE B 166 HIS 0.009 0.002 HIS E 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.24 (22726) covalent geometry : angle 0.57090 / 0.30 (30855) hydrogen bonds : bond 0.04003 / 2.71 ( 980) hydrogen bonds : angle 4.78646 / 3.34 ( 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 137 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.8588 (mmm) cc_final: 0.8282 (mtt) REVERT: A 158 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7809 (mtp) REVERT: D 27 ARG cc_start: 0.7625 (tpp-160) cc_final: 0.7117 (tpm170) REVERT: E 36 ASN cc_start: 0.8074 (t0) cc_final: 0.7632 (t0) REVERT: E 326 MET cc_start: 0.8250 (ttm) cc_final: 0.7855 (mtp) REVERT: F 72 ASP cc_start: 0.7523 (m-30) cc_final: 0.7285 (m-30) REVERT: F 326 MET cc_start: 0.8170 (tpp) cc_final: 0.7940 (ttt) REVERT: G 326 MET cc_start: 0.8049 (tpp) cc_final: 0.7812 (tpp) REVERT: I 34 ASN cc_start: 0.8931 (p0) cc_final: 0.8683 (p0) outliers start: 27 outliers final: 20 residues processed: 126 average time/residue: 0.1613 time to fit residues: 32.2027 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 : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 84 MET 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 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 99 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 83 optimal weight: 3.9990 chunk 96 optimal weight: 20.0000 chunk 57 optimal weight: 8.9990 chunk 281 optimal weight: 20.0000 chunk 173 optimal weight: 5.9990 chunk 201 optimal weight: 6.9990 chunk 219 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 248 optimal weight: 40.0000 chunk 270 optimal weight: 3.9990 chunk 220 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 199 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.066299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.048317 restraints weight = 66919.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.049758 restraints weight = 39450.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.050719 restraints weight = 28409.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.051252 restraints weight = 23161.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.051695 restraints weight = 20570.250| |-----------------------------------------------------------------------------| r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 22726 Z= 0.292 Angle : 0.622 8.979 30855 Z= 0.324 Chirality : 0.045 0.181 3504 Planarity : 0.004 0.049 3846 Dihedral : 12.410 82.680 3415 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.25 % Allowed : 9.68 % 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: -0.11 (0.16), residues: 2754 helix: 0.49 (0.15), residues: 1278 sheet: 1.73 (0.26), residues: 432 loop : -1.57 (0.16), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 306 TYR 0.032 0.002 TYR D 315 PHE 0.022 0.002 PHE E 126 HIS 0.010 0.002 HIS D 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00672 / 0.29 (22726) covalent geometry : angle 0.62208 / 0.32 (30855) hydrogen bonds : bond 0.04314 / 2.92 ( 980) hydrogen bonds : angle 4.84370 / 3.39 ( 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 134 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.880 Fit side-chains REVERT: A 84 MET cc_start: 0.8645 (mmm) cc_final: 0.8354 (mtt) REVERT: A 158 MET cc_start: 0.8238 (ttp) cc_final: 0.7886 (mtp) REVERT: C 99 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8184 (tp) REVERT: C 251 MET cc_start: 0.8407 (tpp) cc_final: 0.8194 (tpp) REVERT: D 27 ARG cc_start: 0.7642 (tpp-160) cc_final: 0.7416 (tpp-160) REVERT: E 36 ASN cc_start: 0.8186 (t0) cc_final: 0.7730 (t0) REVERT: E 326 MET cc_start: 0.8273 (ttm) cc_final: 0.7924 (mtp) REVERT: F 72 ASP cc_start: 0.7625 (m-30) cc_final: 0.6895 (m-30) REVERT: F 326 MET cc_start: 0.8138 (tpp) cc_final: 0.7892 (ttt) REVERT: G 326 MET cc_start: 0.8291 (tpp) cc_final: 0.7952 (tpp) outliers start: 28 outliers final: 23 residues processed: 125 average time/residue: 0.1636 time to fit residues: 33.1637 Evaluate side-chains 127 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 C residue 99 ILE 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 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 99 ILE Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 264 VAL 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: 0.8980 chunk 39 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 262 optimal weight: 10.0000 chunk 195 optimal weight: 10.0000 chunk 162 optimal weight: 7.9990 chunk 119 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 267 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 244 HIS B 36 ASN C 244 HIS G 244 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.067780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.049979 restraints weight = 65346.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.051456 restraints weight = 38140.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.052435 restraints weight = 27338.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.053052 restraints weight = 22222.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.053376 restraints weight = 19558.418| |-----------------------------------------------------------------------------| r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22726 Z= 0.130 Angle : 0.484 8.277 30855 Z= 0.257 Chirality : 0.041 0.143 3504 Planarity : 0.003 0.032 3846 Dihedral : 12.321 82.875 3415 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.94 % Allowed : 10.26 % Favored : 88.80 % 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: 0.07 (0.16), residues: 2754 helix: 0.64 (0.15), residues: 1278 sheet: 1.97 (0.26), residues: 423 loop : -1.54 (0.17), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 306 TYR 0.011 0.001 TYR F 315 PHE 0.011 0.001 PHE B 248 HIS 0.003 0.001 HIS F 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (22726) covalent geometry : angle 0.48423 / 0.26 (30855) hydrogen bonds : bond 0.03393 / 2.30 ( 980) hydrogen bonds : angle 4.48751 / 3.14 ( 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 130 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.843 Fit side-chains REVERT: A 84 MET cc_start: 0.8614 (mmm) cc_final: 0.8300 (mtt) REVERT: A 158 MET cc_start: 0.8184 (ttp) cc_final: 0.7870 (mtp) REVERT: A 326 MET cc_start: 0.8638 (mmm) cc_final: 0.8372 (tpp) REVERT: D 27 ARG cc_start: 0.7619 (tpp-160) cc_final: 0.7332 (tpm170) REVERT: D 235 ARG cc_start: 0.7593 (tpt90) cc_final: 0.7330 (tpt-90) REVERT: E 36 ASN cc_start: 0.8107 (t0) cc_final: 0.7732 (t0) REVERT: E 222 ASP cc_start: 0.8256 (t0) cc_final: 0.7879 (t70) REVERT: E 326 MET cc_start: 0.8206 (ttm) cc_final: 0.7869 (mtp) REVERT: G 27 ARG cc_start: 0.7776 (tpp-160) cc_final: 0.7202 (tpm170) REVERT: G 326 MET cc_start: 0.8124 (tpp) cc_final: 0.7856 (tpp) outliers start: 21 outliers final: 17 residues processed: 124 average time/residue: 0.1391 time to fit residues: 27.7659 Evaluate side-chains 125 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 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 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 61 ILE Chi-restraints excluded: chain H residue 99 ILE 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: 6.9990 chunk 245 optimal weight: 4.9990 chunk 281 optimal weight: 20.0000 chunk 64 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 44 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.3091 r_free = 0.3091 target = 0.068800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.051283 restraints weight = 64231.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.052831 restraints weight = 36986.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.053842 restraints weight = 26233.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.054494 restraints weight = 21199.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.054840 restraints weight = 18557.832| |-----------------------------------------------------------------------------| r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22726 Z= 0.130 Angle : 0.468 12.025 30855 Z= 0.248 Chirality : 0.040 0.142 3504 Planarity : 0.003 0.032 3846 Dihedral : 12.285 84.164 3415 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.99 % Allowed : 10.13 % Favored : 88.89 % 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: 0.51 (0.16), residues: 2754 helix: 0.99 (0.15), residues: 1215 sheet: 1.99 (0.26), residues: 423 loop : -1.06 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 306 TYR 0.011 0.001 TYR D 315 PHE 0.010 0.001 PHE G 248 HIS 0.003 0.001 HIS D 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (22726) covalent geometry : angle 0.46783 / 0.25 (30855) hydrogen bonds : bond 0.03149 / 2.14 ( 980) hydrogen bonds : angle 4.34639 / 3.04 ( 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 137 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.802 Fit side-chains REVERT: A 84 MET cc_start: 0.8593 (mmm) cc_final: 0.8270 (mtt) REVERT: A 158 MET cc_start: 0.8109 (ttp) cc_final: 0.7896 (mtp) REVERT: A 326 MET cc_start: 0.8470 (mmm) cc_final: 0.8216 (tpt) REVERT: D 27 ARG cc_start: 0.7672 (tpp-160) cc_final: 0.7435 (tpm170) REVERT: E 36 ASN cc_start: 0.8013 (t0) cc_final: 0.7694 (t0) REVERT: E 326 MET cc_start: 0.8126 (ttm) cc_final: 0.7831 (mtp) REVERT: G 27 ARG cc_start: 0.7782 (tpp-160) cc_final: 0.7420 (tpm170) REVERT: G 84 MET cc_start: 0.8586 (mmm) cc_final: 0.8252 (mmm) REVERT: G 326 MET cc_start: 0.8112 (tpp) cc_final: 0.7871 (tpp) outliers start: 22 outliers final: 21 residues processed: 131 average time/residue: 0.1607 time to fit residues: 33.3912 Evaluate side-chains 129 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 270 VAL Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 270 VAL 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 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 61 ILE Chi-restraints excluded: chain H residue 99 ILE 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: 7.9990 chunk 146 optimal weight: 4.9990 chunk 252 optimal weight: 20.0000 chunk 194 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 230 optimal weight: 20.0000 chunk 51 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.3034 r_free = 0.3034 target = 0.066623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.048708 restraints weight = 66247.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.050165 restraints weight = 39183.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.051112 restraints weight = 28210.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.051714 restraints weight = 23030.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.051954 restraints weight = 20339.186| |-----------------------------------------------------------------------------| r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 22726 Z= 0.257 Angle : 0.572 10.637 30855 Z= 0.299 Chirality : 0.043 0.177 3504 Planarity : 0.004 0.052 3846 Dihedral : 12.392 86.584 3415 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.03 % Allowed : 10.22 % Favored : 88.75 % 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: 0.36 (0.16), residues: 2754 helix: 0.96 (0.15), residues: 1224 sheet: 1.71 (0.26), residues: 432 loop : -1.20 (0.17), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 306 TYR 0.024 0.002 TYR D 315 PHE 0.019 0.002 PHE B 248 HIS 0.007 0.001 HIS D 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.26 (22726) covalent geometry : angle 0.57212 / 0.30 (30855) hydrogen bonds : bond 0.03941 / 2.67 ( 980) hydrogen bonds : angle 4.59668 / 3.22 ( 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: 23 poor density : 107 time to evaluate : 0.864 Fit side-chains REVERT: A 84 MET cc_start: 0.8635 (mmm) cc_final: 0.8350 (mtt) REVERT: A 158 MET cc_start: 0.8282 (ttp) cc_final: 0.7977 (mtp) REVERT: D 27 ARG cc_start: 0.7682 (tpp-160) cc_final: 0.7038 (tpm170) REVERT: D 30 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7116 (mp10) REVERT: E 36 ASN cc_start: 0.8063 (t0) cc_final: 0.7664 (t0) REVERT: E 326 MET cc_start: 0.8244 (ttm) cc_final: 0.7935 (mtp) REVERT: G 27 ARG cc_start: 0.7776 (tpp-160) cc_final: 0.7382 (tpm170) REVERT: G 326 MET cc_start: 0.8133 (tpp) cc_final: 0.7866 (tpp) outliers start: 23 outliers final: 22 residues processed: 125 average time/residue: 0.1588 time to fit residues: 31.8772 Evaluate side-chains 129 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 270 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 30 GLN 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 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 99 ILE 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: 8.9990 chunk 165 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 264 optimal weight: 0.2980 chunk 42 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 266 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 76 optimal weight: 0.0980 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.3068 r_free = 0.3068 target = 0.068118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.050394 restraints weight = 65620.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.051881 restraints weight = 38226.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.052860 restraints weight = 27321.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.053425 restraints weight = 22162.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.053884 restraints weight = 19554.724| |-----------------------------------------------------------------------------| r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22726 Z= 0.115 Angle : 0.469 11.312 30855 Z= 0.249 Chirality : 0.040 0.148 3504 Planarity : 0.003 0.051 3846 Dihedral : 12.315 86.420 3415 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.76 % Allowed : 10.57 % Favored : 88.66 % 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: 1.04 (0.15), residues: 1215 sheet: 1.92 (0.26), residues: 423 loop : -1.12 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 306 TYR 0.009 0.001 TYR F 315 PHE 0.010 0.001 PHE G 248 HIS 0.003 0.001 HIS E 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (22726) covalent geometry : angle 0.46877 / 0.25 (30855) hydrogen bonds : bond 0.03035 / 2.07 ( 980) hydrogen bonds : angle 4.24372 / 2.97 ( 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 130 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.596 Fit side-chains REVERT: A 84 MET cc_start: 0.8710 (mmm) cc_final: 0.8333 (mtt) REVERT: A 158 MET cc_start: 0.8121 (ttp) cc_final: 0.7863 (mtp) REVERT: D 27 ARG cc_start: 0.7793 (tpp-160) cc_final: 0.7495 (tpm170) REVERT: E 36 ASN cc_start: 0.7958 (t0) cc_final: 0.7601 (t0) REVERT: E 326 MET cc_start: 0.8183 (ttm) cc_final: 0.7916 (mtp) REVERT: G 27 ARG cc_start: 0.7747 (tpp-160) cc_final: 0.7406 (tpm170) REVERT: G 84 MET cc_start: 0.8575 (mmm) cc_final: 0.8268 (mmm) REVERT: G 326 MET cc_start: 0.8146 (tpp) cc_final: 0.7900 (tpp) outliers start: 17 outliers final: 16 residues processed: 125 average time/residue: 0.1383 time to fit residues: 28.3762 Evaluate side-chains 124 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL 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 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 99 ILE 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 181 optimal weight: 8.9990 chunk 176 optimal weight: 4.9990 chunk 231 optimal weight: 0.9990 chunk 125 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 chunk 138 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 236 optimal weight: 1.9990 chunk 276 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.067633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.049787 restraints weight = 65687.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.051269 restraints weight = 38539.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.052247 restraints weight = 27640.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.052863 restraints weight = 22446.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.053108 restraints weight = 19758.334| |-----------------------------------------------------------------------------| r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22726 Z= 0.161 Angle : 0.489 10.782 30855 Z= 0.259 Chirality : 0.041 0.151 3504 Planarity : 0.003 0.057 3846 Dihedral : 12.329 87.733 3415 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.85 % Allowed : 10.44 % Favored : 88.71 % 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: 0.51 (0.16), residues: 2754 helix: 1.05 (0.15), residues: 1215 sheet: 1.91 (0.26), residues: 423 loop : -1.11 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 306 TYR 0.014 0.001 TYR C 315 PHE 0.017 0.001 PHE B 46 HIS 0.004 0.001 HIS C 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (22726) covalent geometry : angle 0.48902 / 0.26 (30855) hydrogen bonds : bond 0.03262 / 2.21 ( 980) hydrogen bonds : angle 4.29134 / 3.00 ( 2700) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2926.32 seconds wall clock time: 51 minutes 40.93 seconds (3100.93 seconds total)