Starting phenix.real_space_refine on Thu Jun 19 07:17:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bq2_16170/06_2025/8bq2_16170.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bq2_16170/06_2025/8bq2_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8bq2_16170/06_2025/8bq2_16170.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bq2_16170/06_2025/8bq2_16170.map" model { file = "/net/cci-nas-00/data/ceres_data/8bq2_16170/06_2025/8bq2_16170.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bq2_16170/06_2025/8bq2_16170.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.024 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.23, per 1000 atoms: 0.59 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: 5.94 Conformation dependent library (CDL) restraints added in 3.1 seconds 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5094 Finding SS restraints... Secondary structure from input PDB file: 153 helices and 18 sheets defined 54.2% alpha, 16.4% beta 0 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 7.81 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: 7.74 Time building geometry restraints manager: 6.97 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=" O4' DG W 14 " pdb=" C1' DG W 14 " ideal model delta sigma weight residual 1.414 1.449 -0.035 2.00e-02 2.50e+03 3.04e+00 bond pdb=" O5' DG W 29 " pdb=" C5' DG W 29 " ideal model delta sigma weight residual 1.423 1.473 -0.050 3.00e-02 1.11e+03 2.76e+00 bond pdb=" C5' DG W 29 " pdb=" C4' DG W 29 " ideal model delta sigma weight residual 1.518 1.551 -0.033 2.00e-02 2.50e+03 2.64e+00 bond pdb=" CB ARG G 235 " pdb=" CG ARG G 235 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.69e+00 bond pdb=" CB ARG B 235 " pdb=" CG ARG B 235 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.67e+00 ... (remaining 22721 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 30303 1.69 - 3.37: 452 3.37 - 5.06: 79 5.06 - 6.74: 20 6.74 - 8.43: 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 108.40 99.97 8.43 1.50e+00 4.44e-01 3.16e+01 angle pdb=" O3' DG W 29 " pdb=" C3' DG W 29 " pdb=" C2' DG W 29 " ideal model delta sigma weight residual 111.50 105.18 6.32 1.50e+00 4.44e-01 1.77e+01 angle pdb=" CA ARG G 27 " pdb=" CB ARG G 27 " pdb=" CG ARG G 27 " ideal model delta sigma weight residual 114.10 120.50 -6.40 2.00e+00 2.50e-01 1.03e+01 angle pdb=" CA ARG B 27 " pdb=" CB ARG B 27 " pdb=" CG ARG B 27 " ideal model delta sigma weight residual 114.10 120.50 -6.40 2.00e+00 2.50e-01 1.02e+01 angle pdb=" CA ARG H 27 " pdb=" CB ARG H 27 " pdb=" CG ARG H 27 " ideal model delta sigma weight residual 114.10 120.48 -6.38 2.00e+00 2.50e-01 1.02e+01 ... (remaining 30850 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 12434 16.69 - 33.37: 977 33.37 - 50.06: 283 50.06 - 66.74: 136 66.74 - 83.43: 52 Dihedral angle restraints: 13882 sinusoidal: 5926 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 13879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2950 0.053 - 0.106: 474 0.106 - 0.158: 79 0.158 - 0.211: 0 0.211 - 0.264: 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 2.35 -2.08 0.26 2.00e-01 2.50e+01 1.74e+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 2.42 2.56 -0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA ILE G 160 " pdb=" N ILE G 160 " pdb=" C ILE G 160 " pdb=" CB ILE G 160 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.72e-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 339 or resid 401 through 402)) selection = (chain 'B' and (resid 21 through 339 or resid 400 through 401)) selection = (chain 'C' and (resid 21 through 339 or resid 400 through 401)) selection = (chain 'D' and (resid 21 through 339 or resid 400 through 401)) selection = (chain 'E' and (resid 21 through 339 or resid 400 through 401)) selection = (chain 'F' and (resid 21 through 339 or resid 400 through 401)) selection = (chain 'G' and (resid 21 through 339 or resid 400 through 401)) selection = (chain 'H' and (resid 21 through 339 or resid 400 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: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.910 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 56.210 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 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 0.050 22726 Z= 0.117 Angle : 0.543 8.428 30855 Z= 0.315 Chirality : 0.039 0.264 3504 Planarity : 0.006 0.061 3846 Dihedral : 15.173 83.429 8788 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.91 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (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 HIS 0.014 0.003 HIS F 47 PHE 0.015 0.002 PHE F 195 TYR 0.018 0.002 TYR F 228 ARG 0.023 0.002 ARG G 229 Details of bonding type rmsd hydrogen bonds : bond 0.18017 ( 980) hydrogen bonds : angle 7.27245 ( 2700) covalent geometry : bond 0.00252 (22726) covalent geometry : angle 0.54348 (30855) *********************** 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 : 2.771 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: 0.7698 (mtt) REVERT: A 253 LEU cc_start: 0.9290 (tp) cc_final: 0.8935 (tt) REVERT: B 36 ASN cc_start: 0.7169 (t0) cc_final: 0.6961 (t0) REVERT: B 158 MET cc_start: 0.8276 (ttm) cc_final: 0.8064 (ttm) REVERT: C 36 ASN cc_start: 0.8119 (t0) cc_final: 0.7892 (t0) REVERT: C 251 MET cc_start: 0.8038 (tpp) cc_final: 0.7747 (tpt) REVERT: E 36 ASN cc_start: 0.7981 (t0) cc_final: 0.7720 (t0) REVERT: E 222 ASP cc_start: 0.8265 (t0) cc_final: 0.7925 (t70) REVERT: E 326 MET cc_start: 0.8111 (ttm) cc_final: 0.7894 (ttt) REVERT: I 34 ASN cc_start: 0.8241 (p0) cc_final: 0.7990 (p0) REVERT: I 62 ASN cc_start: 0.8303 (m-40) cc_final: 0.7780 (m110) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.4022 time to fit residues: 119.2241 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 : 2.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 238 optimal weight: 0.0170 chunk 213 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 144 optimal weight: 6.9990 chunk 114 optimal weight: 0.7980 chunk 221 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 164 optimal weight: 9.9990 chunk 256 optimal weight: 9.9990 overall best weight: 2.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 244 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.070330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.052614 restraints weight = 65121.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.054147 restraints weight = 37703.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.055173 restraints weight = 26795.389| |-----------------------------------------------------------------------------| r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 22726 Z= 0.137 Angle : 0.492 5.333 30855 Z= 0.265 Chirality : 0.040 0.136 3504 Planarity : 0.003 0.030 3846 Dihedral : 13.542 82.332 3694 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.90 % Allowed : 7.66 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.15), residues: 2754 helix: 0.12 (0.14), residues: 1278 sheet: 3.03 (0.24), residues: 432 loop : -1.65 (0.16), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 199 PHE 0.019 0.001 PHE C 259 TYR 0.014 0.001 TYR C 315 ARG 0.006 0.001 ARG E 27 Details of bonding type rmsd hydrogen bonds : bond 0.03369 ( 980) hydrogen bonds : angle 4.94943 ( 2700) covalent geometry : bond 0.00309 (22726) covalent geometry : angle 0.49197 (30855) *********************** 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 149 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 2.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8493 (mmm) cc_final: 0.8191 (mtt) REVERT: B 84 MET cc_start: 0.8395 (mmm) cc_final: 0.8078 (mtt) REVERT: C 70 LYS cc_start: 0.8808 (mttt) cc_final: 0.8470 (mmmt) REVERT: C 84 MET cc_start: 0.8689 (mmm) cc_final: 0.8369 (mtt) REVERT: C 251 MET cc_start: 0.8139 (tpp) cc_final: 0.7907 (tpp) REVERT: E 36 ASN cc_start: 0.8315 (t0) cc_final: 0.7907 (t0) REVERT: E 222 ASP cc_start: 0.8219 (t0) cc_final: 0.7808 (t70) REVERT: E 326 MET cc_start: 0.8139 (ttm) cc_final: 0.7917 (ttt) REVERT: F 158 MET cc_start: 0.8391 (ttm) cc_final: 0.8089 (ttm) REVERT: H 211 MET cc_start: 0.8404 (ttm) cc_final: 0.7948 (ttm) REVERT: I 34 ASN cc_start: 0.8740 (p0) cc_final: 0.8531 (p0) REVERT: I 211 MET cc_start: 0.8250 (ttm) cc_final: 0.8049 (ttm) outliers start: 20 outliers final: 14 residues processed: 141 average time/residue: 0.3349 time to fit residues: 75.7805 Evaluate side-chains 123 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 211 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 270 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 287 ILE 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 34 optimal weight: 20.0000 chunk 113 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 261 optimal weight: 30.0000 chunk 188 optimal weight: 2.9990 chunk 273 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 263 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3095 r_free = 0.3095 target = 0.068899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.051447 restraints weight = 64052.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.052999 restraints weight = 36996.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.054003 restraints weight = 26209.027| |-----------------------------------------------------------------------------| r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 22726 Z= 0.183 Angle : 0.512 7.914 30855 Z= 0.272 Chirality : 0.041 0.140 3504 Planarity : 0.003 0.044 3846 Dihedral : 13.438 84.257 3694 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.85 % Allowed : 9.09 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.16), residues: 2754 helix: 0.62 (0.15), residues: 1215 sheet: 2.50 (0.26), residues: 432 loop : -0.98 (0.17), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 199 PHE 0.017 0.002 PHE A 327 TYR 0.021 0.002 TYR C 315 ARG 0.007 0.001 ARG C 306 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 980) hydrogen bonds : angle 4.64638 ( 2700) covalent geometry : bond 0.00422 (22726) covalent geometry : angle 0.51221 (30855) *********************** 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 145 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 2.437 Fit side-chains revert: symmetry clash REVERT: A 62 ASN cc_start: 0.8433 (t0) cc_final: 0.8174 (t0) REVERT: A 84 MET cc_start: 0.8528 (mmm) cc_final: 0.8253 (mtt) REVERT: A 158 MET cc_start: 0.8265 (ttm) cc_final: 0.7914 (mtp) REVERT: C 84 MET cc_start: 0.8716 (mmm) cc_final: 0.8501 (mtt) REVERT: C 99 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8596 (tp) REVERT: E 222 ASP cc_start: 0.8256 (t0) cc_final: 0.7832 (t70) REVERT: F 72 ASP cc_start: 0.7481 (m-30) cc_final: 0.7237 (m-30) REVERT: G 27 ARG cc_start: 0.7687 (tpp-160) cc_final: 0.7483 (tpm170) REVERT: I 211 MET cc_start: 0.8184 (ttm) cc_final: 0.7910 (ttm) outliers start: 19 outliers final: 13 residues processed: 135 average time/residue: 0.3871 time to fit residues: 80.4250 Evaluate side-chains 123 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 2.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain F residue 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 28 LEU 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 160 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 272 optimal weight: 6.9990 chunk 230 optimal weight: 20.0000 chunk 179 optimal weight: 0.9990 chunk 252 optimal weight: 20.0000 chunk 165 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 112 optimal weight: 7.9990 chunk 220 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 244 HIS F 244 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.068355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.050817 restraints weight = 65143.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.052357 restraints weight = 37465.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.053375 restraints weight = 26579.416| |-----------------------------------------------------------------------------| r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22726 Z= 0.196 Angle : 0.506 7.727 30855 Z= 0.268 Chirality : 0.041 0.130 3504 Planarity : 0.003 0.049 3846 Dihedral : 13.417 83.069 3694 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.16 % Allowed : 9.50 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.16), residues: 2754 helix: 0.79 (0.15), residues: 1224 sheet: 2.48 (0.26), residues: 423 loop : -1.07 (0.17), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 244 PHE 0.015 0.002 PHE B 248 TYR 0.019 0.001 TYR D 315 ARG 0.009 0.000 ARG C 306 Details of bonding type rmsd hydrogen bonds : bond 0.03551 ( 980) hydrogen bonds : angle 4.52160 ( 2700) covalent geometry : bond 0.00450 (22726) covalent geometry : angle 0.50554 (30855) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 2.554 Fit side-chains revert: symmetry clash REVERT: A 62 ASN cc_start: 0.8502 (t0) cc_final: 0.8231 (t0) REVERT: A 84 MET cc_start: 0.8706 (mmm) cc_final: 0.8325 (mtt) REVERT: A 158 MET cc_start: 0.8254 (ttm) cc_final: 0.7974 (mtp) REVERT: C 84 MET cc_start: 0.8602 (mmm) cc_final: 0.8384 (mtt) REVERT: E 222 ASP cc_start: 0.8291 (t0) cc_final: 0.7852 (t70) REVERT: E 326 MET cc_start: 0.7913 (ttt) cc_final: 0.7681 (mtp) REVERT: G 27 ARG cc_start: 0.7573 (tpp-160) cc_final: 0.7348 (tpm170) REVERT: I 158 MET cc_start: 0.8298 (ttm) cc_final: 0.7969 (ttm) outliers start: 26 outliers final: 17 residues processed: 130 average time/residue: 0.3394 time to fit residues: 70.7572 Evaluate side-chains 127 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 2.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain 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 192 optimal weight: 7.9990 chunk 221 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 233 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 chunk 100 optimal weight: 0.4980 chunk 160 optimal weight: 6.9990 chunk 167 optimal weight: 0.0470 chunk 31 optimal weight: 20.0000 overall best weight: 2.5084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS C 244 HIS G 244 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.069243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.051687 restraints weight = 64542.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.053214 restraints weight = 37309.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.054231 restraints weight = 26603.188| |-----------------------------------------------------------------------------| r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 22726 Z= 0.139 Angle : 0.448 6.826 30855 Z= 0.240 Chirality : 0.039 0.135 3504 Planarity : 0.003 0.054 3846 Dihedral : 13.190 87.329 3694 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.30 % Allowed : 9.50 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.16), residues: 2754 helix: 0.94 (0.15), residues: 1224 sheet: 2.40 (0.26), residues: 423 loop : -1.07 (0.17), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 244 PHE 0.011 0.001 PHE G 248 TYR 0.013 0.001 TYR C 315 ARG 0.010 0.000 ARG C 306 Details of bonding type rmsd hydrogen bonds : bond 0.03021 ( 980) hydrogen bonds : angle 4.24191 ( 2700) covalent geometry : bond 0.00315 (22726) covalent geometry : angle 0.44804 (30855) *********************** 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 146 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 2.624 Fit side-chains revert: symmetry clash REVERT: A 62 ASN cc_start: 0.8510 (t0) cc_final: 0.8217 (t0) REVERT: A 84 MET cc_start: 0.8656 (mmm) cc_final: 0.8326 (mtt) REVERT: A 158 MET cc_start: 0.8264 (ttm) cc_final: 0.7992 (mtp) REVERT: D 27 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.6712 (tpm170) REVERT: D 84 MET cc_start: 0.8667 (mmm) cc_final: 0.8448 (mtp) REVERT: E 222 ASP cc_start: 0.8219 (t0) cc_final: 0.7800 (t70) REVERT: E 326 MET cc_start: 0.7888 (ttt) cc_final: 0.7655 (mtp) REVERT: F 72 ASP cc_start: 0.7624 (m-30) cc_final: 0.6995 (m-30) REVERT: G 27 ARG cc_start: 0.7479 (tpp-160) cc_final: 0.7262 (tpm170) REVERT: H 211 MET cc_start: 0.8480 (ttm) cc_final: 0.8262 (ttm) REVERT: I 158 MET cc_start: 0.8260 (ttm) cc_final: 0.7937 (ttm) outliers start: 29 outliers final: 17 residues processed: 136 average time/residue: 0.3700 time to fit residues: 80.2290 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 : 2.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 211 MET Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 76 optimal weight: 7.9990 chunk 47 optimal weight: 0.7980 chunk 243 optimal weight: 0.9980 chunk 169 optimal weight: 5.9990 chunk 278 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 204 optimal weight: 7.9990 chunk 176 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 chunk 167 optimal weight: 4.9990 chunk 267 optimal weight: 5.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.069133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.051681 restraints weight = 64096.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.053227 restraints weight = 36967.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.054261 restraints weight = 26223.591| |-----------------------------------------------------------------------------| r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 22726 Z= 0.139 Angle : 0.447 6.794 30855 Z= 0.239 Chirality : 0.039 0.123 3504 Planarity : 0.003 0.056 3846 Dihedral : 13.090 84.609 3694 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.16 % Allowed : 9.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.16), residues: 2754 helix: 1.05 (0.15), residues: 1224 sheet: 2.37 (0.26), residues: 423 loop : -1.04 (0.17), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 244 PHE 0.011 0.001 PHE B 248 TYR 0.012 0.001 TYR C 315 ARG 0.011 0.000 ARG C 306 Details of bonding type rmsd hydrogen bonds : bond 0.02997 ( 980) hydrogen bonds : angle 4.14975 ( 2700) covalent geometry : bond 0.00316 (22726) covalent geometry : angle 0.44746 (30855) *********************** 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 140 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 2.532 Fit side-chains REVERT: A 62 ASN cc_start: 0.8530 (t0) cc_final: 0.8250 (t0) REVERT: A 84 MET cc_start: 0.8656 (mmm) cc_final: 0.8339 (mtt) REVERT: A 158 MET cc_start: 0.8264 (ttm) cc_final: 0.8003 (mtp) REVERT: D 30 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7796 (mp10) REVERT: D 84 MET cc_start: 0.8649 (mmm) cc_final: 0.8432 (mtp) REVERT: E 222 ASP cc_start: 0.8214 (t0) cc_final: 0.7789 (t70) REVERT: E 326 MET cc_start: 0.7901 (ttt) cc_final: 0.7695 (mtp) outliers start: 26 outliers final: 20 residues processed: 130 average time/residue: 0.3469 time to fit residues: 72.1743 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 : 2.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 270 VAL 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 211 MET Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 180 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 203 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 225 optimal weight: 9.9990 chunk 166 optimal weight: 0.7980 chunk 196 optimal weight: 6.9990 chunk 271 optimal weight: 10.0000 chunk 244 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 199 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.068321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.051324 restraints weight = 65268.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.052795 restraints weight = 36447.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.053172 restraints weight = 25287.401| |-----------------------------------------------------------------------------| r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22726 Z= 0.184 Angle : 0.488 7.956 30855 Z= 0.258 Chirality : 0.040 0.150 3504 Planarity : 0.003 0.055 3846 Dihedral : 13.208 86.703 3694 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.21 % Allowed : 10.22 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.16), residues: 2754 helix: 0.97 (0.15), residues: 1233 sheet: 1.67 (0.26), residues: 468 loop : -1.04 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 244 PHE 0.014 0.002 PHE B 248 TYR 0.015 0.001 TYR C 315 ARG 0.011 0.000 ARG C 306 Details of bonding type rmsd hydrogen bonds : bond 0.03428 ( 980) hydrogen bonds : angle 4.29329 ( 2700) covalent geometry : bond 0.00424 (22726) covalent geometry : angle 0.48775 (30855) *********************** 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 135 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 2.486 Fit side-chains REVERT: A 62 ASN cc_start: 0.8552 (t0) cc_final: 0.8265 (t0) REVERT: A 84 MET cc_start: 0.8636 (mmm) cc_final: 0.8347 (mtt) REVERT: A 158 MET cc_start: 0.8302 (ttm) cc_final: 0.8011 (mtp) REVERT: D 30 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7699 (mp10) REVERT: D 84 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8501 (mtp) REVERT: E 326 MET cc_start: 0.7923 (ttt) cc_final: 0.7703 (mtp) outliers start: 27 outliers final: 20 residues processed: 124 average time/residue: 0.3522 time to fit residues: 70.0818 Evaluate side-chains 126 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 30 GLN 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 E residue 106 SER 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 125 MET Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 46 optimal weight: 0.9980 chunk 195 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 278 optimal weight: 9.9990 chunk 204 optimal weight: 6.9990 chunk 267 optimal weight: 20.0000 chunk 146 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 131 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN H 244 HIS I 272 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.068588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.050988 restraints weight = 64667.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.052537 restraints weight = 37292.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.053559 restraints weight = 26442.733| |-----------------------------------------------------------------------------| r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 22726 Z= 0.165 Angle : 0.471 9.442 30855 Z= 0.249 Chirality : 0.040 0.150 3504 Planarity : 0.003 0.056 3846 Dihedral : 13.099 88.881 3694 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.99 % Allowed : 10.57 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.16), residues: 2754 helix: 1.01 (0.15), residues: 1233 sheet: 2.19 (0.27), residues: 423 loop : -1.09 (0.17), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 244 PHE 0.013 0.001 PHE B 248 TYR 0.013 0.001 TYR D 315 ARG 0.012 0.000 ARG C 306 Details of bonding type rmsd hydrogen bonds : bond 0.03203 ( 980) hydrogen bonds : angle 4.18570 ( 2700) covalent geometry : bond 0.00379 (22726) covalent geometry : angle 0.47114 (30855) *********************** 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 130 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 2.456 Fit side-chains REVERT: A 62 ASN cc_start: 0.8542 (t0) cc_final: 0.8263 (t0) REVERT: A 84 MET cc_start: 0.8601 (mmm) cc_final: 0.8303 (mtt) REVERT: A 158 MET cc_start: 0.8227 (ttm) cc_final: 0.8003 (mtp) REVERT: D 30 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7623 (mp10) REVERT: D 84 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8386 (mtp) REVERT: E 326 MET cc_start: 0.7903 (ttt) cc_final: 0.7701 (mtp) outliers start: 22 outliers final: 18 residues processed: 122 average time/residue: 0.3508 time to fit residues: 68.4121 Evaluate side-chains 125 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 30 GLN 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 36 ASN Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 120 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 188 optimal weight: 2.9990 chunk 274 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 172 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.067041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.049176 restraints weight = 66228.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.050645 restraints weight = 39029.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.051615 restraints weight = 28055.018| |-----------------------------------------------------------------------------| r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 22726 Z= 0.205 Angle : 0.514 8.140 30855 Z= 0.272 Chirality : 0.041 0.145 3504 Planarity : 0.003 0.062 3846 Dihedral : 13.185 88.380 3694 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.94 % Allowed : 10.84 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.16), residues: 2754 helix: 1.00 (0.15), residues: 1224 sheet: 1.83 (0.26), residues: 450 loop : -1.18 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 244 PHE 0.014 0.002 PHE B 248 TYR 0.017 0.001 TYR D 315 ARG 0.013 0.000 ARG C 306 Details of bonding type rmsd hydrogen bonds : bond 0.03629 ( 980) hydrogen bonds : angle 4.33420 ( 2700) covalent geometry : bond 0.00473 (22726) covalent geometry : angle 0.51449 (30855) *********************** 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 124 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 2.501 Fit side-chains REVERT: A 62 ASN cc_start: 0.8583 (t0) cc_final: 0.8297 (t0) REVERT: A 84 MET cc_start: 0.8599 (mmm) cc_final: 0.8363 (mtt) REVERT: A 158 MET cc_start: 0.8297 (ttm) cc_final: 0.8005 (mtp) REVERT: D 30 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7644 (mp10) REVERT: D 84 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8452 (mtp) outliers start: 21 outliers final: 18 residues processed: 117 average time/residue: 0.3206 time to fit residues: 61.6176 Evaluate side-chains 122 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 2.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 30 GLN 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 E residue 106 SER 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 125 MET Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 71 optimal weight: 8.9990 chunk 106 optimal weight: 20.0000 chunk 227 optimal weight: 9.9990 chunk 111 optimal weight: 0.9980 chunk 280 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 179 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 210 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.068401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.051375 restraints weight = 64917.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.052842 restraints weight = 36036.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.053636 restraints weight = 24745.385| |-----------------------------------------------------------------------------| r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 22726 Z= 0.169 Angle : 0.480 9.751 30855 Z= 0.254 Chirality : 0.040 0.137 3504 Planarity : 0.003 0.067 3846 Dihedral : 13.071 87.095 3694 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.90 % Allowed : 11.20 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.16), residues: 2754 helix: 1.03 (0.15), residues: 1224 sheet: 1.81 (0.26), residues: 450 loop : -1.16 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 244 PHE 0.013 0.001 PHE B 248 TYR 0.014 0.001 TYR D 315 ARG 0.014 0.000 ARG C 306 Details of bonding type rmsd hydrogen bonds : bond 0.03241 ( 980) hydrogen bonds : angle 4.20189 ( 2700) covalent geometry : bond 0.00387 (22726) covalent geometry : angle 0.47959 (30855) ********************** 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 126 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 2.728 Fit side-chains REVERT: A 62 ASN cc_start: 0.8633 (t0) cc_final: 0.8342 (t0) REVERT: A 84 MET cc_start: 0.8568 (mmm) cc_final: 0.8340 (mtt) REVERT: A 158 MET cc_start: 0.8266 (ttm) cc_final: 0.7983 (mtp) REVERT: D 30 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7571 (mp10) REVERT: D 84 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8314 (mtp) outliers start: 20 outliers final: 17 residues processed: 120 average time/residue: 0.3455 time to fit residues: 67.3655 Evaluate side-chains 121 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 2.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 30 GLN 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 106 SER 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 125 MET Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 16 optimal weight: 0.9990 chunk 209 optimal weight: 0.7980 chunk 143 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 266 optimal weight: 1.9990 chunk 276 optimal weight: 6.9990 chunk 198 optimal weight: 0.0010 chunk 63 optimal weight: 8.9990 chunk 272 optimal weight: 4.9990 chunk 221 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.070512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.053106 restraints weight = 64154.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.054682 restraints weight = 36937.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.055732 restraints weight = 26130.214| |-----------------------------------------------------------------------------| r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22726 Z= 0.089 Angle : 0.417 9.870 30855 Z= 0.222 Chirality : 0.038 0.141 3504 Planarity : 0.003 0.040 3846 Dihedral : 12.698 87.957 3694 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.76 % Allowed : 11.29 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.16), residues: 2754 helix: 1.17 (0.16), residues: 1233 sheet: 2.09 (0.26), residues: 441 loop : -1.07 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS G 199 PHE 0.009 0.001 PHE G 86 TYR 0.008 0.001 TYR G 54 ARG 0.009 0.000 ARG C 306 Details of bonding type rmsd hydrogen bonds : bond 0.02281 ( 980) hydrogen bonds : angle 3.81828 ( 2700) covalent geometry : bond 0.00191 (22726) covalent geometry : angle 0.41681 (30855) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5648.36 seconds wall clock time: 100 minutes 12.95 seconds (6012.95 seconds total)