Starting phenix.real_space_refine on Sat Sep 12 21:13:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ufi_26476/09_2026/7ufi_26476.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ufi_26476/09_2026/7ufi_26476.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ufi_26476/09_2026/7ufi_26476.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ufi_26476/09_2026/7ufi_26476.map" model { file = "/net/cci-nas-00/data/ceres_data/7ufi_26476/09_2026/7ufi_26476.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ufi_26476/09_2026/7ufi_26476.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ufi_26476/09_2026/7ufi_26476.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ufi_26476/09_2026/7ufi_26476.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 63 5.49 5 S 77 5.16 5 C 11446 2.51 5 N 3177 2.21 5 O 3556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18319 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 430 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "B" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 431 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "1" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "2" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "3" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "4" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "5" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "6" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "7" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "1" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.47, per 1000 atoms: 0.24 Number of scatterers: 18319 At special positions: 0 Unit cell: (99.594, 144.864, 150.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 77 16.00 P 63 15.00 O 3556 8.00 N 3177 7.00 C 11446 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 718.1 milliseconds 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4102 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 7 sheets defined 56.3% alpha, 3.3% beta 21 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain '1' and resid 5 through 14 Processing helix chain '1' and resid 19 through 36 removed outlier: 3.878A pdb=" N SER 1 36 " --> pdb=" O CYS 1 32 " (cutoff:3.500A) Processing helix chain '1' and resid 54 through 74 removed outlier: 6.885A pdb=" N ALA 1 69 " --> pdb=" O GLN 1 65 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ALA 1 70 " --> pdb=" O ALA 1 66 " (cutoff:3.500A) Processing helix chain '1' and resid 89 through 101 Processing helix chain '1' and resid 113 through 127 Proline residue: 1 124 - end of helix Processing helix chain '1' and resid 136 through 140 removed outlier: 3.550A pdb=" N LEU 1 139 " --> pdb=" O PHE 1 136 " (cutoff:3.500A) Processing helix chain '1' and resid 149 through 162 Processing helix chain '1' and resid 171 through 173 No H-bonds generated for 'chain '1' and resid 171 through 173' Processing helix chain '1' and resid 174 through 181 removed outlier: 3.577A pdb=" N LEU 1 178 " --> pdb=" O SER 1 174 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN 1 181 " --> pdb=" O VAL 1 177 " (cutoff:3.500A) Processing helix chain '1' and resid 181 through 188 Processing helix chain '1' and resid 204 through 217 removed outlier: 3.713A pdb=" N THR 1 208 " --> pdb=" O GLY 1 204 " (cutoff:3.500A) Processing helix chain '1' and resid 227 through 238 removed outlier: 3.720A pdb=" N LYS 1 232 " --> pdb=" O GLU 1 228 " (cutoff:3.500A) Processing helix chain '1' and resid 241 through 259 removed outlier: 3.606A pdb=" N ASN 1 259 " --> pdb=" O GLU 1 255 " (cutoff:3.500A) Processing helix chain '1' and resid 268 through 276 Processing helix chain '1' and resid 308 through 313 Processing helix chain '2' and resid 5 through 14 Processing helix chain '2' and resid 19 through 36 removed outlier: 3.900A pdb=" N SER 2 36 " --> pdb=" O CYS 2 32 " (cutoff:3.500A) Processing helix chain '2' and resid 54 through 74 removed outlier: 6.860A pdb=" N ALA 2 69 " --> pdb=" O GLN 2 65 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ALA 2 70 " --> pdb=" O ALA 2 66 " (cutoff:3.500A) Processing helix chain '2' and resid 89 through 101 Processing helix chain '2' and resid 113 through 127 Proline residue: 2 124 - end of helix Processing helix chain '2' and resid 136 through 140 removed outlier: 3.830A pdb=" N LEU 2 139 " --> pdb=" O PHE 2 136 " (cutoff:3.500A) Processing helix chain '2' and resid 149 through 162 Processing helix chain '2' and resid 171 through 173 No H-bonds generated for 'chain '2' and resid 171 through 173' Processing helix chain '2' and resid 174 through 181 removed outlier: 3.568A pdb=" N LEU 2 178 " --> pdb=" O SER 2 174 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN 2 181 " --> pdb=" O VAL 2 177 " (cutoff:3.500A) Processing helix chain '2' and resid 181 through 188 Processing helix chain '2' and resid 204 through 217 removed outlier: 3.750A pdb=" N THR 2 208 " --> pdb=" O GLY 2 204 " (cutoff:3.500A) Processing helix chain '2' and resid 227 through 238 removed outlier: 3.735A pdb=" N LYS 2 232 " --> pdb=" O GLU 2 228 " (cutoff:3.500A) Processing helix chain '2' and resid 241 through 259 removed outlier: 3.536A pdb=" N ASN 2 259 " --> pdb=" O GLU 2 255 " (cutoff:3.500A) Processing helix chain '2' and resid 268 through 276 Processing helix chain '2' and resid 308 through 313 Processing helix chain '3' and resid 5 through 14 Processing helix chain '3' and resid 19 through 36 removed outlier: 3.887A pdb=" N SER 3 36 " --> pdb=" O CYS 3 32 " (cutoff:3.500A) Processing helix chain '3' and resid 54 through 74 removed outlier: 6.706A pdb=" N ALA 3 69 " --> pdb=" O GLN 3 65 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ALA 3 70 " --> pdb=" O ALA 3 66 " (cutoff:3.500A) Processing helix chain '3' and resid 89 through 101 Processing helix chain '3' and resid 113 through 127 Proline residue: 3 124 - end of helix Processing helix chain '3' and resid 136 through 140 removed outlier: 3.917A pdb=" N LEU 3 139 " --> pdb=" O PHE 3 136 " (cutoff:3.500A) Processing helix chain '3' and resid 149 through 162 Processing helix chain '3' and resid 171 through 173 No H-bonds generated for 'chain '3' and resid 171 through 173' Processing helix chain '3' and resid 174 through 181 removed outlier: 3.559A pdb=" N LEU 3 178 " --> pdb=" O SER 3 174 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN 3 181 " --> pdb=" O VAL 3 177 " (cutoff:3.500A) Processing helix chain '3' and resid 181 through 188 Processing helix chain '3' and resid 204 through 217 removed outlier: 3.759A pdb=" N THR 3 208 " --> pdb=" O GLY 3 204 " (cutoff:3.500A) Processing helix chain '3' and resid 227 through 238 removed outlier: 3.723A pdb=" N LYS 3 232 " --> pdb=" O GLU 3 228 " (cutoff:3.500A) Processing helix chain '3' and resid 241 through 259 removed outlier: 3.515A pdb=" N ASN 3 259 " --> pdb=" O GLU 3 255 " (cutoff:3.500A) Processing helix chain '3' and resid 268 through 276 Processing helix chain '3' and resid 308 through 313 Processing helix chain '4' and resid 5 through 14 Processing helix chain '4' and resid 19 through 36 removed outlier: 3.988A pdb=" N SER 4 36 " --> pdb=" O CYS 4 32 " (cutoff:3.500A) Processing helix chain '4' and resid 54 through 74 removed outlier: 6.768A pdb=" N ALA 4 69 " --> pdb=" O GLN 4 65 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ALA 4 70 " --> pdb=" O ALA 4 66 " (cutoff:3.500A) Processing helix chain '4' and resid 89 through 101 Processing helix chain '4' and resid 113 through 127 Proline residue: 4 124 - end of helix Processing helix chain '4' and resid 136 through 140 removed outlier: 3.726A pdb=" N LEU 4 139 " --> pdb=" O PHE 4 136 " (cutoff:3.500A) Processing helix chain '4' and resid 149 through 162 Processing helix chain '4' and resid 171 through 173 No H-bonds generated for 'chain '4' and resid 171 through 173' Processing helix chain '4' and resid 174 through 181 removed outlier: 3.554A pdb=" N LEU 4 178 " --> pdb=" O SER 4 174 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN 4 181 " --> pdb=" O VAL 4 177 " (cutoff:3.500A) Processing helix chain '4' and resid 181 through 188 Processing helix chain '4' and resid 204 through 217 removed outlier: 3.710A pdb=" N THR 4 208 " --> pdb=" O GLY 4 204 " (cutoff:3.500A) Processing helix chain '4' and resid 227 through 238 removed outlier: 3.741A pdb=" N LYS 4 232 " --> pdb=" O GLU 4 228 " (cutoff:3.500A) Processing helix chain '4' and resid 241 through 259 removed outlier: 3.539A pdb=" N ASN 4 259 " --> pdb=" O GLU 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 268 through 276 Processing helix chain '4' and resid 308 through 313 Processing helix chain '5' and resid 5 through 14 Processing helix chain '5' and resid 19 through 36 removed outlier: 3.900A pdb=" N SER 5 36 " --> pdb=" O CYS 5 32 " (cutoff:3.500A) Processing helix chain '5' and resid 54 through 74 removed outlier: 6.929A pdb=" N ALA 5 69 " --> pdb=" O GLN 5 65 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ALA 5 70 " --> pdb=" O ALA 5 66 " (cutoff:3.500A) Processing helix chain '5' and resid 89 through 101 Processing helix chain '5' and resid 113 through 127 Proline residue: 5 124 - end of helix Processing helix chain '5' and resid 136 through 140 removed outlier: 3.941A pdb=" N LEU 5 139 " --> pdb=" O PHE 5 136 " (cutoff:3.500A) Processing helix chain '5' and resid 149 through 162 Processing helix chain '5' and resid 171 through 173 No H-bonds generated for 'chain '5' and resid 171 through 173' Processing helix chain '5' and resid 174 through 181 removed outlier: 3.594A pdb=" N LEU 5 178 " --> pdb=" O SER 5 174 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN 5 181 " --> pdb=" O VAL 5 177 " (cutoff:3.500A) Processing helix chain '5' and resid 181 through 188 Processing helix chain '5' and resid 204 through 217 removed outlier: 3.727A pdb=" N THR 5 208 " --> pdb=" O GLY 5 204 " (cutoff:3.500A) Processing helix chain '5' and resid 227 through 238 removed outlier: 3.768A pdb=" N LYS 5 232 " --> pdb=" O GLU 5 228 " (cutoff:3.500A) Processing helix chain '5' and resid 241 through 259 removed outlier: 3.540A pdb=" N ASN 5 259 " --> pdb=" O GLU 5 255 " (cutoff:3.500A) Processing helix chain '5' and resid 268 through 276 Processing helix chain '5' and resid 308 through 313 Processing helix chain '6' and resid 5 through 14 Processing helix chain '6' and resid 19 through 36 removed outlier: 3.805A pdb=" N SER 6 36 " --> pdb=" O CYS 6 32 " (cutoff:3.500A) Processing helix chain '6' and resid 54 through 74 removed outlier: 6.810A pdb=" N ALA 6 69 " --> pdb=" O GLN 6 65 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ALA 6 70 " --> pdb=" O ALA 6 66 " (cutoff:3.500A) Processing helix chain '6' and resid 89 through 101 Processing helix chain '6' and resid 113 through 127 Proline residue: 6 124 - end of helix Processing helix chain '6' and resid 136 through 140 removed outlier: 3.882A pdb=" N LEU 6 139 " --> pdb=" O PHE 6 136 " (cutoff:3.500A) Processing helix chain '6' and resid 149 through 162 Processing helix chain '6' and resid 171 through 173 No H-bonds generated for 'chain '6' and resid 171 through 173' Processing helix chain '6' and resid 174 through 181 removed outlier: 3.572A pdb=" N LEU 6 178 " --> pdb=" O SER 6 174 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN 6 181 " --> pdb=" O VAL 6 177 " (cutoff:3.500A) Processing helix chain '6' and resid 181 through 188 Processing helix chain '6' and resid 204 through 217 removed outlier: 3.729A pdb=" N THR 6 208 " --> pdb=" O GLY 6 204 " (cutoff:3.500A) Processing helix chain '6' and resid 227 through 238 removed outlier: 3.695A pdb=" N LYS 6 232 " --> pdb=" O GLU 6 228 " (cutoff:3.500A) Processing helix chain '6' and resid 241 through 259 Processing helix chain '6' and resid 268 through 276 Processing helix chain '6' and resid 308 through 313 Processing helix chain '7' and resid 5 through 14 Processing helix chain '7' and resid 19 through 36 removed outlier: 3.935A pdb=" N SER 7 36 " --> pdb=" O CYS 7 32 " (cutoff:3.500A) Processing helix chain '7' and resid 54 through 74 removed outlier: 6.785A pdb=" N ALA 7 69 " --> pdb=" O GLN 7 65 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ALA 7 70 " --> pdb=" O ALA 7 66 " (cutoff:3.500A) Processing helix chain '7' and resid 89 through 101 Processing helix chain '7' and resid 113 through 127 Proline residue: 7 124 - end of helix Processing helix chain '7' and resid 136 through 140 removed outlier: 3.605A pdb=" N LEU 7 139 " --> pdb=" O PHE 7 136 " (cutoff:3.500A) Processing helix chain '7' and resid 149 through 162 Processing helix chain '7' and resid 171 through 173 No H-bonds generated for 'chain '7' and resid 171 through 173' Processing helix chain '7' and resid 174 through 181 removed outlier: 3.563A pdb=" N LEU 7 178 " --> pdb=" O SER 7 174 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN 7 181 " --> pdb=" O VAL 7 177 " (cutoff:3.500A) Processing helix chain '7' and resid 181 through 188 Processing helix chain '7' and resid 204 through 217 removed outlier: 3.758A pdb=" N THR 7 208 " --> pdb=" O GLY 7 204 " (cutoff:3.500A) Processing helix chain '7' and resid 227 through 238 removed outlier: 3.695A pdb=" N LYS 7 232 " --> pdb=" O GLU 7 228 " (cutoff:3.500A) Processing helix chain '7' and resid 241 through 259 removed outlier: 3.522A pdb=" N ASN 7 259 " --> pdb=" O GLU 7 255 " (cutoff:3.500A) Processing helix chain '7' and resid 268 through 276 Processing helix chain '7' and resid 308 through 313 Processing sheet with id=AA1, first strand: chain '1' and resid 131 through 133 removed outlier: 6.838A pdb=" N ILE 1 131 " --> pdb=" O VAL 1 167 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N PHE 1 169 " --> pdb=" O ILE 1 131 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE 1 133 " --> pdb=" O PHE 1 169 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET 1 45 " --> pdb=" O ILE 1 166 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE 1 168 " --> pdb=" O MET 1 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 131 through 133 removed outlier: 6.822A pdb=" N ILE 2 131 " --> pdb=" O VAL 2 167 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N PHE 2 169 " --> pdb=" O ILE 2 131 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE 2 133 " --> pdb=" O PHE 2 169 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET 2 45 " --> pdb=" O ILE 2 166 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE 2 168 " --> pdb=" O MET 2 45 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '3' and resid 131 through 133 removed outlier: 6.859A pdb=" N ILE 3 131 " --> pdb=" O VAL 3 167 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N PHE 3 169 " --> pdb=" O ILE 3 131 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE 3 133 " --> pdb=" O PHE 3 169 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET 3 45 " --> pdb=" O ILE 3 166 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE 3 168 " --> pdb=" O MET 3 45 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '4' and resid 131 through 133 removed outlier: 6.821A pdb=" N ILE 4 131 " --> pdb=" O VAL 4 167 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N PHE 4 169 " --> pdb=" O ILE 4 131 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE 4 133 " --> pdb=" O PHE 4 169 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '5' and resid 131 through 133 removed outlier: 6.806A pdb=" N ILE 5 131 " --> pdb=" O VAL 5 167 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N PHE 5 169 " --> pdb=" O ILE 5 131 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE 5 133 " --> pdb=" O PHE 5 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '6' and resid 131 through 133 removed outlier: 6.829A pdb=" N ILE 6 131 " --> pdb=" O VAL 6 167 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N PHE 6 169 " --> pdb=" O ILE 6 131 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE 6 133 " --> pdb=" O PHE 6 169 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET 6 45 " --> pdb=" O ILE 6 166 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE 6 168 " --> pdb=" O MET 6 45 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '7' and resid 131 through 133 removed outlier: 6.840A pdb=" N ILE 7 131 " --> pdb=" O VAL 7 167 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N PHE 7 169 " --> pdb=" O ILE 7 131 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE 7 133 " --> pdb=" O PHE 7 169 " (cutoff:3.500A) 761 hydrogen bonds defined for protein. 2262 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 55 hydrogen bonds 110 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 2.87 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3581 1.33 - 1.46: 4386 1.46 - 1.58: 10556 1.58 - 1.70: 116 1.70 - 1.82: 133 Bond restraints: 18772 Sorted by residual: bond pdb=" N ILE 5 76 " pdb=" CA ILE 5 76 " ideal model delta sigma weight residual 1.458 1.497 -0.039 9.00e-03 1.23e+04 1.86e+01 bond pdb=" N ILE 4 76 " pdb=" CA ILE 4 76 " ideal model delta sigma weight residual 1.458 1.496 -0.038 9.00e-03 1.23e+04 1.81e+01 bond pdb=" N ILE 2 76 " pdb=" CA ILE 2 76 " ideal model delta sigma weight residual 1.458 1.496 -0.038 9.00e-03 1.23e+04 1.77e+01 bond pdb=" N ILE 6 76 " pdb=" CA ILE 6 76 " ideal model delta sigma weight residual 1.458 1.496 -0.038 9.00e-03 1.23e+04 1.76e+01 bond pdb=" N ILE 3 76 " pdb=" CA ILE 3 76 " ideal model delta sigma weight residual 1.458 1.496 -0.038 9.00e-03 1.23e+04 1.76e+01 ... (remaining 18767 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.88: 24666 3.88 - 7.76: 924 7.76 - 11.64: 3 11.64 - 15.52: 11 15.52 - 19.40: 8 Bond angle restraints: 25612 Sorted by residual: angle pdb=" PB ATP 2 401 " pdb=" O3B ATP 2 401 " pdb=" PG ATP 2 401 " ideal model delta sigma weight residual 139.87 120.47 19.40 1.00e+00 1.00e+00 3.77e+02 angle pdb=" PB ATP 1 401 " pdb=" O3B ATP 1 401 " pdb=" PG ATP 1 401 " ideal model delta sigma weight residual 139.87 120.58 19.29 1.00e+00 1.00e+00 3.72e+02 angle pdb=" PB ATP 7 401 " pdb=" O3B ATP 7 401 " pdb=" PG ATP 7 401 " ideal model delta sigma weight residual 139.87 120.77 19.10 1.00e+00 1.00e+00 3.65e+02 angle pdb=" PB ATP 3 401 " pdb=" O3B ATP 3 401 " pdb=" PG ATP 3 401 " ideal model delta sigma weight residual 139.87 120.91 18.96 1.00e+00 1.00e+00 3.59e+02 angle pdb=" PB ATP 6 401 " pdb=" O3B ATP 6 401 " pdb=" PG ATP 6 401 " ideal model delta sigma weight residual 139.87 122.05 17.82 1.00e+00 1.00e+00 3.17e+02 ... (remaining 25607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 9230 16.69 - 33.38: 1174 33.38 - 50.07: 678 50.07 - 66.76: 151 66.76 - 83.45: 35 Dihedral angle restraints: 11268 sinusoidal: 4926 harmonic: 6342 Sorted by residual: dihedral pdb=" CA PHE 2 288 " pdb=" C PHE 2 288 " pdb=" N GLU 2 289 " pdb=" CA GLU 2 289 " ideal model delta harmonic sigma weight residual -180.00 -153.78 -26.22 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA PHE 4 288 " pdb=" C PHE 4 288 " pdb=" N GLU 4 289 " pdb=" CA GLU 4 289 " ideal model delta harmonic sigma weight residual -180.00 -154.89 -25.11 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA PHE 5 288 " pdb=" C PHE 5 288 " pdb=" N GLU 5 289 " pdb=" CA GLU 5 289 " ideal model delta harmonic sigma weight residual -180.00 -154.97 -25.03 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 11265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1108 0.045 - 0.089: 938 0.089 - 0.134: 555 0.134 - 0.178: 218 0.178 - 0.223: 44 Chirality restraints: 2863 Sorted by residual: chirality pdb=" CA VAL 1 17 " pdb=" N VAL 1 17 " pdb=" C VAL 1 17 " pdb=" CB VAL 1 17 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA VAL 3 17 " pdb=" N VAL 3 17 " pdb=" C VAL 3 17 " pdb=" CB VAL 3 17 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" C3' DT B 39 " pdb=" C4' DT B 39 " pdb=" O3' DT B 39 " pdb=" C2' DT B 39 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 2860 not shown) Planarity restraints: 3122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ATP 7 401 " -0.020 2.00e-02 2.50e+03 8.57e-03 2.02e+00 pdb=" C2 ATP 7 401 " -0.002 2.00e-02 2.50e+03 pdb=" C4 ATP 7 401 " 0.008 2.00e-02 2.50e+03 pdb=" C5 ATP 7 401 " 0.005 2.00e-02 2.50e+03 pdb=" C6 ATP 7 401 " 0.002 2.00e-02 2.50e+03 pdb=" C8 ATP 7 401 " 0.002 2.00e-02 2.50e+03 pdb=" N1 ATP 7 401 " -0.003 2.00e-02 2.50e+03 pdb=" N3 ATP 7 401 " 0.007 2.00e-02 2.50e+03 pdb=" N6 ATP 7 401 " -0.011 2.00e-02 2.50e+03 pdb=" N7 ATP 7 401 " 0.001 2.00e-02 2.50e+03 pdb=" N9 ATP 7 401 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE 7 168 " 0.006 2.00e-02 2.50e+03 1.28e-02 1.64e+00 pdb=" C ILE 7 168 " -0.022 2.00e-02 2.50e+03 pdb=" O ILE 7 168 " 0.008 2.00e-02 2.50e+03 pdb=" N PHE 7 169 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 2 199 " -0.015 2.00e-02 2.50e+03 9.04e-03 1.63e+00 pdb=" CG TYR 2 199 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR 2 199 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR 2 199 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR 2 199 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR 2 199 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR 2 199 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR 2 199 " -0.005 2.00e-02 2.50e+03 ... (remaining 3119 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 14 2.30 - 2.95: 6840 2.95 - 3.60: 26620 3.60 - 4.25: 40909 4.25 - 4.90: 69158 Nonbonded interactions: 143541 Sorted by model distance: nonbonded pdb=" OE1 GLN 5 200 " pdb=" CG LEU 5 299 " model vdw 1.645 3.470 nonbonded pdb=" OE1 GLN 5 200 " pdb=" CB LEU 5 299 " model vdw 1.709 3.440 nonbonded pdb=" NE2 GLN 5 200 " pdb=" CD2 LEU 5 299 " model vdw 1.874 3.540 nonbonded pdb=" OE1 GLN 5 200 " pdb=" CD1 LEU 5 299 " model vdw 1.929 3.460 nonbonded pdb=" OE1 GLN 5 200 " pdb=" CD2 LEU 5 299 " model vdw 1.953 3.460 ... (remaining 143536 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 '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.250 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 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 : 0.013 0.146 18773 Z= 1.015 Angle : 1.833 19.404 25612 Z= 1.364 Chirality : 0.080 0.223 2863 Planarity : 0.003 0.015 3122 Dihedral : 19.526 83.452 7166 Min Nonbonded Distance : 1.645 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.51 % Allowed : 9.11 % Favored : 90.38 % Rotamer: Outliers : 11.94 % Allowed : 14.23 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.89 (0.15), residues: 2163 helix: -1.98 (0.12), residues: 1127 sheet: -3.45 (0.31), residues: 224 loop : -2.99 (0.18), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 6 195 TYR 0.020 0.003 TYR 2 199 PHE 0.017 0.003 PHE 7 209 TRP 0.021 0.003 TRP 4 154 HIS 0.006 0.001 HIS 2 138 Details of bonding type rmsd/Z covalent geometry : bond 0.01315 / 1.01 (18772) covalent geometry : angle 1.83280 / 1.36 (25612) hydrogen bonds : bond 0.17555 / 19.32 ( 816) hydrogen bonds : angle 7.32010 / 8.41 ( 2372) Misc. bond : bond 0.14647 / 7.32 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 956 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 732 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 19 THR cc_start: 0.7610 (OUTLIER) cc_final: 0.6935 (t) REVERT: 1 22 VAL cc_start: 0.6374 (t) cc_final: 0.6116 (p) REVERT: 1 23 ARG cc_start: 0.8149 (mtm180) cc_final: 0.7830 (mtm110) REVERT: 1 26 LEU cc_start: 0.7049 (mt) cc_final: 0.6679 (mt) REVERT: 1 30 ASP cc_start: 0.7085 (m-30) cc_final: 0.6724 (m-30) REVERT: 1 37 ASP cc_start: 0.7944 (p0) cc_final: 0.6600 (p0) REVERT: 1 38 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.6946 (mp) REVERT: 1 39 GLU cc_start: 0.6615 (mp0) cc_final: 0.5311 (mp0) REVERT: 1 46 MET cc_start: 0.8275 (tpt) cc_final: 0.7632 (tpp) REVERT: 1 60 LYS cc_start: 0.7904 (mmmt) cc_final: 0.7608 (mmmm) REVERT: 1 64 ASN cc_start: 0.7741 (m-40) cc_final: 0.7505 (m110) REVERT: 1 83 GLU cc_start: 0.7792 (tt0) cc_final: 0.7116 (mt-10) REVERT: 1 86 ASP cc_start: 0.7946 (t70) cc_final: 0.7570 (t70) REVERT: 1 92 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7456 (t0) REVERT: 1 109 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.5961 (tt0) REVERT: 1 110 THR cc_start: 0.7681 (OUTLIER) cc_final: 0.6607 (p) REVERT: 1 114 ARG cc_start: 0.6952 (ptp90) cc_final: 0.6619 (mtm-85) REVERT: 1 118 ARG cc_start: 0.7915 (ttm170) cc_final: 0.7704 (ttm-80) REVERT: 1 129 LYS cc_start: 0.8184 (mtpt) cc_final: 0.7954 (mtpt) REVERT: 1 150 GLN cc_start: 0.8078 (mt0) cc_final: 0.7763 (mt0) REVERT: 1 168 ILE cc_start: 0.8087 (pt) cc_final: 0.7574 (pt) REVERT: 1 175 LYS cc_start: 0.7602 (ttmt) cc_final: 0.7172 (tttm) REVERT: 1 179 GLN cc_start: 0.7236 (mt0) cc_final: 0.6837 (mt0) REVERT: 1 187 ARG cc_start: 0.7630 (mtt90) cc_final: 0.7400 (mtt-85) REVERT: 1 192 VAL cc_start: 0.8237 (OUTLIER) cc_final: 0.8031 (m) REVERT: 1 193 GLU cc_start: 0.8014 (tp30) cc_final: 0.7385 (tp30) REVERT: 1 197 PHE cc_start: 0.8456 (m-80) cc_final: 0.8211 (m-10) REVERT: 1 215 LYS cc_start: 0.7779 (mmtt) cc_final: 0.7563 (mmtt) REVERT: 1 259 ASN cc_start: 0.7072 (p0) cc_final: 0.6839 (p0) REVERT: 1 261 HIS cc_start: 0.6245 (m170) cc_final: 0.5829 (m90) REVERT: 1 274 LYS cc_start: 0.8035 (mttt) cc_final: 0.7806 (mtmm) REVERT: 1 285 LYS cc_start: 0.7301 (tppt) cc_final: 0.6783 (tppt) REVERT: 1 300 ARG cc_start: 0.7695 (mtm-85) cc_final: 0.7379 (mtm-85) REVERT: 1 310 ASP cc_start: 0.7342 (m-30) cc_final: 0.7013 (m-30) REVERT: 1 311 TYR cc_start: 0.7894 (t80) cc_final: 0.7546 (t80) REVERT: 2 8 ARG cc_start: 0.7355 (ttm170) cc_final: 0.7105 (ttp-170) REVERT: 2 14 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.7005 (mtm-85) REVERT: 2 24 LYS cc_start: 0.7295 (tttt) cc_final: 0.7037 (ttmm) REVERT: 2 33 ARG cc_start: 0.7829 (ttp80) cc_final: 0.7356 (ttp-170) REVERT: 2 39 GLU cc_start: 0.6237 (mp0) cc_final: 0.5705 (mp0) REVERT: 2 40 SER cc_start: 0.7082 (m) cc_final: 0.6715 (t) REVERT: 2 89 LYS cc_start: 0.7551 (mmmt) cc_final: 0.7119 (mmmt) REVERT: 2 96 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7346 (tm-30) REVERT: 2 100 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7807 (tm-30) REVERT: 2 122 LEU cc_start: 0.7672 (tp) cc_final: 0.7380 (tp) REVERT: 2 141 GLU cc_start: 0.7481 (tt0) cc_final: 0.6901 (tt0) REVERT: 2 150 GLN cc_start: 0.7622 (mt0) cc_final: 0.6909 (mm-40) REVERT: 2 162 THR cc_start: 0.8349 (t) cc_final: 0.7967 (p) REVERT: 2 163 LYS cc_start: 0.8062 (mppt) cc_final: 0.7541 (mmtp) REVERT: 2 164 CYS cc_start: 0.8115 (t) cc_final: 0.7459 (p) REVERT: 2 171 MET cc_start: 0.8519 (mtp) cc_final: 0.8264 (mtp) REVERT: 2 179 GLN cc_start: 0.7721 (mt0) cc_final: 0.7512 (mt0) REVERT: 2 193 GLU cc_start: 0.7542 (tp30) cc_final: 0.7098 (tp30) REVERT: 2 200 GLN cc_start: 0.3923 (OUTLIER) cc_final: 0.3654 (tm-30) REVERT: 2 214 ASP cc_start: 0.7526 (t70) cc_final: 0.7178 (t0) REVERT: 2 235 TYR cc_start: 0.7771 (t80) cc_final: 0.7135 (t80) REVERT: 2 242 MET cc_start: 0.7350 (tpp) cc_final: 0.7052 (tmm) REVERT: 2 255 GLU cc_start: 0.8038 (tp30) cc_final: 0.7205 (mm-30) REVERT: 2 259 ASN cc_start: 0.7530 (p0) cc_final: 0.7318 (p0) REVERT: 2 262 GLU cc_start: 0.6711 (mp0) cc_final: 0.6282 (mp0) REVERT: 2 268 ASP cc_start: 0.6802 (p0) cc_final: 0.6465 (p0) REVERT: 2 286 ASN cc_start: 0.8600 (t0) cc_final: 0.8166 (t0) REVERT: 2 310 ASP cc_start: 0.7014 (m-30) cc_final: 0.6550 (m-30) REVERT: 3 30 ASP cc_start: 0.7717 (m-30) cc_final: 0.6917 (m-30) REVERT: 3 33 ARG cc_start: 0.7943 (ttp80) cc_final: 0.7628 (ttp-110) REVERT: 3 34 ASP cc_start: 0.7513 (m-30) cc_final: 0.6468 (m-30) REVERT: 3 39 GLU cc_start: 0.7284 (mp0) cc_final: 0.6853 (mp0) REVERT: 3 46 MET cc_start: 0.8169 (tpt) cc_final: 0.7540 (tpp) REVERT: 3 48 TYR cc_start: 0.7704 (m-80) cc_final: 0.7472 (m-80) REVERT: 3 61 LYS cc_start: 0.8198 (tptp) cc_final: 0.7846 (tptp) REVERT: 3 81 HIS cc_start: 0.8467 (t70) cc_final: 0.8044 (t-90) REVERT: 3 89 LYS cc_start: 0.8071 (mmmt) cc_final: 0.7790 (mmmt) REVERT: 3 118 ARG cc_start: 0.7660 (ttm170) cc_final: 0.7349 (ttt90) REVERT: 3 126 VAL cc_start: 0.8197 (m) cc_final: 0.7929 (p) REVERT: 3 143 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.7367 (ppt170) REVERT: 3 157 MET cc_start: 0.7671 (ttm) cc_final: 0.7080 (tpp) REVERT: 3 173 TYR cc_start: 0.8455 (p90) cc_final: 0.7759 (p90) REVERT: 3 175 LYS cc_start: 0.7820 (ttmt) cc_final: 0.7351 (ttmm) REVERT: 3 179 GLN cc_start: 0.7736 (mt0) cc_final: 0.7475 (mt0) REVERT: 3 207 LYS cc_start: 0.8144 (tttt) cc_final: 0.7562 (ttmt) REVERT: 3 214 ASP cc_start: 0.7636 (t70) cc_final: 0.7303 (t0) REVERT: 3 220 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.6353 (pm20) REVERT: 3 225 LEU cc_start: 0.7561 (mp) cc_final: 0.7358 (mt) REVERT: 3 233 LYS cc_start: 0.7176 (mtpt) cc_final: 0.6827 (mtmm) REVERT: 3 247 ASN cc_start: 0.8171 (m-40) cc_final: 0.7876 (m-40) REVERT: 3 250 TYR cc_start: 0.7707 (t80) cc_final: 0.7175 (t80) REVERT: 3 268 ASP cc_start: 0.7042 (p0) cc_final: 0.6676 (p0) REVERT: 3 282 ASN cc_start: 0.8012 (t0) cc_final: 0.7732 (t0) REVERT: 3 289 GLU cc_start: 0.5929 (OUTLIER) cc_final: 0.5705 (pt0) REVERT: 3 300 ARG cc_start: 0.8250 (mtm-85) cc_final: 0.7630 (mtt90) REVERT: 4 16 PHE cc_start: 0.7528 (t80) cc_final: 0.7235 (t80) REVERT: 4 18 SER cc_start: 0.7927 (p) cc_final: 0.7408 (p) REVERT: 4 19 THR cc_start: 0.7697 (OUTLIER) cc_final: 0.7075 (p) REVERT: 4 23 ARG cc_start: 0.6925 (mtm180) cc_final: 0.6382 (mtm-85) REVERT: 4 46 MET cc_start: 0.7926 (tpt) cc_final: 0.7615 (tpt) REVERT: 4 53 VAL cc_start: 0.7746 (OUTLIER) cc_final: 0.7512 (m) REVERT: 4 55 LYS cc_start: 0.7047 (mtmt) cc_final: 0.6804 (mtmm) REVERT: 4 62 TYR cc_start: 0.7875 (t80) cc_final: 0.7609 (t80) REVERT: 4 64 ASN cc_start: 0.7528 (m-40) cc_final: 0.7247 (m-40) REVERT: 4 83 GLU cc_start: 0.7323 (tt0) cc_final: 0.6251 (tt0) REVERT: 4 98 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7862 (mm) REVERT: 4 109 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6997 (pp20) REVERT: 4 133 ILE cc_start: 0.6833 (mt) cc_final: 0.6631 (mm) REVERT: 4 149 THR cc_start: 0.5316 (OUTLIER) cc_final: 0.4877 (t) REVERT: 4 154 TRP cc_start: 0.7475 (t60) cc_final: 0.7075 (t60) REVERT: 4 155 LEU cc_start: 0.8123 (mt) cc_final: 0.7865 (mm) REVERT: 4 192 VAL cc_start: 0.7641 (OUTLIER) cc_final: 0.7423 (p) REVERT: 4 220 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7748 (pm20) REVERT: 4 227 ASN cc_start: 0.6222 (m-40) cc_final: 0.6015 (p0) REVERT: 4 238 SER cc_start: 0.7646 (p) cc_final: 0.7398 (p) REVERT: 4 239 GLN cc_start: 0.6386 (mp10) cc_final: 0.6182 (mp10) REVERT: 4 247 ASN cc_start: 0.7610 (m-40) cc_final: 0.7311 (t0) REVERT: 4 253 SER cc_start: 0.7753 (p) cc_final: 0.7420 (p) REVERT: 4 271 PHE cc_start: 0.7634 (t80) cc_final: 0.7377 (t80) REVERT: 4 274 LYS cc_start: 0.7871 (mttt) cc_final: 0.7387 (mttt) REVERT: 4 279 ASP cc_start: 0.7728 (p0) cc_final: 0.7462 (t70) REVERT: 4 295 THR cc_start: 0.7989 (p) cc_final: 0.7539 (p) REVERT: 4 298 MET cc_start: 0.6436 (mtt) cc_final: 0.5909 (mtt) REVERT: 5 60 LYS cc_start: 0.6944 (mmmt) cc_final: 0.6684 (mmtt) REVERT: 5 105 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6508 (mm) REVERT: 5 109 GLU cc_start: 0.3836 (OUTLIER) cc_final: 0.3278 (tt0) REVERT: 5 142 GLU cc_start: 0.4856 (OUTLIER) cc_final: 0.4551 (mm-30) REVERT: 5 171 MET cc_start: 0.7619 (mtp) cc_final: 0.6815 (mtp) REVERT: 5 215 LYS cc_start: 0.7401 (mmtt) cc_final: 0.6911 (tmtt) REVERT: 6 19 THR cc_start: 0.7528 (OUTLIER) cc_final: 0.7228 (p) REVERT: 6 30 ASP cc_start: 0.6853 (m-30) cc_final: 0.6504 (m-30) REVERT: 6 33 ARG cc_start: 0.7847 (ttp80) cc_final: 0.7638 (ttp-110) REVERT: 6 53 VAL cc_start: 0.7553 (OUTLIER) cc_final: 0.7180 (m) REVERT: 6 62 TYR cc_start: 0.7767 (t80) cc_final: 0.7352 (t80) REVERT: 6 64 ASN cc_start: 0.6537 (m-40) cc_final: 0.6292 (m110) REVERT: 6 76 ILE cc_start: 0.6439 (OUTLIER) cc_final: 0.6194 (mm) REVERT: 6 83 GLU cc_start: 0.7076 (tt0) cc_final: 0.6842 (tt0) REVERT: 6 96 GLU cc_start: 0.7501 (tm-30) cc_final: 0.6973 (mt-10) REVERT: 6 105 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7235 (pt) REVERT: 6 111 ASP cc_start: 0.7032 (t70) cc_final: 0.6707 (t0) REVERT: 6 134 ASP cc_start: 0.6673 (t0) cc_final: 0.6095 (t0) REVERT: 6 137 GLN cc_start: 0.7960 (pm20) cc_final: 0.6832 (pm20) REVERT: 6 141 GLU cc_start: 0.7220 (tt0) cc_final: 0.6465 (tt0) REVERT: 6 149 THR cc_start: 0.7696 (OUTLIER) cc_final: 0.7302 (p) REVERT: 6 150 GLN cc_start: 0.7514 (mt0) cc_final: 0.7227 (mt0) REVERT: 6 156 LYS cc_start: 0.7574 (ttpt) cc_final: 0.7302 (ttpp) REVERT: 6 158 ILE cc_start: 0.7359 (tp) cc_final: 0.7098 (mm) REVERT: 6 164 CYS cc_start: 0.7742 (t) cc_final: 0.7164 (p) REVERT: 6 171 MET cc_start: 0.8255 (mtp) cc_final: 0.7950 (mmm) REVERT: 6 175 LYS cc_start: 0.7640 (ttmt) cc_final: 0.7423 (ttmm) REVERT: 6 181 ASN cc_start: 0.7956 (t0) cc_final: 0.7738 (t0) REVERT: 6 187 ARG cc_start: 0.7891 (mtt90) cc_final: 0.7258 (tpp80) REVERT: 6 189 SER cc_start: 0.8548 (p) cc_final: 0.8161 (m) REVERT: 6 191 GLN cc_start: 0.7940 (mt0) cc_final: 0.7715 (mt0) REVERT: 6 192 VAL cc_start: 0.8458 (OUTLIER) cc_final: 0.8182 (t) REVERT: 6 198 SER cc_start: 0.7506 (p) cc_final: 0.6928 (t) REVERT: 6 231 GLN cc_start: 0.8344 (tt0) cc_final: 0.8016 (tt0) REVERT: 6 233 LYS cc_start: 0.7799 (mtpt) cc_final: 0.7501 (mmtm) REVERT: 6 234 LEU cc_start: 0.8154 (mt) cc_final: 0.7933 (mt) REVERT: 6 255 GLU cc_start: 0.7122 (tp30) cc_final: 0.6648 (tt0) REVERT: 6 268 ASP cc_start: 0.8177 (p0) cc_final: 0.7148 (p0) REVERT: 6 274 LYS cc_start: 0.7962 (mttt) cc_final: 0.7717 (mmtt) REVERT: 6 283 SER cc_start: 0.8121 (p) cc_final: 0.7791 (t) REVERT: 7 24 LYS cc_start: 0.7684 (tttt) cc_final: 0.7272 (ttpp) REVERT: 7 28 TYR cc_start: 0.8021 (m-10) cc_final: 0.7769 (m-10) REVERT: 7 33 ARG cc_start: 0.7486 (ttp80) cc_final: 0.6938 (ttm170) REVERT: 7 38 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6967 (mt) REVERT: 7 39 GLU cc_start: 0.7686 (mp0) cc_final: 0.6861 (mp0) REVERT: 7 41 GLU cc_start: 0.7547 (tt0) cc_final: 0.7244 (tt0) REVERT: 7 43 THR cc_start: 0.7429 (OUTLIER) cc_final: 0.7165 (m) REVERT: 7 44 CYS cc_start: 0.7985 (m) cc_final: 0.7598 (m) REVERT: 7 83 GLU cc_start: 0.7206 (tt0) cc_final: 0.6898 (mt-10) REVERT: 7 86 ASP cc_start: 0.8378 (t70) cc_final: 0.8053 (t0) REVERT: 7 98 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6390 (mm) REVERT: 7 111 ASP cc_start: 0.6858 (t70) cc_final: 0.6523 (t70) REVERT: 7 115 LEU cc_start: 0.6541 (pp) cc_final: 0.6335 (pp) REVERT: 7 119 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7477 (pt) REVERT: 7 146 ARG cc_start: 0.7566 (ptm160) cc_final: 0.7225 (ptm160) REVERT: 7 147 VAL cc_start: 0.7468 (m) cc_final: 0.7218 (p) REVERT: 7 156 LYS cc_start: 0.7552 (ttpt) cc_final: 0.7089 (tttm) REVERT: 7 157 MET cc_start: 0.7693 (ttm) cc_final: 0.7164 (ttm) REVERT: 7 160 ASN cc_start: 0.7611 (m-40) cc_final: 0.7263 (p0) REVERT: 7 166 ILE cc_start: 0.8259 (mt) cc_final: 0.7921 (tp) REVERT: 7 175 LYS cc_start: 0.7369 (ttmt) cc_final: 0.7080 (ttmt) REVERT: 7 181 ASN cc_start: 0.7465 (t0) cc_final: 0.6991 (t0) REVERT: 7 192 VAL cc_start: 0.8572 (OUTLIER) cc_final: 0.8318 (t) REVERT: 7 214 ASP cc_start: 0.7416 (t70) cc_final: 0.7009 (t0) REVERT: 7 225 LEU cc_start: 0.7094 (mp) cc_final: 0.6576 (mt) REVERT: 7 232 LYS cc_start: 0.7702 (ttmm) cc_final: 0.7099 (ttpp) REVERT: 7 241 ASN cc_start: 0.7234 (t0) cc_final: 0.6996 (t0) REVERT: 7 246 ARG cc_start: 0.7664 (mmm-85) cc_final: 0.7332 (mmm160) REVERT: 7 250 TYR cc_start: 0.7774 (t80) cc_final: 0.7238 (t80) REVERT: 7 279 ASP cc_start: 0.7862 (p0) cc_final: 0.7532 (p0) REVERT: 7 309 GLU cc_start: 0.6685 (mt-10) cc_final: 0.6460 (mt-10) REVERT: 7 313 ARG cc_start: 0.6960 (ttp-170) cc_final: 0.6450 (ttp-170) outliers start: 224 outliers final: 72 residues processed: 883 average time/residue: 0.1747 time to fit residues: 218.1652 Evaluate side-chains 749 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 645 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 14 ARG Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 1 residue 38 LEU Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 1 residue 92 ASP Chi-restraints excluded: chain 1 residue 109 GLU Chi-restraints excluded: chain 1 residue 110 THR Chi-restraints excluded: chain 1 residue 119 LEU Chi-restraints excluded: chain 1 residue 142 GLU Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 1 residue 149 THR Chi-restraints excluded: chain 1 residue 192 VAL Chi-restraints excluded: chain 1 residue 211 GLU Chi-restraints excluded: chain 1 residue 289 GLU Chi-restraints excluded: chain 1 residue 294 VAL Chi-restraints excluded: chain 2 residue 14 ARG Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 105 LEU Chi-restraints excluded: chain 2 residue 119 LEU Chi-restraints excluded: chain 2 residue 120 THR Chi-restraints excluded: chain 2 residue 149 THR Chi-restraints excluded: chain 2 residue 192 VAL Chi-restraints excluded: chain 2 residue 200 GLN Chi-restraints excluded: chain 2 residue 208 THR Chi-restraints excluded: chain 2 residue 211 GLU Chi-restraints excluded: chain 2 residue 263 THR Chi-restraints excluded: chain 3 residue 19 THR Chi-restraints excluded: chain 3 residue 32 CYS Chi-restraints excluded: chain 3 residue 110 THR Chi-restraints excluded: chain 3 residue 119 LEU Chi-restraints excluded: chain 3 residue 142 GLU Chi-restraints excluded: chain 3 residue 143 ARG Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 149 THR Chi-restraints excluded: chain 3 residue 211 GLU Chi-restraints excluded: chain 3 residue 220 GLU Chi-restraints excluded: chain 3 residue 263 THR Chi-restraints excluded: chain 3 residue 270 VAL Chi-restraints excluded: chain 3 residue 289 GLU Chi-restraints excluded: chain 4 residue 14 ARG Chi-restraints excluded: chain 4 residue 19 THR Chi-restraints excluded: chain 4 residue 29 MET Chi-restraints excluded: chain 4 residue 53 VAL Chi-restraints excluded: chain 4 residue 98 LEU Chi-restraints excluded: chain 4 residue 109 GLU Chi-restraints excluded: chain 4 residue 110 THR Chi-restraints excluded: chain 4 residue 119 LEU Chi-restraints excluded: chain 4 residue 142 GLU Chi-restraints excluded: chain 4 residue 148 LEU Chi-restraints excluded: chain 4 residue 149 THR Chi-restraints excluded: chain 4 residue 192 VAL Chi-restraints excluded: chain 4 residue 211 GLU Chi-restraints excluded: chain 4 residue 220 GLU Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 289 GLU Chi-restraints excluded: chain 4 residue 294 VAL Chi-restraints excluded: chain 5 residue 14 ARG Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 29 MET Chi-restraints excluded: chain 5 residue 32 CYS Chi-restraints excluded: chain 5 residue 76 ILE Chi-restraints excluded: chain 5 residue 77 ILE Chi-restraints excluded: chain 5 residue 105 LEU Chi-restraints excluded: chain 5 residue 109 GLU Chi-restraints excluded: chain 5 residue 110 THR Chi-restraints excluded: chain 5 residue 119 LEU Chi-restraints excluded: chain 5 residue 120 THR Chi-restraints excluded: chain 5 residue 142 GLU Chi-restraints excluded: chain 5 residue 211 GLU Chi-restraints excluded: chain 5 residue 220 GLU Chi-restraints excluded: chain 5 residue 263 THR Chi-restraints excluded: chain 5 residue 289 GLU Chi-restraints excluded: chain 5 residue 293 GLU Chi-restraints excluded: chain 6 residue 6 GLU Chi-restraints excluded: chain 6 residue 14 ARG Chi-restraints excluded: chain 6 residue 19 THR Chi-restraints excluded: chain 6 residue 32 CYS Chi-restraints excluded: chain 6 residue 53 VAL Chi-restraints excluded: chain 6 residue 76 ILE Chi-restraints excluded: chain 6 residue 105 LEU Chi-restraints excluded: chain 6 residue 119 LEU Chi-restraints excluded: chain 6 residue 120 THR Chi-restraints excluded: chain 6 residue 123 ILE Chi-restraints excluded: chain 6 residue 142 GLU Chi-restraints excluded: chain 6 residue 143 ARG Chi-restraints excluded: chain 6 residue 148 LEU Chi-restraints excluded: chain 6 residue 149 THR Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 6 residue 211 GLU Chi-restraints excluded: chain 6 residue 263 THR Chi-restraints excluded: chain 6 residue 289 GLU Chi-restraints excluded: chain 6 residue 293 GLU Chi-restraints excluded: chain 6 residue 294 VAL Chi-restraints excluded: chain 7 residue 14 ARG Chi-restraints excluded: chain 7 residue 19 THR Chi-restraints excluded: chain 7 residue 38 LEU Chi-restraints excluded: chain 7 residue 43 THR Chi-restraints excluded: chain 7 residue 98 LEU Chi-restraints excluded: chain 7 residue 119 LEU Chi-restraints excluded: chain 7 residue 123 ILE Chi-restraints excluded: chain 7 residue 142 GLU Chi-restraints excluded: chain 7 residue 149 THR Chi-restraints excluded: chain 7 residue 192 VAL Chi-restraints excluded: chain 7 residue 270 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 0.8980 chunk 212 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 282 ASN 2 138 HIS 2 231 GLN 2 261 HIS 3 138 HIS 4 138 HIS 4 259 ASN 5 138 HIS 6 138 HIS 6 183 GLN 6 200 GLN 6 314 HIS 7 138 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.170058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.136555 restraints weight = 26380.402| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.27 r_work: 0.3564 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 18773 Z= 0.194 Angle : 0.762 12.650 25612 Z= 0.384 Chirality : 0.045 0.245 2863 Planarity : 0.006 0.100 3122 Dihedral : 17.349 90.664 3050 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 6.93 % Allowed : 23.40 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.17), residues: 2163 helix: -0.42 (0.14), residues: 1183 sheet: -3.15 (0.32), residues: 238 loop : -2.64 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 3 14 TYR 0.023 0.002 TYR 6 199 PHE 0.020 0.002 PHE 2 271 TRP 0.016 0.002 TRP 6 154 HIS 0.006 0.001 HIS 4 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (18772) covalent geometry : angle 0.76223 / 0.38 (25612) hydrogen bonds : bond 0.04483 / 4.95 ( 816) hydrogen bonds : angle 4.38791 / 5.04 ( 2372) Misc. bond : bond 0.00161 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 656 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 6 GLU cc_start: 0.7786 (pm20) cc_final: 0.7541 (pm20) REVERT: 1 14 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.7001 (mtm-85) REVERT: 1 19 THR cc_start: 0.8850 (OUTLIER) cc_final: 0.8188 (t) REVERT: 1 26 LEU cc_start: 0.8472 (mt) cc_final: 0.8020 (mt) REVERT: 1 30 ASP cc_start: 0.7777 (m-30) cc_final: 0.7483 (m-30) REVERT: 1 37 ASP cc_start: 0.8191 (p0) cc_final: 0.7151 (p0) REVERT: 1 38 LEU cc_start: 0.7911 (mp) cc_final: 0.7322 (mt) REVERT: 1 39 GLU cc_start: 0.7144 (mp0) cc_final: 0.5928 (mp0) REVERT: 1 45 MET cc_start: 0.8669 (ttm) cc_final: 0.8358 (ttp) REVERT: 1 46 MET cc_start: 0.8093 (tpt) cc_final: 0.7779 (tpp) REVERT: 1 60 LYS cc_start: 0.8613 (mmmt) cc_final: 0.8264 (mmtp) REVERT: 1 83 GLU cc_start: 0.7116 (tt0) cc_final: 0.6820 (mt-10) REVERT: 1 100 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7164 (tm-30) REVERT: 1 109 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.6335 (tt0) REVERT: 1 114 ARG cc_start: 0.7763 (ptp90) cc_final: 0.7427 (mtm-85) REVERT: 1 129 LYS cc_start: 0.8528 (mtpt) cc_final: 0.8246 (mtpt) REVERT: 1 134 ASP cc_start: 0.7119 (t0) cc_final: 0.6826 (t0) REVERT: 1 149 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8469 (p) REVERT: 1 150 GLN cc_start: 0.8308 (mt0) cc_final: 0.8089 (mt0) REVERT: 1 163 LYS cc_start: 0.8287 (mptt) cc_final: 0.7992 (mmtm) REVERT: 1 261 HIS cc_start: 0.6263 (m170) cc_final: 0.6019 (m90) REVERT: 1 271 PHE cc_start: 0.7916 (t80) cc_final: 0.7319 (t80) REVERT: 1 274 LYS cc_start: 0.8607 (mttt) cc_final: 0.8392 (mtpp) REVERT: 1 285 LYS cc_start: 0.7495 (tppt) cc_final: 0.7166 (tppt) REVERT: 2 33 ARG cc_start: 0.8266 (ttp80) cc_final: 0.7935 (ttp-170) REVERT: 2 39 GLU cc_start: 0.6890 (mp0) cc_final: 0.6442 (mp0) REVERT: 2 89 LYS cc_start: 0.8307 (mmmt) cc_final: 0.7941 (mmmt) REVERT: 2 96 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7487 (tm-30) REVERT: 2 122 LEU cc_start: 0.8462 (tp) cc_final: 0.8210 (tp) REVERT: 2 129 LYS cc_start: 0.8425 (mmpt) cc_final: 0.8165 (mmpt) REVERT: 2 150 GLN cc_start: 0.8146 (mt0) cc_final: 0.7567 (mm-40) REVERT: 2 163 LYS cc_start: 0.8386 (mppt) cc_final: 0.8082 (mmtm) REVERT: 2 164 CYS cc_start: 0.8085 (t) cc_final: 0.7740 (m) REVERT: 2 181 ASN cc_start: 0.7903 (t0) cc_final: 0.7511 (t0) REVERT: 2 200 GLN cc_start: 0.5772 (OUTLIER) cc_final: 0.5325 (tm-30) REVERT: 2 232 LYS cc_start: 0.8190 (ttmm) cc_final: 0.7893 (ttmm) REVERT: 2 259 ASN cc_start: 0.8348 (OUTLIER) cc_final: 0.8124 (p0) REVERT: 2 286 ASN cc_start: 0.8865 (t0) cc_final: 0.8641 (t0) REVERT: 2 310 ASP cc_start: 0.7614 (m-30) cc_final: 0.7320 (m-30) REVERT: 3 34 ASP cc_start: 0.8176 (m-30) cc_final: 0.7744 (m-30) REVERT: 3 38 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7416 (mm) REVERT: 3 39 GLU cc_start: 0.7523 (mp0) cc_final: 0.7162 (mp0) REVERT: 3 46 MET cc_start: 0.7915 (tpt) cc_final: 0.7571 (tpp) REVERT: 3 96 GLU cc_start: 0.7356 (tm-30) cc_final: 0.7116 (tm-30) REVERT: 3 175 LYS cc_start: 0.8435 (ttmt) cc_final: 0.8197 (ttmm) REVERT: 3 181 ASN cc_start: 0.7637 (t0) cc_final: 0.7391 (t0) REVERT: 3 207 LYS cc_start: 0.8623 (tttt) cc_final: 0.8214 (ttmt) REVERT: 3 220 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.6254 (pm20) REVERT: 3 232 LYS cc_start: 0.7885 (ttmm) cc_final: 0.7583 (ttmm) REVERT: 3 233 LYS cc_start: 0.7779 (mtpt) cc_final: 0.7505 (mtmm) REVERT: 3 247 ASN cc_start: 0.8794 (m-40) cc_final: 0.8364 (m-40) REVERT: 3 255 GLU cc_start: 0.8018 (tp30) cc_final: 0.7629 (tp30) REVERT: 3 259 ASN cc_start: 0.7846 (OUTLIER) cc_final: 0.7200 (p0) REVERT: 3 268 ASP cc_start: 0.7342 (p0) cc_final: 0.6928 (p0) REVERT: 3 279 ASP cc_start: 0.6667 (p0) cc_final: 0.6437 (p0) REVERT: 3 282 ASN cc_start: 0.8065 (t0) cc_final: 0.7732 (t0) REVERT: 4 19 THR cc_start: 0.8373 (OUTLIER) cc_final: 0.8090 (p) REVERT: 4 23 ARG cc_start: 0.6884 (mtm180) cc_final: 0.6654 (mtm110) REVERT: 4 29 MET cc_start: 0.7946 (mtt) cc_final: 0.7576 (mmp) REVERT: 4 46 MET cc_start: 0.7820 (tpt) cc_final: 0.7380 (tpt) REVERT: 4 55 LYS cc_start: 0.7874 (mtmt) cc_final: 0.7578 (mtmm) REVERT: 4 62 TYR cc_start: 0.8197 (t80) cc_final: 0.7930 (t80) REVERT: 4 83 GLU cc_start: 0.6960 (tt0) cc_final: 0.6146 (tt0) REVERT: 4 133 ILE cc_start: 0.7778 (mt) cc_final: 0.7535 (mm) REVERT: 4 149 THR cc_start: 0.5098 (OUTLIER) cc_final: 0.4549 (t) REVERT: 4 154 TRP cc_start: 0.7840 (t60) cc_final: 0.7568 (t60) REVERT: 4 155 LEU cc_start: 0.8336 (mt) cc_final: 0.7987 (mm) REVERT: 4 253 SER cc_start: 0.8293 (p) cc_final: 0.7997 (p) REVERT: 4 295 THR cc_start: 0.8753 (p) cc_final: 0.8108 (t) REVERT: 4 298 MET cc_start: 0.6837 (mtt) cc_final: 0.6602 (mtt) REVERT: 4 304 LYS cc_start: 0.7092 (tppt) cc_final: 0.6838 (tppt) REVERT: 4 311 TYR cc_start: 0.6543 (t80) cc_final: 0.6289 (t80) REVERT: 5 55 LYS cc_start: 0.7411 (mtmm) cc_final: 0.6802 (mtmm) REVERT: 5 60 LYS cc_start: 0.7096 (mmmt) cc_final: 0.6732 (mmtt) REVERT: 5 84 LEU cc_start: 0.6995 (mp) cc_final: 0.6771 (mt) REVERT: 5 105 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.6610 (mm) REVERT: 5 118 ARG cc_start: 0.7668 (ttm170) cc_final: 0.7277 (ttm170) REVERT: 5 171 MET cc_start: 0.7724 (mtp) cc_final: 0.6929 (mtp) REVERT: 6 30 ASP cc_start: 0.7443 (m-30) cc_final: 0.7194 (m-30) REVERT: 6 64 ASN cc_start: 0.7139 (m-40) cc_final: 0.6885 (m110) REVERT: 6 111 ASP cc_start: 0.7267 (t70) cc_final: 0.6980 (t0) REVERT: 6 119 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8036 (tp) REVERT: 6 134 ASP cc_start: 0.7351 (t0) cc_final: 0.6943 (t0) REVERT: 6 135 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6798 (mm-30) REVERT: 6 141 GLU cc_start: 0.6362 (tt0) cc_final: 0.5828 (tt0) REVERT: 6 143 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7426 (ppt170) REVERT: 6 144 SER cc_start: 0.6928 (p) cc_final: 0.5204 (p) REVERT: 6 149 THR cc_start: 0.8227 (OUTLIER) cc_final: 0.7815 (p) REVERT: 6 150 GLN cc_start: 0.8261 (mt0) cc_final: 0.8049 (mt0) REVERT: 6 153 ASN cc_start: 0.8053 (m-40) cc_final: 0.7773 (m-40) REVERT: 6 158 ILE cc_start: 0.8479 (tp) cc_final: 0.7866 (mm) REVERT: 6 175 LYS cc_start: 0.8395 (ttmt) cc_final: 0.8054 (ttmm) REVERT: 6 189 SER cc_start: 0.8704 (p) cc_final: 0.8420 (t) REVERT: 6 232 LYS cc_start: 0.8363 (ttmm) cc_final: 0.8064 (mmmm) REVERT: 6 255 GLU cc_start: 0.7569 (tp30) cc_final: 0.7334 (tt0) REVERT: 6 268 ASP cc_start: 0.7887 (p0) cc_final: 0.7324 (p0) REVERT: 6 283 SER cc_start: 0.8292 (p) cc_final: 0.8008 (t) REVERT: 7 39 GLU cc_start: 0.7746 (mp0) cc_final: 0.7139 (mp0) REVERT: 7 43 THR cc_start: 0.8126 (OUTLIER) cc_final: 0.7831 (m) REVERT: 7 60 LYS cc_start: 0.8524 (mtpp) cc_final: 0.8264 (mttp) REVERT: 7 86 ASP cc_start: 0.8370 (t70) cc_final: 0.8167 (t0) REVERT: 7 129 LYS cc_start: 0.8327 (mmmm) cc_final: 0.7782 (mttp) REVERT: 7 156 LYS cc_start: 0.8680 (ttpt) cc_final: 0.8335 (tttp) REVERT: 7 214 ASP cc_start: 0.7558 (t70) cc_final: 0.7330 (t0) REVERT: 7 225 LEU cc_start: 0.8535 (mp) cc_final: 0.8143 (mt) REVERT: 7 232 LYS cc_start: 0.8550 (ttmm) cc_final: 0.7873 (ttpp) REVERT: 7 276 THR cc_start: 0.8792 (t) cc_final: 0.8550 (m) REVERT: 7 286 ASN cc_start: 0.8559 (OUTLIER) cc_final: 0.8318 (t0) REVERT: 7 313 ARG cc_start: 0.7063 (ttp-170) cc_final: 0.6776 (ttp-170) outliers start: 130 outliers final: 68 residues processed: 722 average time/residue: 0.1722 time to fit residues: 175.3965 Evaluate side-chains 704 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 619 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 14 ARG Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 1 residue 53 VAL Chi-restraints excluded: chain 1 residue 109 GLU Chi-restraints excluded: chain 1 residue 110 THR Chi-restraints excluded: chain 1 residue 117 LYS Chi-restraints excluded: chain 1 residue 119 LEU Chi-restraints excluded: chain 1 residue 142 GLU Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 1 residue 149 THR Chi-restraints excluded: chain 1 residue 158 ILE Chi-restraints excluded: chain 1 residue 176 VAL Chi-restraints excluded: chain 1 residue 295 THR Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 22 VAL Chi-restraints excluded: chain 2 residue 46 MET Chi-restraints excluded: chain 2 residue 149 THR Chi-restraints excluded: chain 2 residue 200 GLN Chi-restraints excluded: chain 2 residue 259 ASN Chi-restraints excluded: chain 2 residue 261 HIS Chi-restraints excluded: chain 2 residue 294 VAL Chi-restraints excluded: chain 2 residue 314 HIS Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 19 THR Chi-restraints excluded: chain 3 residue 38 LEU Chi-restraints excluded: chain 3 residue 63 LEU Chi-restraints excluded: chain 3 residue 110 THR Chi-restraints excluded: chain 3 residue 142 GLU Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 149 THR Chi-restraints excluded: chain 3 residue 220 GLU Chi-restraints excluded: chain 3 residue 259 ASN Chi-restraints excluded: chain 3 residue 270 VAL Chi-restraints excluded: chain 3 residue 273 SER Chi-restraints excluded: chain 4 residue 10 SER Chi-restraints excluded: chain 4 residue 14 ARG Chi-restraints excluded: chain 4 residue 19 THR Chi-restraints excluded: chain 4 residue 27 SER Chi-restraints excluded: chain 4 residue 47 VAL Chi-restraints excluded: chain 4 residue 110 THR Chi-restraints excluded: chain 4 residue 119 LEU Chi-restraints excluded: chain 4 residue 142 GLU Chi-restraints excluded: chain 4 residue 148 LEU Chi-restraints excluded: chain 4 residue 149 THR Chi-restraints excluded: chain 4 residue 211 GLU Chi-restraints excluded: chain 4 residue 230 LEU Chi-restraints excluded: chain 4 residue 231 GLN Chi-restraints excluded: chain 4 residue 269 PHE Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 38 LEU Chi-restraints excluded: chain 5 residue 76 ILE Chi-restraints excluded: chain 5 residue 97 LEU Chi-restraints excluded: chain 5 residue 99 VAL Chi-restraints excluded: chain 5 residue 105 LEU Chi-restraints excluded: chain 5 residue 110 THR Chi-restraints excluded: chain 5 residue 142 GLU Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 211 GLU Chi-restraints excluded: chain 5 residue 259 ASN Chi-restraints excluded: chain 6 residue 6 GLU Chi-restraints excluded: chain 6 residue 14 ARG Chi-restraints excluded: chain 6 residue 99 VAL Chi-restraints excluded: chain 6 residue 118 ARG Chi-restraints excluded: chain 6 residue 119 LEU Chi-restraints excluded: chain 6 residue 142 GLU Chi-restraints excluded: chain 6 residue 143 ARG Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 148 LEU Chi-restraints excluded: chain 6 residue 149 THR Chi-restraints excluded: chain 6 residue 259 ASN Chi-restraints excluded: chain 6 residue 263 THR Chi-restraints excluded: chain 7 residue 19 THR Chi-restraints excluded: chain 7 residue 43 THR Chi-restraints excluded: chain 7 residue 53 VAL Chi-restraints excluded: chain 7 residue 63 LEU Chi-restraints excluded: chain 7 residue 77 ILE Chi-restraints excluded: chain 7 residue 117 LYS Chi-restraints excluded: chain 7 residue 119 LEU Chi-restraints excluded: chain 7 residue 120 THR Chi-restraints excluded: chain 7 residue 142 GLU Chi-restraints excluded: chain 7 residue 148 LEU Chi-restraints excluded: chain 7 residue 149 THR Chi-restraints excluded: chain 7 residue 286 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 37 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 174 optimal weight: 0.5980 chunk 220 optimal weight: 0.7980 chunk 206 optimal weight: 1.9990 chunk 177 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 64 ASN 1 87 ASN 1 231 GLN 2 179 GLN 2 231 GLN 2 261 HIS 3 259 ASN 4 259 ASN 6 160 ASN 6 183 GLN 6 227 ASN 7 87 ASN 7 247 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.169466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.134023 restraints weight = 26531.380| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.26 r_work: 0.3537 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 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 : 0.004 0.054 18773 Z= 0.169 Angle : 0.690 10.930 25612 Z= 0.349 Chirality : 0.043 0.269 2863 Planarity : 0.005 0.080 3122 Dihedral : 16.038 90.059 2933 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 6.61 % Allowed : 25.75 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.18), residues: 2163 helix: 0.22 (0.15), residues: 1183 sheet: -2.90 (0.33), residues: 238 loop : -2.48 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 1 33 TYR 0.026 0.002 TYR 3 199 PHE 0.022 0.002 PHE 1 269 TRP 0.017 0.002 TRP 6 154 HIS 0.012 0.001 HIS 2 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (18772) covalent geometry : angle 0.68993 / 0.35 (25612) hydrogen bonds : bond 0.03985 / 4.40 ( 816) hydrogen bonds : angle 4.02945 / 4.65 ( 2372) Misc. bond : bond 0.00301 / 0.15 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 637 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 19 THR cc_start: 0.8917 (OUTLIER) cc_final: 0.8360 (t) REVERT: 1 23 ARG cc_start: 0.8429 (mtm110) cc_final: 0.8169 (mtm110) REVERT: 1 29 MET cc_start: 0.8633 (mmm) cc_final: 0.8293 (mtm) REVERT: 1 30 ASP cc_start: 0.7836 (m-30) cc_final: 0.7526 (m-30) REVERT: 1 37 ASP cc_start: 0.8026 (p0) cc_final: 0.7337 (p0) REVERT: 1 38 LEU cc_start: 0.8129 (mp) cc_final: 0.7911 (mt) REVERT: 1 39 GLU cc_start: 0.7145 (mp0) cc_final: 0.6085 (mp0) REVERT: 1 45 MET cc_start: 0.8650 (ttm) cc_final: 0.8351 (ttp) REVERT: 1 60 LYS cc_start: 0.8571 (mmmt) cc_final: 0.8263 (mmtp) REVERT: 1 83 GLU cc_start: 0.7201 (tt0) cc_final: 0.6931 (mt-10) REVERT: 1 100 GLU cc_start: 0.7556 (tm-30) cc_final: 0.7140 (tm-30) REVERT: 1 101 MET cc_start: 0.7774 (ttp) cc_final: 0.7399 (ttp) REVERT: 1 109 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.6359 (tt0) REVERT: 1 114 ARG cc_start: 0.7774 (ptp90) cc_final: 0.7513 (mtm-85) REVERT: 1 129 LYS cc_start: 0.8528 (mtpt) cc_final: 0.8210 (mtpt) REVERT: 1 134 ASP cc_start: 0.7223 (t0) cc_final: 0.6881 (t0) REVERT: 1 149 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8493 (p) REVERT: 1 163 LYS cc_start: 0.8243 (mptt) cc_final: 0.7999 (mmtm) REVERT: 1 269 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.7709 (m-80) REVERT: 1 274 LYS cc_start: 0.8644 (mttt) cc_final: 0.8401 (mtpp) REVERT: 1 279 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.8110 (p0) REVERT: 1 285 LYS cc_start: 0.7618 (tppt) cc_final: 0.7232 (tppt) REVERT: 1 310 ASP cc_start: 0.7880 (m-30) cc_final: 0.7524 (t0) REVERT: 2 24 LYS cc_start: 0.8275 (ttpp) cc_final: 0.7988 (ttmm) REVERT: 2 89 LYS cc_start: 0.8335 (mmmt) cc_final: 0.7932 (mmmt) REVERT: 2 96 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7471 (tp30) REVERT: 2 116 THR cc_start: 0.8104 (m) cc_final: 0.7660 (p) REVERT: 2 122 LEU cc_start: 0.8513 (tp) cc_final: 0.8196 (tp) REVERT: 2 129 LYS cc_start: 0.8432 (mmpt) cc_final: 0.8178 (mmpt) REVERT: 2 163 LYS cc_start: 0.8405 (mppt) cc_final: 0.7862 (mmtm) REVERT: 2 181 ASN cc_start: 0.7995 (t0) cc_final: 0.7609 (t0) REVERT: 2 193 GLU cc_start: 0.7535 (tp30) cc_final: 0.7180 (tp30) REVERT: 2 200 GLN cc_start: 0.6177 (OUTLIER) cc_final: 0.5843 (tm-30) REVERT: 2 211 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7239 (mm-30) REVERT: 2 232 LYS cc_start: 0.8245 (ttmm) cc_final: 0.7855 (ttmm) REVERT: 3 30 ASP cc_start: 0.8060 (m-30) cc_final: 0.7741 (m-30) REVERT: 3 34 ASP cc_start: 0.8227 (m-30) cc_final: 0.7744 (m-30) REVERT: 3 38 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7357 (mm) REVERT: 3 39 GLU cc_start: 0.7522 (mp0) cc_final: 0.7097 (mp0) REVERT: 3 46 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7580 (tpt) REVERT: 3 65 GLN cc_start: 0.8282 (pt0) cc_final: 0.7970 (pp30) REVERT: 3 87 ASN cc_start: 0.7978 (t0) cc_final: 0.7575 (t0) REVERT: 3 92 ASP cc_start: 0.7759 (t0) cc_final: 0.7483 (t0) REVERT: 3 96 GLU cc_start: 0.7402 (tm-30) cc_final: 0.7120 (tm-30) REVERT: 3 181 ASN cc_start: 0.7691 (t0) cc_final: 0.7392 (t0) REVERT: 3 207 LYS cc_start: 0.8649 (tttt) cc_final: 0.8032 (ttmm) REVERT: 3 228 GLU cc_start: 0.6580 (tm-30) cc_final: 0.6065 (tm-30) REVERT: 3 232 LYS cc_start: 0.7957 (ttmm) cc_final: 0.7651 (ttmm) REVERT: 3 233 LYS cc_start: 0.7710 (mtpt) cc_final: 0.7429 (mtmm) REVERT: 3 247 ASN cc_start: 0.8785 (m-40) cc_final: 0.8406 (m-40) REVERT: 3 255 GLU cc_start: 0.8039 (tp30) cc_final: 0.7533 (tp30) REVERT: 3 259 ASN cc_start: 0.7758 (OUTLIER) cc_final: 0.7166 (p0) REVERT: 3 268 ASP cc_start: 0.7503 (p0) cc_final: 0.7108 (p0) REVERT: 3 269 PHE cc_start: 0.7232 (OUTLIER) cc_final: 0.5533 (t80) REVERT: 3 282 ASN cc_start: 0.8086 (t0) cc_final: 0.7780 (t0) REVERT: 4 19 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.8018 (p) REVERT: 4 23 ARG cc_start: 0.6652 (mtm180) cc_final: 0.6381 (mtm110) REVERT: 4 29 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7665 (mmp) REVERT: 4 33 ARG cc_start: 0.8065 (ttp80) cc_final: 0.7798 (ttp80) REVERT: 4 45 MET cc_start: 0.7648 (ttp) cc_final: 0.6650 (ttp) REVERT: 4 46 MET cc_start: 0.8227 (tpt) cc_final: 0.7344 (tpt) REVERT: 4 55 LYS cc_start: 0.7864 (mtmt) cc_final: 0.7607 (mtmm) REVERT: 4 62 TYR cc_start: 0.8165 (t80) cc_final: 0.7740 (t80) REVERT: 4 83 GLU cc_start: 0.6792 (tt0) cc_final: 0.6119 (tt0) REVERT: 4 133 ILE cc_start: 0.7811 (mt) cc_final: 0.7594 (mm) REVERT: 4 137 GLN cc_start: 0.7048 (pt0) cc_final: 0.6309 (pt0) REVERT: 4 149 THR cc_start: 0.5220 (OUTLIER) cc_final: 0.4694 (t) REVERT: 4 154 TRP cc_start: 0.7916 (t60) cc_final: 0.7617 (t60) REVERT: 4 155 LEU cc_start: 0.8364 (mt) cc_final: 0.8041 (mm) REVERT: 4 171 MET cc_start: 0.8531 (mtp) cc_final: 0.8022 (mtp) REVERT: 4 178 LEU cc_start: 0.7352 (tp) cc_final: 0.7049 (pp) REVERT: 4 190 ILE cc_start: 0.8408 (mt) cc_final: 0.8092 (pt) REVERT: 4 228 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7421 (tm-30) REVERT: 4 253 SER cc_start: 0.8282 (p) cc_final: 0.8068 (p) REVERT: 4 274 LYS cc_start: 0.8218 (mttt) cc_final: 0.7802 (mtmt) REVERT: 4 285 LYS cc_start: 0.7000 (OUTLIER) cc_final: 0.6760 (mtmm) REVERT: 4 295 THR cc_start: 0.8613 (p) cc_final: 0.8062 (t) REVERT: 4 304 LYS cc_start: 0.7299 (tppt) cc_final: 0.6989 (tppt) REVERT: 5 60 LYS cc_start: 0.7122 (mmmt) cc_final: 0.6803 (mmtt) REVERT: 5 105 LEU cc_start: 0.6708 (OUTLIER) cc_final: 0.6498 (mm) REVERT: 5 171 MET cc_start: 0.7775 (mtp) cc_final: 0.7044 (mtp) REVERT: 6 5 ARG cc_start: 0.6669 (tpp80) cc_final: 0.6326 (tpp-160) REVERT: 6 30 ASP cc_start: 0.7331 (m-30) cc_final: 0.7095 (m-30) REVERT: 6 64 ASN cc_start: 0.7019 (m-40) cc_final: 0.6773 (m110) REVERT: 6 95 ARG cc_start: 0.8068 (ttm170) cc_final: 0.7850 (ttp80) REVERT: 6 96 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7622 (tm-30) REVERT: 6 119 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8010 (tp) REVERT: 6 134 ASP cc_start: 0.7335 (t0) cc_final: 0.7047 (t0) REVERT: 6 149 THR cc_start: 0.8195 (OUTLIER) cc_final: 0.7788 (p) REVERT: 6 150 GLN cc_start: 0.8327 (mt0) cc_final: 0.7964 (mt0) REVERT: 6 153 ASN cc_start: 0.8048 (m-40) cc_final: 0.7706 (m-40) REVERT: 6 162 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8253 (p) REVERT: 6 164 CYS cc_start: 0.7969 (t) cc_final: 0.7576 (p) REVERT: 6 168 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7912 (mm) REVERT: 6 175 LYS cc_start: 0.8317 (ttmt) cc_final: 0.7941 (ttmm) REVERT: 6 181 ASN cc_start: 0.8446 (t0) cc_final: 0.8217 (t0) REVERT: 6 189 SER cc_start: 0.8694 (p) cc_final: 0.8397 (t) REVERT: 6 192 VAL cc_start: 0.8953 (OUTLIER) cc_final: 0.8725 (t) REVERT: 6 230 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7923 (tp) REVERT: 6 255 GLU cc_start: 0.7401 (tp30) cc_final: 0.6786 (mm-30) REVERT: 6 283 SER cc_start: 0.8219 (p) cc_final: 0.8018 (t) REVERT: 7 14 ARG cc_start: 0.8254 (mtm-85) cc_final: 0.8026 (mtt90) REVERT: 7 24 LYS cc_start: 0.8337 (ttpp) cc_final: 0.8071 (ttpp) REVERT: 7 39 GLU cc_start: 0.7685 (mp0) cc_final: 0.6947 (mp0) REVERT: 7 48 TYR cc_start: 0.8384 (m-80) cc_final: 0.8123 (m-80) REVERT: 7 65 GLN cc_start: 0.8239 (tm-30) cc_final: 0.8016 (tt0) REVERT: 7 86 ASP cc_start: 0.8310 (t70) cc_final: 0.8064 (t0) REVERT: 7 129 LYS cc_start: 0.8392 (mmmm) cc_final: 0.7986 (mmtp) REVERT: 7 156 LYS cc_start: 0.8705 (ttpt) cc_final: 0.8378 (tttp) REVERT: 7 162 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8397 (p) REVERT: 7 163 LYS cc_start: 0.8750 (mppt) cc_final: 0.8362 (mttp) REVERT: 7 232 LYS cc_start: 0.8552 (ttmm) cc_final: 0.7838 (ttpp) REVERT: 7 286 ASN cc_start: 0.8562 (t0) cc_final: 0.8349 (t0) outliers start: 124 outliers final: 69 residues processed: 698 average time/residue: 0.1735 time to fit residues: 171.7287 Evaluate side-chains 694 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 603 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 1 residue 53 VAL Chi-restraints excluded: chain 1 residue 99 VAL Chi-restraints excluded: chain 1 residue 107 LEU Chi-restraints excluded: chain 1 residue 109 GLU Chi-restraints excluded: chain 1 residue 110 THR Chi-restraints excluded: chain 1 residue 117 LYS Chi-restraints excluded: chain 1 residue 119 LEU Chi-restraints excluded: chain 1 residue 142 GLU Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 1 residue 149 THR Chi-restraints excluded: chain 1 residue 176 VAL Chi-restraints excluded: chain 1 residue 217 LEU Chi-restraints excluded: chain 1 residue 269 PHE Chi-restraints excluded: chain 1 residue 279 ASP Chi-restraints excluded: chain 1 residue 295 THR Chi-restraints excluded: chain 1 residue 309 GLU Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 22 VAL Chi-restraints excluded: chain 2 residue 45 MET Chi-restraints excluded: chain 2 residue 149 THR Chi-restraints excluded: chain 2 residue 200 GLN Chi-restraints excluded: chain 2 residue 213 LEU Chi-restraints excluded: chain 2 residue 261 HIS Chi-restraints excluded: chain 2 residue 262 GLU Chi-restraints excluded: chain 2 residue 294 VAL Chi-restraints excluded: chain 2 residue 314 HIS Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 19 THR Chi-restraints excluded: chain 3 residue 35 LEU Chi-restraints excluded: chain 3 residue 38 LEU Chi-restraints excluded: chain 3 residue 41 GLU Chi-restraints excluded: chain 3 residue 46 MET Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 110 THR Chi-restraints excluded: chain 3 residue 142 GLU Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 149 THR Chi-restraints excluded: chain 3 residue 259 ASN Chi-restraints excluded: chain 3 residue 269 PHE Chi-restraints excluded: chain 3 residue 270 VAL Chi-restraints excluded: chain 4 residue 10 SER Chi-restraints excluded: chain 4 residue 19 THR Chi-restraints excluded: chain 4 residue 27 SER Chi-restraints excluded: chain 4 residue 29 MET Chi-restraints excluded: chain 4 residue 110 THR Chi-restraints excluded: chain 4 residue 119 LEU Chi-restraints excluded: chain 4 residue 130 LEU Chi-restraints excluded: chain 4 residue 131 ILE Chi-restraints excluded: chain 4 residue 142 GLU Chi-restraints excluded: chain 4 residue 148 LEU Chi-restraints excluded: chain 4 residue 149 THR Chi-restraints excluded: chain 4 residue 198 SER Chi-restraints excluded: chain 4 residue 211 GLU Chi-restraints excluded: chain 4 residue 231 GLN Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 285 LYS Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 29 MET Chi-restraints excluded: chain 5 residue 46 MET Chi-restraints excluded: chain 5 residue 92 ASP Chi-restraints excluded: chain 5 residue 97 LEU Chi-restraints excluded: chain 5 residue 105 LEU Chi-restraints excluded: chain 5 residue 110 THR Chi-restraints excluded: chain 5 residue 142 GLU Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 211 GLU Chi-restraints excluded: chain 6 residue 6 GLU Chi-restraints excluded: chain 6 residue 63 LEU Chi-restraints excluded: chain 6 residue 99 VAL Chi-restraints excluded: chain 6 residue 118 ARG Chi-restraints excluded: chain 6 residue 119 LEU Chi-restraints excluded: chain 6 residue 142 GLU Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 148 LEU Chi-restraints excluded: chain 6 residue 149 THR Chi-restraints excluded: chain 6 residue 162 THR Chi-restraints excluded: chain 6 residue 168 ILE Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 6 residue 230 LEU Chi-restraints excluded: chain 6 residue 269 PHE Chi-restraints excluded: chain 7 residue 19 THR Chi-restraints excluded: chain 7 residue 53 VAL Chi-restraints excluded: chain 7 residue 117 LYS Chi-restraints excluded: chain 7 residue 119 LEU Chi-restraints excluded: chain 7 residue 142 GLU Chi-restraints excluded: chain 7 residue 148 LEU Chi-restraints excluded: chain 7 residue 149 THR Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 309 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 3 optimal weight: 60.0000 chunk 14 optimal weight: 0.6980 chunk 78 optimal weight: 0.2980 chunk 1 optimal weight: 60.0000 chunk 99 optimal weight: 0.8980 chunk 129 optimal weight: 0.6980 chunk 193 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 64 ASN 1 138 HIS 1 183 GLN ** 1 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 282 ASN 3 183 GLN 3 239 GLN 4 231 GLN 6 227 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.168879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.133284 restraints weight = 26598.329| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.25 r_work: 0.3547 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18773 Z= 0.153 Angle : 0.661 11.562 25612 Z= 0.334 Chirality : 0.042 0.181 2863 Planarity : 0.005 0.055 3122 Dihedral : 15.685 88.914 2910 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 6.40 % Allowed : 26.28 % Favored : 67.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.18), residues: 2163 helix: 0.54 (0.15), residues: 1190 sheet: -2.46 (0.36), residues: 224 loop : -2.45 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 1 33 TYR 0.021 0.002 TYR 6 199 PHE 0.017 0.002 PHE 1 237 TRP 0.016 0.002 TRP 6 154 HIS 0.012 0.001 HIS 2 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (18772) covalent geometry : angle 0.66101 / 0.33 (25612) hydrogen bonds : bond 0.03550 / 3.92 ( 816) hydrogen bonds : angle 3.84167 / 4.48 ( 2372) Misc. bond : bond 0.00342 / 0.17 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 618 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 19 THR cc_start: 0.8858 (OUTLIER) cc_final: 0.8430 (t) REVERT: 1 29 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8333 (mtm) REVERT: 1 30 ASP cc_start: 0.7861 (m-30) cc_final: 0.7554 (m-30) REVERT: 1 37 ASP cc_start: 0.8033 (p0) cc_final: 0.7346 (p0) REVERT: 1 38 LEU cc_start: 0.8164 (mp) cc_final: 0.7901 (mt) REVERT: 1 39 GLU cc_start: 0.7129 (mp0) cc_final: 0.6162 (mp0) REVERT: 1 45 MET cc_start: 0.8636 (ttm) cc_final: 0.8417 (ttp) REVERT: 1 46 MET cc_start: 0.8030 (tpp) cc_final: 0.7763 (tpt) REVERT: 1 60 LYS cc_start: 0.8548 (mmmt) cc_final: 0.8138 (mmtp) REVERT: 1 83 GLU cc_start: 0.7286 (tt0) cc_final: 0.6976 (mt-10) REVERT: 1 100 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7147 (tm-30) REVERT: 1 101 MET cc_start: 0.7881 (ttp) cc_final: 0.7525 (ttp) REVERT: 1 105 LEU cc_start: 0.7640 (pp) cc_final: 0.7353 (mp) REVERT: 1 109 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6583 (tt0) REVERT: 1 129 LYS cc_start: 0.8543 (mtpt) cc_final: 0.8218 (mtpt) REVERT: 1 134 ASP cc_start: 0.7259 (t0) cc_final: 0.6957 (t0) REVERT: 1 149 THR cc_start: 0.8640 (p) cc_final: 0.8274 (p) REVERT: 1 162 THR cc_start: 0.8222 (OUTLIER) cc_final: 0.7987 (t) REVERT: 1 163 LYS cc_start: 0.8209 (mptt) cc_final: 0.7958 (mmtm) REVERT: 1 171 MET cc_start: 0.8471 (mtp) cc_final: 0.8269 (mmm) REVERT: 1 269 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7752 (m-80) REVERT: 1 274 LYS cc_start: 0.8637 (mttt) cc_final: 0.8357 (mtpp) REVERT: 1 279 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.8063 (p0) REVERT: 1 285 LYS cc_start: 0.7583 (tppt) cc_final: 0.7304 (tppt) REVERT: 1 297 ASP cc_start: 0.8045 (t0) cc_final: 0.7720 (t0) REVERT: 2 33 ARG cc_start: 0.8334 (ttp80) cc_final: 0.8016 (ttp-170) REVERT: 2 46 MET cc_start: 0.8070 (ttt) cc_final: 0.7814 (ttt) REVERT: 2 96 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7434 (tp30) REVERT: 2 116 THR cc_start: 0.8012 (m) cc_final: 0.7658 (p) REVERT: 2 122 LEU cc_start: 0.8512 (tp) cc_final: 0.8235 (tp) REVERT: 2 135 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7074 (mm-30) REVERT: 2 146 ARG cc_start: 0.7251 (ptm-80) cc_final: 0.6805 (ptm-80) REVERT: 2 150 GLN cc_start: 0.8083 (mt0) cc_final: 0.7729 (mt0) REVERT: 2 163 LYS cc_start: 0.8328 (mppt) cc_final: 0.7944 (mmtm) REVERT: 2 175 LYS cc_start: 0.8912 (ttmt) cc_final: 0.8625 (ttmm) REVERT: 2 211 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7163 (mp0) REVERT: 2 228 GLU cc_start: 0.7725 (tp30) cc_final: 0.7388 (tp30) REVERT: 2 242 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.7946 (tmm) REVERT: 2 261 HIS cc_start: 0.7759 (OUTLIER) cc_final: 0.7130 (t-90) REVERT: 3 27 SER cc_start: 0.8975 (m) cc_final: 0.8493 (p) REVERT: 3 30 ASP cc_start: 0.8130 (m-30) cc_final: 0.7870 (m-30) REVERT: 3 34 ASP cc_start: 0.8237 (m-30) cc_final: 0.7800 (m-30) REVERT: 3 38 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7338 (mm) REVERT: 3 39 GLU cc_start: 0.7491 (mp0) cc_final: 0.7033 (mp0) REVERT: 3 46 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7553 (tpp) REVERT: 3 61 LYS cc_start: 0.8341 (tptp) cc_final: 0.8095 (tptp) REVERT: 3 86 ASP cc_start: 0.8362 (t70) cc_final: 0.8085 (t0) REVERT: 3 87 ASN cc_start: 0.7894 (t0) cc_final: 0.7597 (t0) REVERT: 3 92 ASP cc_start: 0.7767 (t0) cc_final: 0.7520 (t0) REVERT: 3 96 GLU cc_start: 0.7435 (tm-30) cc_final: 0.7154 (tm-30) REVERT: 3 149 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.8150 (p) REVERT: 3 181 ASN cc_start: 0.7654 (t0) cc_final: 0.7339 (t0) REVERT: 3 207 LYS cc_start: 0.8639 (tttt) cc_final: 0.8000 (ttmm) REVERT: 3 220 GLU cc_start: 0.6686 (OUTLIER) cc_final: 0.6350 (pm20) REVERT: 3 228 GLU cc_start: 0.6629 (tm-30) cc_final: 0.6041 (tm-30) REVERT: 3 232 LYS cc_start: 0.8114 (ttmm) cc_final: 0.7844 (ttmm) REVERT: 3 247 ASN cc_start: 0.8712 (m-40) cc_final: 0.8401 (m-40) REVERT: 3 255 GLU cc_start: 0.8006 (tp30) cc_final: 0.7776 (tp30) REVERT: 3 259 ASN cc_start: 0.8096 (OUTLIER) cc_final: 0.7396 (p0) REVERT: 3 268 ASP cc_start: 0.7454 (p0) cc_final: 0.7095 (p0) REVERT: 3 269 PHE cc_start: 0.7217 (OUTLIER) cc_final: 0.5564 (t80) REVERT: 3 282 ASN cc_start: 0.8034 (t0) cc_final: 0.7780 (t0) REVERT: 3 300 ARG cc_start: 0.8451 (ptp90) cc_final: 0.8222 (ptp90) REVERT: 4 19 THR cc_start: 0.8436 (OUTLIER) cc_final: 0.8180 (p) REVERT: 4 23 ARG cc_start: 0.6748 (mtm180) cc_final: 0.6483 (mtm110) REVERT: 4 29 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7600 (mmp) REVERT: 4 45 MET cc_start: 0.7529 (ttp) cc_final: 0.6524 (ttp) REVERT: 4 46 MET cc_start: 0.8302 (tpt) cc_final: 0.7480 (tpt) REVERT: 4 55 LYS cc_start: 0.7856 (mtmt) cc_final: 0.7596 (mtmm) REVERT: 4 62 TYR cc_start: 0.8101 (t80) cc_final: 0.7629 (t80) REVERT: 4 63 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7351 (tp) REVERT: 4 83 GLU cc_start: 0.6784 (tt0) cc_final: 0.6019 (tt0) REVERT: 4 118 ARG cc_start: 0.6939 (mtp180) cc_final: 0.6679 (mtp180) REVERT: 4 133 ILE cc_start: 0.7790 (mt) cc_final: 0.7574 (mm) REVERT: 4 137 GLN cc_start: 0.7176 (OUTLIER) cc_final: 0.6474 (pt0) REVERT: 4 149 THR cc_start: 0.5307 (OUTLIER) cc_final: 0.4746 (t) REVERT: 4 154 TRP cc_start: 0.7944 (t60) cc_final: 0.7598 (t60) REVERT: 4 155 LEU cc_start: 0.8396 (mt) cc_final: 0.8073 (mm) REVERT: 4 171 MET cc_start: 0.8649 (mtp) cc_final: 0.8187 (mtp) REVERT: 4 178 LEU cc_start: 0.7409 (tp) cc_final: 0.7116 (pp) REVERT: 4 253 SER cc_start: 0.8263 (p) cc_final: 0.8045 (p) REVERT: 4 274 LYS cc_start: 0.8209 (mttt) cc_final: 0.7772 (mtmt) REVERT: 4 295 THR cc_start: 0.8472 (p) cc_final: 0.8175 (t) REVERT: 4 300 ARG cc_start: 0.7755 (mtm-85) cc_final: 0.7510 (mtm-85) REVERT: 4 304 LYS cc_start: 0.7397 (tppt) cc_final: 0.7097 (tppt) REVERT: 5 105 LEU cc_start: 0.6749 (OUTLIER) cc_final: 0.6529 (mm) REVERT: 5 157 MET cc_start: 0.6841 (tmm) cc_final: 0.6562 (ppp) REVERT: 5 171 MET cc_start: 0.7684 (mtp) cc_final: 0.7108 (mtp) REVERT: 6 30 ASP cc_start: 0.7391 (m-30) cc_final: 0.7145 (m-30) REVERT: 6 64 ASN cc_start: 0.6999 (m-40) cc_final: 0.6775 (m-40) REVERT: 6 115 LEU cc_start: 0.7161 (pp) cc_final: 0.6676 (tp) REVERT: 6 119 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8005 (tp) REVERT: 6 149 THR cc_start: 0.8305 (p) cc_final: 0.7901 (p) REVERT: 6 150 GLN cc_start: 0.8373 (mt0) cc_final: 0.8039 (mt0) REVERT: 6 153 ASN cc_start: 0.8092 (m-40) cc_final: 0.7725 (m-40) REVERT: 6 164 CYS cc_start: 0.7956 (t) cc_final: 0.7582 (p) REVERT: 6 175 LYS cc_start: 0.8316 (ttmt) cc_final: 0.7966 (ttmm) REVERT: 6 181 ASN cc_start: 0.8485 (t0) cc_final: 0.8277 (t0) REVERT: 6 189 SER cc_start: 0.8678 (p) cc_final: 0.8393 (t) REVERT: 6 192 VAL cc_start: 0.8936 (OUTLIER) cc_final: 0.8719 (t) REVERT: 6 219 PHE cc_start: 0.6335 (m-80) cc_final: 0.6132 (m-80) REVERT: 6 237 PHE cc_start: 0.8124 (t80) cc_final: 0.7483 (t80) REVERT: 6 247 ASN cc_start: 0.8389 (m-40) cc_final: 0.7592 (m-40) REVERT: 6 255 GLU cc_start: 0.7377 (tp30) cc_final: 0.6433 (mm-30) REVERT: 6 259 ASN cc_start: 0.7214 (OUTLIER) cc_final: 0.6815 (p0) REVERT: 6 270 VAL cc_start: 0.7987 (p) cc_final: 0.7779 (m) REVERT: 6 275 LEU cc_start: 0.6751 (tp) cc_final: 0.6386 (mp) REVERT: 7 8 ARG cc_start: 0.8802 (mtm180) cc_final: 0.8592 (mtm-85) REVERT: 7 24 LYS cc_start: 0.8353 (ttpp) cc_final: 0.8147 (ttpt) REVERT: 7 28 TYR cc_start: 0.8925 (m-10) cc_final: 0.8624 (m-80) REVERT: 7 39 GLU cc_start: 0.7573 (mp0) cc_final: 0.6962 (mp0) REVERT: 7 46 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7398 (tpp) REVERT: 7 48 TYR cc_start: 0.8493 (m-80) cc_final: 0.8106 (m-10) REVERT: 7 86 ASP cc_start: 0.8366 (t70) cc_final: 0.8101 (t0) REVERT: 7 95 ARG cc_start: 0.8395 (ptp90) cc_final: 0.8139 (ptm160) REVERT: 7 119 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7844 (tt) REVERT: 7 129 LYS cc_start: 0.8353 (mmmm) cc_final: 0.7955 (mttp) REVERT: 7 156 LYS cc_start: 0.8732 (ttpt) cc_final: 0.8388 (tttp) REVERT: 7 232 LYS cc_start: 0.8473 (ttmm) cc_final: 0.7830 (ttpp) outliers start: 120 outliers final: 70 residues processed: 680 average time/residue: 0.1717 time to fit residues: 165.9346 Evaluate side-chains 692 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 596 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 1 residue 29 MET Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 1 residue 53 VAL Chi-restraints excluded: chain 1 residue 99 VAL Chi-restraints excluded: chain 1 residue 109 GLU Chi-restraints excluded: chain 1 residue 110 THR Chi-restraints excluded: chain 1 residue 117 LYS Chi-restraints excluded: chain 1 residue 119 LEU Chi-restraints excluded: chain 1 residue 142 GLU Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 1 residue 162 THR Chi-restraints excluded: chain 1 residue 176 VAL Chi-restraints excluded: chain 1 residue 217 LEU Chi-restraints excluded: chain 1 residue 269 PHE Chi-restraints excluded: chain 1 residue 279 ASP Chi-restraints excluded: chain 1 residue 295 THR Chi-restraints excluded: chain 1 residue 309 GLU Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 22 VAL Chi-restraints excluded: chain 2 residue 45 MET Chi-restraints excluded: chain 2 residue 96 GLU Chi-restraints excluded: chain 2 residue 213 LEU Chi-restraints excluded: chain 2 residue 242 MET Chi-restraints excluded: chain 2 residue 261 HIS Chi-restraints excluded: chain 2 residue 294 VAL Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 35 LEU Chi-restraints excluded: chain 3 residue 38 LEU Chi-restraints excluded: chain 3 residue 41 GLU Chi-restraints excluded: chain 3 residue 45 MET Chi-restraints excluded: chain 3 residue 46 MET Chi-restraints excluded: chain 3 residue 63 LEU Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 142 GLU Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 149 THR Chi-restraints excluded: chain 3 residue 220 GLU Chi-restraints excluded: chain 3 residue 259 ASN Chi-restraints excluded: chain 3 residue 269 PHE Chi-restraints excluded: chain 3 residue 270 VAL Chi-restraints excluded: chain 3 residue 312 LEU Chi-restraints excluded: chain 4 residue 10 SER Chi-restraints excluded: chain 4 residue 19 THR Chi-restraints excluded: chain 4 residue 27 SER Chi-restraints excluded: chain 4 residue 29 MET Chi-restraints excluded: chain 4 residue 60 LYS Chi-restraints excluded: chain 4 residue 63 LEU Chi-restraints excluded: chain 4 residue 110 THR Chi-restraints excluded: chain 4 residue 119 LEU Chi-restraints excluded: chain 4 residue 130 LEU Chi-restraints excluded: chain 4 residue 131 ILE Chi-restraints excluded: chain 4 residue 137 GLN Chi-restraints excluded: chain 4 residue 142 GLU Chi-restraints excluded: chain 4 residue 148 LEU Chi-restraints excluded: chain 4 residue 149 THR Chi-restraints excluded: chain 4 residue 162 THR Chi-restraints excluded: chain 4 residue 211 GLU Chi-restraints excluded: chain 4 residue 230 LEU Chi-restraints excluded: chain 4 residue 269 PHE Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 279 ASP Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 38 LEU Chi-restraints excluded: chain 5 residue 46 MET Chi-restraints excluded: chain 5 residue 97 LEU Chi-restraints excluded: chain 5 residue 99 VAL Chi-restraints excluded: chain 5 residue 105 LEU Chi-restraints excluded: chain 5 residue 142 GLU Chi-restraints excluded: chain 5 residue 147 VAL Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 211 GLU Chi-restraints excluded: chain 5 residue 259 ASN Chi-restraints excluded: chain 5 residue 299 LEU Chi-restraints excluded: chain 6 residue 6 GLU Chi-restraints excluded: chain 6 residue 63 LEU Chi-restraints excluded: chain 6 residue 99 VAL Chi-restraints excluded: chain 6 residue 119 LEU Chi-restraints excluded: chain 6 residue 142 GLU Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 148 LEU Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 6 residue 259 ASN Chi-restraints excluded: chain 6 residue 269 PHE Chi-restraints excluded: chain 7 residue 19 THR Chi-restraints excluded: chain 7 residue 40 SER Chi-restraints excluded: chain 7 residue 46 MET Chi-restraints excluded: chain 7 residue 53 VAL Chi-restraints excluded: chain 7 residue 117 LYS Chi-restraints excluded: chain 7 residue 119 LEU Chi-restraints excluded: chain 7 residue 142 GLU Chi-restraints excluded: chain 7 residue 146 ARG Chi-restraints excluded: chain 7 residue 148 LEU Chi-restraints excluded: chain 7 residue 149 THR Chi-restraints excluded: chain 7 residue 214 ASP Chi-restraints excluded: chain 7 residue 309 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 139 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 215 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 64 ASN ** 1 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 259 ASN 1 282 ASN ** 3 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 259 ASN 4 247 ASN 4 261 HIS 7 247 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.167116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.133468 restraints weight = 26329.593| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.20 r_work: 0.3519 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 18773 Z= 0.175 Angle : 0.677 10.907 25612 Z= 0.338 Chirality : 0.043 0.195 2863 Planarity : 0.004 0.040 3122 Dihedral : 15.438 88.710 2901 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 6.93 % Allowed : 26.07 % Favored : 67.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.18), residues: 2163 helix: 0.68 (0.15), residues: 1190 sheet: -2.35 (0.37), residues: 224 loop : -2.34 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG 4 14 TYR 0.026 0.002 TYR 6 199 PHE 0.014 0.002 PHE 1 237 TRP 0.017 0.002 TRP 6 154 HIS 0.007 0.001 HIS 4 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (18772) covalent geometry : angle 0.67744 / 0.34 (25612) hydrogen bonds : bond 0.03600 / 3.98 ( 816) hydrogen bonds : angle 3.83425 / 4.46 ( 2372) Misc. bond : bond 0.00242 / 0.12 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 606 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 11 ARG cc_start: 0.8193 (mtp180) cc_final: 0.7760 (mtp85) REVERT: 1 19 THR cc_start: 0.8892 (OUTLIER) cc_final: 0.8450 (t) REVERT: 1 23 ARG cc_start: 0.8396 (mtm110) cc_final: 0.8176 (mtm110) REVERT: 1 29 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8271 (mtm) REVERT: 1 30 ASP cc_start: 0.8080 (m-30) cc_final: 0.7829 (m-30) REVERT: 1 31 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7365 (ttt90) REVERT: 1 37 ASP cc_start: 0.7967 (p0) cc_final: 0.7609 (p0) REVERT: 1 38 LEU cc_start: 0.8085 (mp) cc_final: 0.7788 (mt) REVERT: 1 39 GLU cc_start: 0.7140 (mp0) cc_final: 0.6645 (mp0) REVERT: 1 60 LYS cc_start: 0.8561 (mmmt) cc_final: 0.8273 (mmtp) REVERT: 1 81 HIS cc_start: 0.7994 (t70) cc_final: 0.7746 (t70) REVERT: 1 83 GLU cc_start: 0.7267 (tt0) cc_final: 0.6986 (mt-10) REVERT: 1 100 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7137 (tm-30) REVERT: 1 101 MET cc_start: 0.7842 (ttp) cc_final: 0.7492 (ttp) REVERT: 1 105 LEU cc_start: 0.7663 (pp) cc_final: 0.7344 (mp) REVERT: 1 129 LYS cc_start: 0.8566 (mtpt) cc_final: 0.8215 (mtpt) REVERT: 1 149 THR cc_start: 0.8617 (p) cc_final: 0.8267 (p) REVERT: 1 162 THR cc_start: 0.8253 (OUTLIER) cc_final: 0.7992 (t) REVERT: 1 163 LYS cc_start: 0.8214 (mptt) cc_final: 0.7989 (mmtt) REVERT: 1 228 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7316 (tm-30) REVERT: 1 269 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7819 (m-80) REVERT: 1 274 LYS cc_start: 0.8649 (mttt) cc_final: 0.8275 (mtpp) REVERT: 1 279 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.8090 (p0) REVERT: 1 285 LYS cc_start: 0.7677 (tppt) cc_final: 0.7392 (tppt) REVERT: 2 33 ARG cc_start: 0.8336 (ttp80) cc_final: 0.8006 (ttp-170) REVERT: 2 46 MET cc_start: 0.7965 (ttt) cc_final: 0.7716 (ttt) REVERT: 2 65 GLN cc_start: 0.7858 (pp30) cc_final: 0.7531 (pt0) REVERT: 2 96 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7407 (tp30) REVERT: 2 116 THR cc_start: 0.8079 (m) cc_final: 0.7651 (p) REVERT: 2 122 LEU cc_start: 0.8568 (tp) cc_final: 0.8213 (tp) REVERT: 2 129 LYS cc_start: 0.8532 (mmtt) cc_final: 0.8269 (mmmt) REVERT: 2 135 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7043 (mm-30) REVERT: 2 150 GLN cc_start: 0.8095 (mt0) cc_final: 0.7778 (mt0) REVERT: 2 163 LYS cc_start: 0.8266 (mppt) cc_final: 0.7946 (mmtm) REVERT: 2 175 LYS cc_start: 0.8869 (ttmt) cc_final: 0.8624 (ttmm) REVERT: 2 211 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7167 (mp0) REVERT: 2 228 GLU cc_start: 0.7679 (tp30) cc_final: 0.7383 (tp30) REVERT: 2 242 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.7849 (tmm) REVERT: 2 309 GLU cc_start: 0.7021 (pm20) cc_final: 0.6782 (mp0) REVERT: 3 27 SER cc_start: 0.8888 (m) cc_final: 0.8441 (p) REVERT: 3 30 ASP cc_start: 0.8198 (m-30) cc_final: 0.7903 (m-30) REVERT: 3 34 ASP cc_start: 0.8253 (m-30) cc_final: 0.7821 (m-30) REVERT: 3 39 GLU cc_start: 0.7455 (mp0) cc_final: 0.7003 (mp0) REVERT: 3 46 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7633 (tpp) REVERT: 3 61 LYS cc_start: 0.8689 (tptp) cc_final: 0.8460 (tptp) REVERT: 3 87 ASN cc_start: 0.8025 (t0) cc_final: 0.7802 (t0) REVERT: 3 92 ASP cc_start: 0.7807 (t0) cc_final: 0.7482 (t0) REVERT: 3 96 GLU cc_start: 0.7355 (tm-30) cc_final: 0.7088 (tm-30) REVERT: 3 149 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.8215 (p) REVERT: 3 181 ASN cc_start: 0.7657 (t0) cc_final: 0.7318 (t0) REVERT: 3 207 LYS cc_start: 0.8684 (tttt) cc_final: 0.8059 (ttmm) REVERT: 3 228 GLU cc_start: 0.6722 (tm-30) cc_final: 0.6064 (tm-30) REVERT: 3 232 LYS cc_start: 0.8185 (ttmm) cc_final: 0.7935 (ttmm) REVERT: 3 247 ASN cc_start: 0.8694 (m-40) cc_final: 0.8428 (m-40) REVERT: 3 255 GLU cc_start: 0.7987 (tp30) cc_final: 0.7567 (tp30) REVERT: 3 259 ASN cc_start: 0.7955 (OUTLIER) cc_final: 0.7469 (p0) REVERT: 3 268 ASP cc_start: 0.7573 (p0) cc_final: 0.7156 (p0) REVERT: 3 269 PHE cc_start: 0.7240 (OUTLIER) cc_final: 0.5528 (t80) REVERT: 3 282 ASN cc_start: 0.8075 (t0) cc_final: 0.7823 (t0) REVERT: 3 300 ARG cc_start: 0.8431 (ptp90) cc_final: 0.8190 (ptp90) REVERT: 4 19 THR cc_start: 0.8565 (p) cc_final: 0.8349 (p) REVERT: 4 29 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7818 (mmp) REVERT: 4 46 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7398 (tpt) REVERT: 4 55 LYS cc_start: 0.8083 (mtmt) cc_final: 0.7853 (mtmm) REVERT: 4 62 TYR cc_start: 0.8178 (t80) cc_final: 0.7719 (t80) REVERT: 4 63 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7366 (tp) REVERT: 4 83 GLU cc_start: 0.6798 (tt0) cc_final: 0.6082 (tt0) REVERT: 4 118 ARG cc_start: 0.6903 (mtp180) cc_final: 0.6644 (mtp180) REVERT: 4 133 ILE cc_start: 0.7814 (mt) cc_final: 0.7590 (mm) REVERT: 4 137 GLN cc_start: 0.7114 (OUTLIER) cc_final: 0.6639 (pm20) REVERT: 4 149 THR cc_start: 0.4918 (OUTLIER) cc_final: 0.4379 (t) REVERT: 4 154 TRP cc_start: 0.7986 (t60) cc_final: 0.7643 (t60) REVERT: 4 155 LEU cc_start: 0.8393 (mt) cc_final: 0.8079 (mm) REVERT: 4 171 MET cc_start: 0.8643 (mtp) cc_final: 0.8284 (mtp) REVERT: 4 190 ILE cc_start: 0.8383 (mt) cc_final: 0.8055 (pt) REVERT: 4 193 GLU cc_start: 0.7504 (tp30) cc_final: 0.7295 (tp30) REVERT: 4 247 ASN cc_start: 0.7745 (OUTLIER) cc_final: 0.7525 (t0) REVERT: 4 253 SER cc_start: 0.8309 (p) cc_final: 0.8087 (p) REVERT: 4 300 ARG cc_start: 0.7835 (mtm-85) cc_final: 0.7568 (mtm-85) REVERT: 4 304 LYS cc_start: 0.7431 (tppt) cc_final: 0.7153 (tppt) REVERT: 5 55 LYS cc_start: 0.7100 (mtmm) cc_final: 0.6234 (mtmm) REVERT: 5 60 LYS cc_start: 0.7118 (mmmt) cc_final: 0.6779 (tppt) REVERT: 5 105 LEU cc_start: 0.6795 (OUTLIER) cc_final: 0.6528 (mm) REVERT: 5 157 MET cc_start: 0.6939 (tmm) cc_final: 0.6656 (ppp) REVERT: 5 171 MET cc_start: 0.7604 (mtp) cc_final: 0.7066 (mtp) REVERT: 5 241 ASN cc_start: 0.7337 (t0) cc_final: 0.6754 (t0) REVERT: 6 30 ASP cc_start: 0.7393 (m-30) cc_final: 0.7164 (m-30) REVERT: 6 64 ASN cc_start: 0.6927 (m-40) cc_final: 0.6689 (m-40) REVERT: 6 80 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6937 (mt) REVERT: 6 119 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.7988 (tp) REVERT: 6 135 GLU cc_start: 0.6460 (mm-30) cc_final: 0.5873 (mm-30) REVERT: 6 137 GLN cc_start: 0.7900 (pm20) cc_final: 0.7572 (pm20) REVERT: 6 149 THR cc_start: 0.8402 (p) cc_final: 0.8009 (p) REVERT: 6 150 GLN cc_start: 0.8446 (mt0) cc_final: 0.8133 (mt0) REVERT: 6 153 ASN cc_start: 0.8098 (m-40) cc_final: 0.7730 (m-40) REVERT: 6 162 THR cc_start: 0.8519 (OUTLIER) cc_final: 0.8226 (p) REVERT: 6 164 CYS cc_start: 0.7900 (t) cc_final: 0.7698 (m) REVERT: 6 175 LYS cc_start: 0.8314 (ttmt) cc_final: 0.7965 (ttmm) REVERT: 6 181 ASN cc_start: 0.8451 (t0) cc_final: 0.8220 (t0) REVERT: 6 189 SER cc_start: 0.8692 (p) cc_final: 0.8375 (t) REVERT: 6 192 VAL cc_start: 0.8955 (OUTLIER) cc_final: 0.8735 (t) REVERT: 6 255 GLU cc_start: 0.7364 (tp30) cc_final: 0.6436 (mm-30) REVERT: 6 259 ASN cc_start: 0.7226 (OUTLIER) cc_final: 0.6838 (p0) REVERT: 6 262 GLU cc_start: 0.6500 (mp0) cc_final: 0.6066 (mp0) REVERT: 6 275 LEU cc_start: 0.7054 (tp) cc_final: 0.6696 (mp) REVERT: 7 16 PHE cc_start: 0.8589 (t80) cc_final: 0.8385 (t80) REVERT: 7 39 GLU cc_start: 0.7655 (mp0) cc_final: 0.7175 (mp0) REVERT: 7 46 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7263 (tpp) REVERT: 7 48 TYR cc_start: 0.8529 (m-80) cc_final: 0.8099 (m-10) REVERT: 7 61 LYS cc_start: 0.8490 (ttmm) cc_final: 0.8272 (ttmm) REVERT: 7 86 ASP cc_start: 0.8388 (t70) cc_final: 0.7984 (t0) REVERT: 7 99 VAL cc_start: 0.8930 (p) cc_final: 0.8601 (t) REVERT: 7 119 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7841 (tt) REVERT: 7 129 LYS cc_start: 0.8379 (mmmm) cc_final: 0.8006 (mttm) REVERT: 7 156 LYS cc_start: 0.8756 (ttpt) cc_final: 0.8399 (tttp) REVERT: 7 162 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8340 (p) REVERT: 7 228 GLU cc_start: 0.7045 (tm-30) cc_final: 0.6467 (tm-30) REVERT: 7 232 LYS cc_start: 0.8479 (ttmm) cc_final: 0.7826 (ttpp) outliers start: 130 outliers final: 76 residues processed: 677 average time/residue: 0.1681 time to fit residues: 162.7894 Evaluate side-chains 699 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 596 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 1 residue 26 LEU Chi-restraints excluded: chain 1 residue 29 MET Chi-restraints excluded: chain 1 residue 31 ARG Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 1 residue 82 ILE Chi-restraints excluded: chain 1 residue 99 VAL Chi-restraints excluded: chain 1 residue 107 LEU Chi-restraints excluded: chain 1 residue 110 THR Chi-restraints excluded: chain 1 residue 117 LYS Chi-restraints excluded: chain 1 residue 119 LEU Chi-restraints excluded: chain 1 residue 142 GLU Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 1 residue 162 THR Chi-restraints excluded: chain 1 residue 176 VAL Chi-restraints excluded: chain 1 residue 215 LYS Chi-restraints excluded: chain 1 residue 217 LEU Chi-restraints excluded: chain 1 residue 269 PHE Chi-restraints excluded: chain 1 residue 279 ASP Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 22 VAL Chi-restraints excluded: chain 2 residue 45 MET Chi-restraints excluded: chain 2 residue 96 GLU Chi-restraints excluded: chain 2 residue 107 LEU Chi-restraints excluded: chain 2 residue 192 VAL Chi-restraints excluded: chain 2 residue 213 LEU Chi-restraints excluded: chain 2 residue 242 MET Chi-restraints excluded: chain 2 residue 294 VAL Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 19 THR Chi-restraints excluded: chain 3 residue 35 LEU Chi-restraints excluded: chain 3 residue 46 MET Chi-restraints excluded: chain 3 residue 63 LEU Chi-restraints excluded: chain 3 residue 65 GLN Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 99 VAL Chi-restraints excluded: chain 3 residue 142 GLU Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 149 THR Chi-restraints excluded: chain 3 residue 193 GLU Chi-restraints excluded: chain 3 residue 259 ASN Chi-restraints excluded: chain 3 residue 269 PHE Chi-restraints excluded: chain 3 residue 270 VAL Chi-restraints excluded: chain 3 residue 312 LEU Chi-restraints excluded: chain 4 residue 10 SER Chi-restraints excluded: chain 4 residue 27 SER Chi-restraints excluded: chain 4 residue 29 MET Chi-restraints excluded: chain 4 residue 30 ASP Chi-restraints excluded: chain 4 residue 46 MET Chi-restraints excluded: chain 4 residue 60 LYS Chi-restraints excluded: chain 4 residue 63 LEU Chi-restraints excluded: chain 4 residue 110 THR Chi-restraints excluded: chain 4 residue 119 LEU Chi-restraints excluded: chain 4 residue 130 LEU Chi-restraints excluded: chain 4 residue 131 ILE Chi-restraints excluded: chain 4 residue 137 GLN Chi-restraints excluded: chain 4 residue 142 GLU Chi-restraints excluded: chain 4 residue 148 LEU Chi-restraints excluded: chain 4 residue 149 THR Chi-restraints excluded: chain 4 residue 211 GLU Chi-restraints excluded: chain 4 residue 230 LEU Chi-restraints excluded: chain 4 residue 231 GLN Chi-restraints excluded: chain 4 residue 247 ASN Chi-restraints excluded: chain 4 residue 269 PHE Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 279 ASP Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 46 MET Chi-restraints excluded: chain 5 residue 97 LEU Chi-restraints excluded: chain 5 residue 105 LEU Chi-restraints excluded: chain 5 residue 142 GLU Chi-restraints excluded: chain 5 residue 147 VAL Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 183 GLN Chi-restraints excluded: chain 5 residue 211 GLU Chi-restraints excluded: chain 5 residue 299 LEU Chi-restraints excluded: chain 6 residue 63 LEU Chi-restraints excluded: chain 6 residue 80 LEU Chi-restraints excluded: chain 6 residue 99 VAL Chi-restraints excluded: chain 6 residue 119 LEU Chi-restraints excluded: chain 6 residue 143 ARG Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 148 LEU Chi-restraints excluded: chain 6 residue 162 THR Chi-restraints excluded: chain 6 residue 179 GLN Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 6 residue 259 ASN Chi-restraints excluded: chain 6 residue 263 THR Chi-restraints excluded: chain 6 residue 269 PHE Chi-restraints excluded: chain 6 residue 304 LYS Chi-restraints excluded: chain 7 residue 19 THR Chi-restraints excluded: chain 7 residue 46 MET Chi-restraints excluded: chain 7 residue 53 VAL Chi-restraints excluded: chain 7 residue 117 LYS Chi-restraints excluded: chain 7 residue 119 LEU Chi-restraints excluded: chain 7 residue 142 GLU Chi-restraints excluded: chain 7 residue 146 ARG Chi-restraints excluded: chain 7 residue 148 LEU Chi-restraints excluded: chain 7 residue 149 THR Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 214 ASP Chi-restraints excluded: chain 7 residue 309 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 63 optimal weight: 0.3980 chunk 26 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 140 optimal weight: 0.0050 chunk 150 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 64 ASN 1 87 ASN 1 145 ASN ** 1 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 282 ASN ** 2 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 261 HIS 3 261 HIS 4 231 GLN ** 6 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 247 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.167987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.134186 restraints weight = 26069.687| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.29 r_work: 0.3537 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 18773 Z= 0.142 Angle : 0.668 10.931 25612 Z= 0.332 Chirality : 0.041 0.189 2863 Planarity : 0.004 0.048 3122 Dihedral : 15.116 88.488 2891 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 6.77 % Allowed : 25.80 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.18), residues: 2163 helix: 0.79 (0.15), residues: 1190 sheet: -2.17 (0.37), residues: 224 loop : -2.22 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 1 33 TYR 0.024 0.002 TYR 5 62 PHE 0.014 0.001 PHE 7 16 TRP 0.020 0.002 TRP 6 154 HIS 0.004 0.001 HIS 3 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (18772) covalent geometry : angle 0.66756 / 0.33 (25612) hydrogen bonds : bond 0.03353 / 3.75 ( 816) hydrogen bonds : angle 3.75366 / 4.39 ( 2372) Misc. bond : bond 0.00282 / 0.14 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 587 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 11 ARG cc_start: 0.8157 (mtp180) cc_final: 0.7700 (mtp85) REVERT: 1 29 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8300 (mtm) REVERT: 1 30 ASP cc_start: 0.8086 (m-30) cc_final: 0.7861 (m-30) REVERT: 1 37 ASP cc_start: 0.8006 (p0) cc_final: 0.7672 (p0) REVERT: 1 38 LEU cc_start: 0.8094 (mp) cc_final: 0.7796 (mt) REVERT: 1 39 GLU cc_start: 0.7133 (mp0) cc_final: 0.6635 (mp0) REVERT: 1 60 LYS cc_start: 0.8539 (mmmt) cc_final: 0.8274 (mmtp) REVERT: 1 81 HIS cc_start: 0.7999 (t70) cc_final: 0.7751 (t70) REVERT: 1 83 GLU cc_start: 0.7338 (tt0) cc_final: 0.7030 (mt-10) REVERT: 1 100 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7126 (tm-30) REVERT: 1 101 MET cc_start: 0.7959 (ttp) cc_final: 0.7600 (ttp) REVERT: 1 105 LEU cc_start: 0.7596 (pp) cc_final: 0.7297 (mp) REVERT: 1 129 LYS cc_start: 0.8552 (mtpt) cc_final: 0.8199 (mtpt) REVERT: 1 149 THR cc_start: 0.8577 (p) cc_final: 0.8280 (p) REVERT: 1 162 THR cc_start: 0.8230 (OUTLIER) cc_final: 0.7981 (t) REVERT: 1 163 LYS cc_start: 0.8252 (mptt) cc_final: 0.8035 (mmtt) REVERT: 1 228 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7335 (tm-30) REVERT: 1 269 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7674 (m-80) REVERT: 1 274 LYS cc_start: 0.8681 (mttt) cc_final: 0.8343 (mtpp) REVERT: 1 279 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.8113 (p0) REVERT: 1 285 LYS cc_start: 0.7679 (tppt) cc_final: 0.7356 (tppt) REVERT: 2 33 ARG cc_start: 0.8333 (ttp80) cc_final: 0.8079 (ttp-170) REVERT: 2 65 GLN cc_start: 0.7846 (pp30) cc_final: 0.7508 (pt0) REVERT: 2 116 THR cc_start: 0.8029 (m) cc_final: 0.7650 (p) REVERT: 2 122 LEU cc_start: 0.8577 (tp) cc_final: 0.8183 (tp) REVERT: 2 129 LYS cc_start: 0.8410 (mmtt) cc_final: 0.8118 (mmmm) REVERT: 2 135 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7048 (mm-30) REVERT: 2 141 GLU cc_start: 0.6348 (tm-30) cc_final: 0.5937 (tm-30) REVERT: 2 146 ARG cc_start: 0.7223 (ptm-80) cc_final: 0.6550 (ptm-80) REVERT: 2 150 GLN cc_start: 0.8118 (mt0) cc_final: 0.7788 (mt0) REVERT: 2 163 LYS cc_start: 0.8280 (mppt) cc_final: 0.7961 (mmtm) REVERT: 2 175 LYS cc_start: 0.8915 (ttmt) cc_final: 0.8635 (ttmm) REVERT: 2 211 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7339 (mt-10) REVERT: 2 228 GLU cc_start: 0.7602 (tp30) cc_final: 0.7294 (tp30) REVERT: 2 235 TYR cc_start: 0.8206 (t80) cc_final: 0.7774 (t80) REVERT: 2 242 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.7886 (tmm) REVERT: 2 309 GLU cc_start: 0.6988 (pm20) cc_final: 0.6655 (mp0) REVERT: 3 24 LYS cc_start: 0.8718 (tttt) cc_final: 0.8357 (ttpp) REVERT: 3 27 SER cc_start: 0.8867 (m) cc_final: 0.8415 (p) REVERT: 3 39 GLU cc_start: 0.7433 (mp0) cc_final: 0.6978 (mp0) REVERT: 3 46 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7677 (tpp) REVERT: 3 61 LYS cc_start: 0.8648 (tptp) cc_final: 0.8324 (tptp) REVERT: 3 86 ASP cc_start: 0.8392 (t0) cc_final: 0.8158 (t0) REVERT: 3 92 ASP cc_start: 0.7790 (t0) cc_final: 0.7475 (t0) REVERT: 3 96 GLU cc_start: 0.7377 (tm-30) cc_final: 0.7084 (tm-30) REVERT: 3 175 LYS cc_start: 0.8355 (ttmm) cc_final: 0.7950 (mtpp) REVERT: 3 181 ASN cc_start: 0.7665 (t0) cc_final: 0.7307 (t0) REVERT: 3 207 LYS cc_start: 0.8779 (tttt) cc_final: 0.8055 (ttmm) REVERT: 3 228 GLU cc_start: 0.6692 (tm-30) cc_final: 0.5970 (tm-30) REVERT: 3 232 LYS cc_start: 0.8101 (ttmm) cc_final: 0.7864 (ttmm) REVERT: 3 242 MET cc_start: 0.8256 (tpp) cc_final: 0.8039 (mmm) REVERT: 3 255 GLU cc_start: 0.8059 (tp30) cc_final: 0.7782 (tp30) REVERT: 3 268 ASP cc_start: 0.7511 (p0) cc_final: 0.7134 (p0) REVERT: 3 269 PHE cc_start: 0.7205 (OUTLIER) cc_final: 0.5503 (t80) REVERT: 3 282 ASN cc_start: 0.8091 (t0) cc_final: 0.7804 (t0) REVERT: 3 300 ARG cc_start: 0.8434 (ptp90) cc_final: 0.8196 (ptp90) REVERT: 4 14 ARG cc_start: 0.7887 (mtm110) cc_final: 0.7663 (ptp90) REVERT: 4 29 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7878 (mmp) REVERT: 4 46 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.7440 (tpt) REVERT: 4 55 LYS cc_start: 0.8067 (mtmt) cc_final: 0.7818 (mtmm) REVERT: 4 62 TYR cc_start: 0.8174 (t80) cc_final: 0.7763 (t80) REVERT: 4 63 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7340 (tp) REVERT: 4 83 GLU cc_start: 0.6884 (tt0) cc_final: 0.6037 (tt0) REVERT: 4 114 ARG cc_start: 0.7873 (ttp80) cc_final: 0.7603 (ptt90) REVERT: 4 133 ILE cc_start: 0.7816 (mt) cc_final: 0.7566 (mm) REVERT: 4 154 TRP cc_start: 0.7932 (t60) cc_final: 0.7566 (t60) REVERT: 4 155 LEU cc_start: 0.8433 (mt) cc_final: 0.8124 (mm) REVERT: 4 178 LEU cc_start: 0.7265 (pp) cc_final: 0.7041 (pp) REVERT: 4 190 ILE cc_start: 0.8357 (mt) cc_final: 0.8040 (pt) REVERT: 4 193 GLU cc_start: 0.7544 (tp30) cc_final: 0.7260 (tp30) REVERT: 4 255 GLU cc_start: 0.7247 (tp30) cc_final: 0.6978 (tt0) REVERT: 4 274 LYS cc_start: 0.8166 (mttt) cc_final: 0.7725 (mtmt) REVERT: 5 30 ASP cc_start: 0.7115 (OUTLIER) cc_final: 0.6901 (t0) REVERT: 5 55 LYS cc_start: 0.7079 (mtmm) cc_final: 0.6275 (mtmm) REVERT: 5 60 LYS cc_start: 0.7097 (mmmt) cc_final: 0.6756 (tppt) REVERT: 5 105 LEU cc_start: 0.6788 (OUTLIER) cc_final: 0.6477 (mp) REVERT: 5 157 MET cc_start: 0.6913 (tmm) cc_final: 0.6629 (ppp) REVERT: 5 171 MET cc_start: 0.7677 (mtp) cc_final: 0.7115 (mtp) REVERT: 5 241 ASN cc_start: 0.7286 (t0) cc_final: 0.6703 (t0) REVERT: 6 24 LYS cc_start: 0.8508 (ttpp) cc_final: 0.8248 (ttmm) REVERT: 6 30 ASP cc_start: 0.7408 (m-30) cc_final: 0.7170 (m-30) REVERT: 6 107 LEU cc_start: 0.8378 (pt) cc_final: 0.7937 (tp) REVERT: 6 119 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8011 (tp) REVERT: 6 135 GLU cc_start: 0.6414 (mm-30) cc_final: 0.5578 (mm-30) REVERT: 6 137 GLN cc_start: 0.7904 (pm20) cc_final: 0.7396 (pm20) REVERT: 6 142 GLU cc_start: 0.6625 (OUTLIER) cc_final: 0.6223 (pm20) REVERT: 6 149 THR cc_start: 0.8405 (p) cc_final: 0.8013 (p) REVERT: 6 150 GLN cc_start: 0.8426 (mt0) cc_final: 0.8089 (mt0) REVERT: 6 153 ASN cc_start: 0.8104 (m-40) cc_final: 0.7734 (m-40) REVERT: 6 162 THR cc_start: 0.8489 (OUTLIER) cc_final: 0.8217 (p) REVERT: 6 175 LYS cc_start: 0.8343 (ttmt) cc_final: 0.7960 (ttmm) REVERT: 6 181 ASN cc_start: 0.8489 (t0) cc_final: 0.8253 (t0) REVERT: 6 189 SER cc_start: 0.8670 (p) cc_final: 0.8413 (m) REVERT: 6 192 VAL cc_start: 0.8969 (OUTLIER) cc_final: 0.8747 (t) REVERT: 6 237 PHE cc_start: 0.8078 (t80) cc_final: 0.7427 (t80) REVERT: 6 255 GLU cc_start: 0.7251 (tp30) cc_final: 0.6306 (mm-30) REVERT: 6 259 ASN cc_start: 0.7337 (OUTLIER) cc_final: 0.6959 (p0) REVERT: 6 262 GLU cc_start: 0.6516 (mp0) cc_final: 0.6195 (mp0) REVERT: 6 266 GLU cc_start: 0.6958 (tp30) cc_final: 0.6252 (tp30) REVERT: 6 275 LEU cc_start: 0.7033 (tp) cc_final: 0.6610 (mp) REVERT: 7 37 ASP cc_start: 0.7581 (p0) cc_final: 0.5992 (p0) REVERT: 7 39 GLU cc_start: 0.7642 (mp0) cc_final: 0.6847 (mp0) REVERT: 7 46 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7393 (tpp) REVERT: 7 48 TYR cc_start: 0.8475 (m-80) cc_final: 0.8023 (m-10) REVERT: 7 61 LYS cc_start: 0.8386 (ttmm) cc_final: 0.8160 (ttmm) REVERT: 7 86 ASP cc_start: 0.8386 (t70) cc_final: 0.7983 (t0) REVERT: 7 99 VAL cc_start: 0.8940 (p) cc_final: 0.8637 (t) REVERT: 7 119 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7848 (tt) REVERT: 7 129 LYS cc_start: 0.8365 (mmmm) cc_final: 0.7984 (mttm) REVERT: 7 156 LYS cc_start: 0.8742 (ttpt) cc_final: 0.8395 (tttp) REVERT: 7 162 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.8314 (p) REVERT: 7 228 GLU cc_start: 0.7041 (tm-30) cc_final: 0.6443 (tm-30) REVERT: 7 232 LYS cc_start: 0.8447 (ttmm) cc_final: 0.7785 (ttpp) REVERT: 7 255 GLU cc_start: 0.7475 (tp30) cc_final: 0.6928 (tp30) outliers start: 127 outliers final: 80 residues processed: 658 average time/residue: 0.1637 time to fit residues: 155.0314 Evaluate side-chains 689 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 589 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 26 LEU Chi-restraints excluded: chain 1 residue 29 MET Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 1 residue 82 ILE Chi-restraints excluded: chain 1 residue 99 VAL Chi-restraints excluded: chain 1 residue 107 LEU Chi-restraints excluded: chain 1 residue 110 THR Chi-restraints excluded: chain 1 residue 117 LYS Chi-restraints excluded: chain 1 residue 119 LEU Chi-restraints excluded: chain 1 residue 142 GLU Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 1 residue 162 THR Chi-restraints excluded: chain 1 residue 176 VAL Chi-restraints excluded: chain 1 residue 215 LYS Chi-restraints excluded: chain 1 residue 217 LEU Chi-restraints excluded: chain 1 residue 269 PHE Chi-restraints excluded: chain 1 residue 279 ASP Chi-restraints excluded: chain 1 residue 309 GLU Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 22 VAL Chi-restraints excluded: chain 2 residue 45 MET Chi-restraints excluded: chain 2 residue 192 VAL Chi-restraints excluded: chain 2 residue 208 THR Chi-restraints excluded: chain 2 residue 213 LEU Chi-restraints excluded: chain 2 residue 242 MET Chi-restraints excluded: chain 2 residue 294 VAL Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 19 THR Chi-restraints excluded: chain 3 residue 35 LEU Chi-restraints excluded: chain 3 residue 45 MET Chi-restraints excluded: chain 3 residue 46 MET Chi-restraints excluded: chain 3 residue 63 LEU Chi-restraints excluded: chain 3 residue 65 GLN Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 99 VAL Chi-restraints excluded: chain 3 residue 115 LEU Chi-restraints excluded: chain 3 residue 142 GLU Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 193 GLU Chi-restraints excluded: chain 3 residue 269 PHE Chi-restraints excluded: chain 3 residue 270 VAL Chi-restraints excluded: chain 3 residue 312 LEU Chi-restraints excluded: chain 4 residue 27 SER Chi-restraints excluded: chain 4 residue 29 MET Chi-restraints excluded: chain 4 residue 30 ASP Chi-restraints excluded: chain 4 residue 46 MET Chi-restraints excluded: chain 4 residue 60 LYS Chi-restraints excluded: chain 4 residue 63 LEU Chi-restraints excluded: chain 4 residue 110 THR Chi-restraints excluded: chain 4 residue 119 LEU Chi-restraints excluded: chain 4 residue 130 LEU Chi-restraints excluded: chain 4 residue 131 ILE Chi-restraints excluded: chain 4 residue 142 GLU Chi-restraints excluded: chain 4 residue 148 LEU Chi-restraints excluded: chain 4 residue 162 THR Chi-restraints excluded: chain 4 residue 211 GLU Chi-restraints excluded: chain 4 residue 230 LEU Chi-restraints excluded: chain 4 residue 231 GLN Chi-restraints excluded: chain 4 residue 269 PHE Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 279 ASP Chi-restraints excluded: chain 5 residue 30 ASP Chi-restraints excluded: chain 5 residue 38 LEU Chi-restraints excluded: chain 5 residue 46 MET Chi-restraints excluded: chain 5 residue 97 LEU Chi-restraints excluded: chain 5 residue 105 LEU Chi-restraints excluded: chain 5 residue 142 GLU Chi-restraints excluded: chain 5 residue 147 VAL Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 158 ILE Chi-restraints excluded: chain 5 residue 168 ILE Chi-restraints excluded: chain 5 residue 183 GLN Chi-restraints excluded: chain 5 residue 211 GLU Chi-restraints excluded: chain 5 residue 299 LEU Chi-restraints excluded: chain 6 residue 63 LEU Chi-restraints excluded: chain 6 residue 99 VAL Chi-restraints excluded: chain 6 residue 115 LEU Chi-restraints excluded: chain 6 residue 118 ARG Chi-restraints excluded: chain 6 residue 119 LEU Chi-restraints excluded: chain 6 residue 142 GLU Chi-restraints excluded: chain 6 residue 143 ARG Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 148 LEU Chi-restraints excluded: chain 6 residue 162 THR Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 6 residue 259 ASN Chi-restraints excluded: chain 6 residue 263 THR Chi-restraints excluded: chain 6 residue 269 PHE Chi-restraints excluded: chain 7 residue 46 MET Chi-restraints excluded: chain 7 residue 53 VAL Chi-restraints excluded: chain 7 residue 117 LYS Chi-restraints excluded: chain 7 residue 119 LEU Chi-restraints excluded: chain 7 residue 142 GLU Chi-restraints excluded: chain 7 residue 146 ARG Chi-restraints excluded: chain 7 residue 148 LEU Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 214 ASP Chi-restraints excluded: chain 7 residue 269 PHE Chi-restraints excluded: chain 7 residue 309 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 94 optimal weight: 0.8980 chunk 154 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 220 optimal weight: 0.8980 chunk 209 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 198 optimal weight: 0.0770 chunk 72 optimal weight: 0.0270 chunk 178 optimal weight: 0.0000 overall best weight: 0.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 64 ASN 1 87 ASN 1 145 ASN ** 1 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 282 ASN ** 2 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 261 HIS 3 261 HIS ** 4 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 183 GLN ** 6 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 247 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.169275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.134272 restraints weight = 26424.931| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.23 r_work: 0.3556 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 18773 Z= 0.129 Angle : 0.663 15.063 25612 Z= 0.326 Chirality : 0.041 0.205 2863 Planarity : 0.004 0.052 3122 Dihedral : 14.961 88.783 2885 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 5.92 % Allowed : 26.71 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.19), residues: 2163 helix: 0.84 (0.15), residues: 1204 sheet: -2.01 (0.38), residues: 224 loop : -2.05 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 1 33 TYR 0.023 0.001 TYR 5 62 PHE 0.012 0.001 PHE 6 269 TRP 0.022 0.002 TRP 6 154 HIS 0.002 0.000 HIS 3 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (18772) covalent geometry : angle 0.66287 / 0.33 (25612) hydrogen bonds : bond 0.03150 / 3.51 ( 816) hydrogen bonds : angle 3.67665 / 4.32 ( 2372) Misc. bond : bond 0.00171 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 587 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 11 ARG cc_start: 0.8203 (mtp180) cc_final: 0.7728 (mtp85) REVERT: 1 23 ARG cc_start: 0.8386 (mtm110) cc_final: 0.7852 (mtm-85) REVERT: 1 29 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8368 (mtm) REVERT: 1 37 ASP cc_start: 0.8025 (p0) cc_final: 0.7713 (p0) REVERT: 1 38 LEU cc_start: 0.8005 (mp) cc_final: 0.7741 (mt) REVERT: 1 39 GLU cc_start: 0.7145 (mp0) cc_final: 0.6683 (mp0) REVERT: 1 48 TYR cc_start: 0.8618 (m-80) cc_final: 0.8098 (m-80) REVERT: 1 57 THR cc_start: 0.8269 (t) cc_final: 0.8031 (t) REVERT: 1 60 LYS cc_start: 0.8506 (mmmt) cc_final: 0.8167 (mttp) REVERT: 1 83 GLU cc_start: 0.7279 (tt0) cc_final: 0.7002 (mt-10) REVERT: 1 100 GLU cc_start: 0.7466 (tm-30) cc_final: 0.7097 (tm-30) REVERT: 1 101 MET cc_start: 0.7855 (ttp) cc_final: 0.7520 (ttp) REVERT: 1 105 LEU cc_start: 0.7580 (pp) cc_final: 0.7285 (mp) REVERT: 1 129 LYS cc_start: 0.8512 (mtpt) cc_final: 0.8152 (mtpt) REVERT: 1 149 THR cc_start: 0.8602 (p) cc_final: 0.8297 (p) REVERT: 1 162 THR cc_start: 0.8232 (OUTLIER) cc_final: 0.7993 (t) REVERT: 1 163 LYS cc_start: 0.8233 (mptt) cc_final: 0.8025 (mmtt) REVERT: 1 228 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7389 (tm-30) REVERT: 1 269 PHE cc_start: 0.8049 (OUTLIER) cc_final: 0.7741 (m-80) REVERT: 1 274 LYS cc_start: 0.8652 (mttt) cc_final: 0.8308 (mtpp) REVERT: 1 279 ASP cc_start: 0.8571 (OUTLIER) cc_final: 0.8206 (p0) REVERT: 1 285 LYS cc_start: 0.7653 (tppt) cc_final: 0.7347 (tppt) REVERT: 2 33 ARG cc_start: 0.8312 (ttp80) cc_final: 0.8079 (ttp-170) REVERT: 2 65 GLN cc_start: 0.7705 (pp30) cc_final: 0.7347 (pt0) REVERT: 2 96 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7377 (tm-30) REVERT: 2 116 THR cc_start: 0.8018 (m) cc_final: 0.7621 (p) REVERT: 2 122 LEU cc_start: 0.8581 (tp) cc_final: 0.8164 (tp) REVERT: 2 129 LYS cc_start: 0.8423 (mmtt) cc_final: 0.8078 (mmmm) REVERT: 2 135 GLU cc_start: 0.7458 (mm-30) cc_final: 0.6943 (mm-30) REVERT: 2 146 ARG cc_start: 0.7193 (ptm-80) cc_final: 0.6451 (ptm-80) REVERT: 2 150 GLN cc_start: 0.8092 (mt0) cc_final: 0.7633 (mt0) REVERT: 2 163 LYS cc_start: 0.8269 (mppt) cc_final: 0.7997 (mmtm) REVERT: 2 175 LYS cc_start: 0.8899 (ttmt) cc_final: 0.8600 (ttmm) REVERT: 2 235 TYR cc_start: 0.8081 (t80) cc_final: 0.7692 (t80) REVERT: 2 242 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.7923 (tmm) REVERT: 2 309 GLU cc_start: 0.6933 (pm20) cc_final: 0.6578 (pm20) REVERT: 3 24 LYS cc_start: 0.8694 (tttt) cc_final: 0.8214 (ttpp) REVERT: 3 27 SER cc_start: 0.8824 (m) cc_final: 0.8360 (p) REVERT: 3 39 GLU cc_start: 0.7448 (mp0) cc_final: 0.6978 (mp0) REVERT: 3 46 MET cc_start: 0.7906 (tpt) cc_final: 0.7630 (tpp) REVERT: 3 61 LYS cc_start: 0.8663 (tptp) cc_final: 0.8109 (tptp) REVERT: 3 92 ASP cc_start: 0.7771 (t0) cc_final: 0.7460 (t0) REVERT: 3 96 GLU cc_start: 0.7395 (tm-30) cc_final: 0.7128 (tm-30) REVERT: 3 175 LYS cc_start: 0.8357 (ttmm) cc_final: 0.7954 (mtpp) REVERT: 3 181 ASN cc_start: 0.7687 (t0) cc_final: 0.7345 (t0) REVERT: 3 207 LYS cc_start: 0.8795 (tttt) cc_final: 0.8095 (ttmm) REVERT: 3 220 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6578 (pm20) REVERT: 3 228 GLU cc_start: 0.6774 (tm-30) cc_final: 0.6031 (tm-30) REVERT: 3 232 LYS cc_start: 0.8201 (ttmm) cc_final: 0.7944 (ttmm) REVERT: 3 255 GLU cc_start: 0.7984 (tp30) cc_final: 0.7762 (tp30) REVERT: 3 268 ASP cc_start: 0.7556 (p0) cc_final: 0.7112 (p0) REVERT: 3 269 PHE cc_start: 0.7192 (OUTLIER) cc_final: 0.5522 (t80) REVERT: 3 282 ASN cc_start: 0.8049 (t0) cc_final: 0.7768 (t0) REVERT: 4 23 ARG cc_start: 0.7087 (mtm180) cc_final: 0.6750 (mtm110) REVERT: 4 29 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7873 (mmp) REVERT: 4 46 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7562 (tpt) REVERT: 4 62 TYR cc_start: 0.8137 (t80) cc_final: 0.7716 (t80) REVERT: 4 63 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7339 (tp) REVERT: 4 83 GLU cc_start: 0.6771 (tt0) cc_final: 0.5931 (tt0) REVERT: 4 96 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6679 (tp30) REVERT: 4 118 ARG cc_start: 0.6865 (mtp180) cc_final: 0.6644 (mtp180) REVERT: 4 131 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.7966 (tp) REVERT: 4 133 ILE cc_start: 0.7805 (mt) cc_final: 0.7564 (mm) REVERT: 4 154 TRP cc_start: 0.7900 (t60) cc_final: 0.7576 (t60) REVERT: 4 155 LEU cc_start: 0.8432 (mt) cc_final: 0.8148 (mm) REVERT: 4 193 GLU cc_start: 0.7566 (tp30) cc_final: 0.7257 (tp30) REVERT: 4 254 ILE cc_start: 0.7747 (pt) cc_final: 0.7291 (mm) REVERT: 4 274 LYS cc_start: 0.8173 (mttt) cc_final: 0.7727 (mtmt) REVERT: 5 55 LYS cc_start: 0.7130 (mtmm) cc_final: 0.6315 (mtmm) REVERT: 5 60 LYS cc_start: 0.7087 (mmmt) cc_final: 0.6750 (tppt) REVERT: 5 105 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6498 (mp) REVERT: 5 171 MET cc_start: 0.7782 (mtp) cc_final: 0.7204 (mtp) REVERT: 6 24 LYS cc_start: 0.8515 (ttpp) cc_final: 0.8272 (ttmm) REVERT: 6 30 ASP cc_start: 0.7380 (m-30) cc_final: 0.7120 (m-30) REVERT: 6 107 LEU cc_start: 0.8355 (pt) cc_final: 0.8044 (tp) REVERT: 6 119 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8031 (tp) REVERT: 6 142 GLU cc_start: 0.6623 (OUTLIER) cc_final: 0.6245 (pm20) REVERT: 6 149 THR cc_start: 0.8380 (p) cc_final: 0.7999 (p) REVERT: 6 150 GLN cc_start: 0.8388 (mt0) cc_final: 0.8101 (mt0) REVERT: 6 153 ASN cc_start: 0.8114 (m-40) cc_final: 0.7734 (m-40) REVERT: 6 175 LYS cc_start: 0.8334 (ttmt) cc_final: 0.7974 (ttmm) REVERT: 6 181 ASN cc_start: 0.8530 (t0) cc_final: 0.8293 (t0) REVERT: 6 185 HIS cc_start: 0.8151 (t70) cc_final: 0.7819 (t70) REVERT: 6 189 SER cc_start: 0.8615 (p) cc_final: 0.8330 (m) REVERT: 6 192 VAL cc_start: 0.8960 (OUTLIER) cc_final: 0.8759 (t) REVERT: 6 237 PHE cc_start: 0.8079 (t80) cc_final: 0.7662 (t80) REVERT: 6 255 GLU cc_start: 0.7308 (tp30) cc_final: 0.6566 (mm-30) REVERT: 6 259 ASN cc_start: 0.7388 (OUTLIER) cc_final: 0.6833 (p0) REVERT: 6 262 GLU cc_start: 0.6505 (mp0) cc_final: 0.6195 (mp0) REVERT: 6 266 GLU cc_start: 0.7256 (tp30) cc_final: 0.6851 (tp30) REVERT: 6 271 PHE cc_start: 0.7114 (t80) cc_final: 0.6429 (t80) REVERT: 6 275 LEU cc_start: 0.7033 (tp) cc_final: 0.6650 (mt) REVERT: 7 37 ASP cc_start: 0.7560 (p0) cc_final: 0.5985 (p0) REVERT: 7 39 GLU cc_start: 0.7691 (mp0) cc_final: 0.6856 (mp0) REVERT: 7 46 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7275 (tpp) REVERT: 7 61 LYS cc_start: 0.8302 (ttmm) cc_final: 0.8067 (ttmm) REVERT: 7 86 ASP cc_start: 0.8299 (t70) cc_final: 0.7819 (t0) REVERT: 7 99 VAL cc_start: 0.8912 (p) cc_final: 0.8625 (t) REVERT: 7 119 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7872 (tt) REVERT: 7 129 LYS cc_start: 0.8340 (mmmm) cc_final: 0.7988 (mttm) REVERT: 7 156 LYS cc_start: 0.8778 (ttpt) cc_final: 0.8443 (tttp) REVERT: 7 162 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.8301 (p) REVERT: 7 228 GLU cc_start: 0.7084 (tm-30) cc_final: 0.6498 (tm-30) REVERT: 7 232 LYS cc_start: 0.8414 (ttmm) cc_final: 0.7759 (ttpp) REVERT: 7 255 GLU cc_start: 0.7420 (tp30) cc_final: 0.6886 (tp30) outliers start: 111 outliers final: 75 residues processed: 647 average time/residue: 0.1704 time to fit residues: 157.3741 Evaluate side-chains 675 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 580 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 29 MET Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 1 residue 82 ILE Chi-restraints excluded: chain 1 residue 99 VAL Chi-restraints excluded: chain 1 residue 107 LEU Chi-restraints excluded: chain 1 residue 110 THR Chi-restraints excluded: chain 1 residue 117 LYS Chi-restraints excluded: chain 1 residue 119 LEU Chi-restraints excluded: chain 1 residue 142 GLU Chi-restraints excluded: chain 1 residue 145 ASN Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 1 residue 162 THR Chi-restraints excluded: chain 1 residue 215 LYS Chi-restraints excluded: chain 1 residue 217 LEU Chi-restraints excluded: chain 1 residue 269 PHE Chi-restraints excluded: chain 1 residue 279 ASP Chi-restraints excluded: chain 1 residue 309 GLU Chi-restraints excluded: chain 2 residue 22 VAL Chi-restraints excluded: chain 2 residue 192 VAL Chi-restraints excluded: chain 2 residue 208 THR Chi-restraints excluded: chain 2 residue 213 LEU Chi-restraints excluded: chain 2 residue 242 MET Chi-restraints excluded: chain 2 residue 294 VAL Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 19 THR Chi-restraints excluded: chain 3 residue 35 LEU Chi-restraints excluded: chain 3 residue 45 MET Chi-restraints excluded: chain 3 residue 65 GLN Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 99 VAL Chi-restraints excluded: chain 3 residue 115 LEU Chi-restraints excluded: chain 3 residue 142 GLU Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 193 GLU Chi-restraints excluded: chain 3 residue 220 GLU Chi-restraints excluded: chain 3 residue 261 HIS Chi-restraints excluded: chain 3 residue 269 PHE Chi-restraints excluded: chain 3 residue 270 VAL Chi-restraints excluded: chain 3 residue 312 LEU Chi-restraints excluded: chain 4 residue 29 MET Chi-restraints excluded: chain 4 residue 46 MET Chi-restraints excluded: chain 4 residue 60 LYS Chi-restraints excluded: chain 4 residue 63 LEU Chi-restraints excluded: chain 4 residue 96 GLU Chi-restraints excluded: chain 4 residue 110 THR Chi-restraints excluded: chain 4 residue 119 LEU Chi-restraints excluded: chain 4 residue 130 LEU Chi-restraints excluded: chain 4 residue 131 ILE Chi-restraints excluded: chain 4 residue 142 GLU Chi-restraints excluded: chain 4 residue 148 LEU Chi-restraints excluded: chain 4 residue 162 THR Chi-restraints excluded: chain 4 residue 211 GLU Chi-restraints excluded: chain 4 residue 263 THR Chi-restraints excluded: chain 4 residue 269 PHE Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 279 ASP Chi-restraints excluded: chain 5 residue 38 LEU Chi-restraints excluded: chain 5 residue 46 MET Chi-restraints excluded: chain 5 residue 97 LEU Chi-restraints excluded: chain 5 residue 105 LEU Chi-restraints excluded: chain 5 residue 142 GLU Chi-restraints excluded: chain 5 residue 147 VAL Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 158 ILE Chi-restraints excluded: chain 5 residue 168 ILE Chi-restraints excluded: chain 5 residue 183 GLN Chi-restraints excluded: chain 5 residue 211 GLU Chi-restraints excluded: chain 5 residue 259 ASN Chi-restraints excluded: chain 5 residue 299 LEU Chi-restraints excluded: chain 6 residue 63 LEU Chi-restraints excluded: chain 6 residue 115 LEU Chi-restraints excluded: chain 6 residue 118 ARG Chi-restraints excluded: chain 6 residue 119 LEU Chi-restraints excluded: chain 6 residue 142 GLU Chi-restraints excluded: chain 6 residue 143 ARG Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 148 LEU Chi-restraints excluded: chain 6 residue 178 LEU Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 6 residue 259 ASN Chi-restraints excluded: chain 6 residue 263 THR Chi-restraints excluded: chain 6 residue 269 PHE Chi-restraints excluded: chain 6 residue 304 LYS Chi-restraints excluded: chain 7 residue 46 MET Chi-restraints excluded: chain 7 residue 107 LEU Chi-restraints excluded: chain 7 residue 117 LYS Chi-restraints excluded: chain 7 residue 119 LEU Chi-restraints excluded: chain 7 residue 142 GLU Chi-restraints excluded: chain 7 residue 146 ARG Chi-restraints excluded: chain 7 residue 148 LEU Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 214 ASP Chi-restraints excluded: chain 7 residue 269 PHE Chi-restraints excluded: chain 7 residue 305 ASP Chi-restraints excluded: chain 7 residue 309 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 64 optimal weight: 0.0570 chunk 169 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 chunk 12 optimal weight: 0.0370 chunk 177 optimal weight: 1.9990 chunk 204 optimal weight: 0.0870 chunk 105 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 64 ASN 1 87 ASN ** 1 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 282 ASN 2 183 GLN ** 2 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 261 HIS 3 183 GLN 3 261 HIS 4 222 GLN ** 6 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 247 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.168871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.133614 restraints weight = 26400.255| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.24 r_work: 0.3561 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18773 Z= 0.128 Angle : 0.674 14.231 25612 Z= 0.332 Chirality : 0.041 0.266 2863 Planarity : 0.004 0.048 3122 Dihedral : 14.873 88.989 2884 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 5.86 % Allowed : 27.67 % Favored : 66.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.19), residues: 2163 helix: 0.93 (0.15), residues: 1204 sheet: -1.90 (0.39), residues: 224 loop : -1.99 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 1 33 TYR 0.023 0.001 TYR 6 199 PHE 0.010 0.001 PHE 1 237 TRP 0.035 0.002 TRP 6 154 HIS 0.015 0.001 HIS 3 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (18772) covalent geometry : angle 0.67427 / 0.33 (25612) hydrogen bonds : bond 0.03031 / 3.36 ( 816) hydrogen bonds : angle 3.63656 / 4.26 ( 2372) Misc. bond : bond 0.00195 / 0.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 587 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 11 ARG cc_start: 0.8199 (mtp180) cc_final: 0.7878 (ttp-170) REVERT: 1 23 ARG cc_start: 0.8421 (mtm110) cc_final: 0.8166 (mtm110) REVERT: 1 29 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8304 (mtm) REVERT: 1 37 ASP cc_start: 0.8007 (p0) cc_final: 0.7685 (p0) REVERT: 1 38 LEU cc_start: 0.7954 (mp) cc_final: 0.7653 (mt) REVERT: 1 39 GLU cc_start: 0.7094 (mp0) cc_final: 0.6648 (mp0) REVERT: 1 48 TYR cc_start: 0.8639 (m-80) cc_final: 0.8128 (m-80) REVERT: 1 60 LYS cc_start: 0.8496 (mmmt) cc_final: 0.8083 (mttp) REVERT: 1 83 GLU cc_start: 0.7278 (tt0) cc_final: 0.7004 (mt-10) REVERT: 1 100 GLU cc_start: 0.7469 (tm-30) cc_final: 0.7100 (tm-30) REVERT: 1 101 MET cc_start: 0.7853 (ttp) cc_final: 0.7538 (ttp) REVERT: 1 129 LYS cc_start: 0.8509 (mtpt) cc_final: 0.8140 (mtpt) REVERT: 1 149 THR cc_start: 0.8588 (p) cc_final: 0.8277 (p) REVERT: 1 162 THR cc_start: 0.8208 (OUTLIER) cc_final: 0.7956 (t) REVERT: 1 163 LYS cc_start: 0.8234 (mptt) cc_final: 0.7980 (mmtt) REVERT: 1 228 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7352 (tm-30) REVERT: 1 269 PHE cc_start: 0.8034 (OUTLIER) cc_final: 0.7740 (m-80) REVERT: 1 274 LYS cc_start: 0.8616 (mttt) cc_final: 0.8355 (mtpp) REVERT: 1 285 LYS cc_start: 0.7625 (tppt) cc_final: 0.7321 (tppt) REVERT: 2 33 ARG cc_start: 0.8298 (ttp80) cc_final: 0.8075 (ttp-170) REVERT: 2 65 GLN cc_start: 0.7664 (pp30) cc_final: 0.7369 (pt0) REVERT: 2 96 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7387 (tm-30) REVERT: 2 116 THR cc_start: 0.7943 (m) cc_final: 0.7580 (p) REVERT: 2 121 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7882 (mt-10) REVERT: 2 122 LEU cc_start: 0.8571 (tp) cc_final: 0.8163 (tp) REVERT: 2 129 LYS cc_start: 0.8420 (mmtt) cc_final: 0.8129 (mmpt) REVERT: 2 135 GLU cc_start: 0.7499 (mm-30) cc_final: 0.6982 (mm-30) REVERT: 2 146 ARG cc_start: 0.7215 (ptm-80) cc_final: 0.6411 (ptm-80) REVERT: 2 150 GLN cc_start: 0.8091 (mt0) cc_final: 0.7645 (mt0) REVERT: 2 163 LYS cc_start: 0.8344 (mppt) cc_final: 0.8000 (mmtm) REVERT: 2 175 LYS cc_start: 0.8912 (ttmt) cc_final: 0.8624 (ttmm) REVERT: 2 211 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7306 (mp0) REVERT: 2 235 TYR cc_start: 0.8054 (t80) cc_final: 0.7659 (t80) REVERT: 3 24 LYS cc_start: 0.8709 (tttt) cc_final: 0.8217 (ttpp) REVERT: 3 27 SER cc_start: 0.8821 (m) cc_final: 0.8363 (p) REVERT: 3 39 GLU cc_start: 0.7448 (mp0) cc_final: 0.7032 (mp0) REVERT: 3 46 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7626 (tpp) REVERT: 3 61 LYS cc_start: 0.8647 (tptp) cc_final: 0.8310 (tptt) REVERT: 3 92 ASP cc_start: 0.7767 (t0) cc_final: 0.7459 (t0) REVERT: 3 96 GLU cc_start: 0.7389 (tm-30) cc_final: 0.7144 (tm-30) REVERT: 3 175 LYS cc_start: 0.8338 (ttmm) cc_final: 0.7961 (mtpp) REVERT: 3 181 ASN cc_start: 0.7677 (t0) cc_final: 0.7348 (t0) REVERT: 3 207 LYS cc_start: 0.8797 (tttt) cc_final: 0.8092 (ttmm) REVERT: 3 220 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.6585 (pm20) REVERT: 3 228 GLU cc_start: 0.6791 (tm-30) cc_final: 0.6001 (tm-30) REVERT: 3 255 GLU cc_start: 0.8017 (tp30) cc_final: 0.7813 (tp30) REVERT: 3 268 ASP cc_start: 0.7506 (p0) cc_final: 0.7132 (p0) REVERT: 3 269 PHE cc_start: 0.7157 (OUTLIER) cc_final: 0.5510 (t80) REVERT: 3 300 ARG cc_start: 0.8320 (ptp90) cc_final: 0.8047 (ptp90) REVERT: 4 23 ARG cc_start: 0.7083 (mtm180) cc_final: 0.6751 (mtm110) REVERT: 4 29 MET cc_start: 0.7988 (mtt) cc_final: 0.7559 (mmp) REVERT: 4 45 MET cc_start: 0.7318 (ttp) cc_final: 0.6268 (ttp) REVERT: 4 46 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7573 (tpt) REVERT: 4 62 TYR cc_start: 0.8090 (t80) cc_final: 0.7750 (t80) REVERT: 4 63 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7325 (tp) REVERT: 4 83 GLU cc_start: 0.6746 (tt0) cc_final: 0.5995 (tt0) REVERT: 4 96 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6682 (tp30) REVERT: 4 154 TRP cc_start: 0.7852 (t60) cc_final: 0.7579 (t60) REVERT: 4 155 LEU cc_start: 0.8440 (mt) cc_final: 0.8164 (mm) REVERT: 4 193 GLU cc_start: 0.7550 (tp30) cc_final: 0.7241 (tp30) REVERT: 4 228 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7450 (tm-30) REVERT: 4 254 ILE cc_start: 0.7701 (pt) cc_final: 0.7264 (mm) REVERT: 4 255 GLU cc_start: 0.7322 (tp30) cc_final: 0.7013 (tt0) REVERT: 4 274 LYS cc_start: 0.8156 (mttt) cc_final: 0.7709 (mtmt) REVERT: 5 55 LYS cc_start: 0.7114 (mtmm) cc_final: 0.6312 (mtmm) REVERT: 5 60 LYS cc_start: 0.7074 (mmmt) cc_final: 0.6694 (tppt) REVERT: 5 105 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6516 (mp) REVERT: 5 142 GLU cc_start: 0.4192 (OUTLIER) cc_final: 0.3477 (mm-30) REVERT: 5 171 MET cc_start: 0.7769 (mtp) cc_final: 0.7183 (mtp) REVERT: 5 182 SER cc_start: 0.7834 (t) cc_final: 0.7404 (m) REVERT: 6 5 ARG cc_start: 0.7010 (tpp-160) cc_final: 0.6621 (tpm170) REVERT: 6 24 LYS cc_start: 0.8502 (ttpp) cc_final: 0.8272 (ttmm) REVERT: 6 30 ASP cc_start: 0.7397 (m-30) cc_final: 0.7129 (m-30) REVERT: 6 107 LEU cc_start: 0.8361 (pt) cc_final: 0.8075 (tp) REVERT: 6 119 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8096 (tp) REVERT: 6 142 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.6269 (pm20) REVERT: 6 149 THR cc_start: 0.8230 (p) cc_final: 0.7884 (p) REVERT: 6 150 GLN cc_start: 0.8354 (mt0) cc_final: 0.8073 (mt0) REVERT: 6 153 ASN cc_start: 0.8071 (m-40) cc_final: 0.7681 (m-40) REVERT: 6 162 THR cc_start: 0.8503 (OUTLIER) cc_final: 0.8192 (p) REVERT: 6 175 LYS cc_start: 0.8340 (ttmt) cc_final: 0.7973 (ttmm) REVERT: 6 181 ASN cc_start: 0.8560 (t0) cc_final: 0.8312 (t0) REVERT: 6 185 HIS cc_start: 0.8151 (t70) cc_final: 0.7788 (t70) REVERT: 6 231 GLN cc_start: 0.8091 (tt0) cc_final: 0.7339 (mt0) REVERT: 6 237 PHE cc_start: 0.8138 (t80) cc_final: 0.7782 (t80) REVERT: 6 255 GLU cc_start: 0.7313 (tp30) cc_final: 0.6280 (mm-30) REVERT: 6 259 ASN cc_start: 0.7303 (OUTLIER) cc_final: 0.6902 (p0) REVERT: 6 262 GLU cc_start: 0.6524 (mp0) cc_final: 0.6147 (mp0) REVERT: 6 263 THR cc_start: 0.5645 (OUTLIER) cc_final: 0.5416 (m) REVERT: 6 266 GLU cc_start: 0.7294 (tp30) cc_final: 0.6846 (tp30) REVERT: 6 271 PHE cc_start: 0.7061 (t80) cc_final: 0.6279 (t80) REVERT: 6 275 LEU cc_start: 0.7062 (tp) cc_final: 0.6553 (mp) REVERT: 7 37 ASP cc_start: 0.7577 (p0) cc_final: 0.6013 (p0) REVERT: 7 39 GLU cc_start: 0.7696 (mp0) cc_final: 0.6892 (mp0) REVERT: 7 46 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7222 (tpp) REVERT: 7 61 LYS cc_start: 0.8302 (ttmm) cc_final: 0.8049 (ttmm) REVERT: 7 86 ASP cc_start: 0.8285 (t70) cc_final: 0.7870 (t0) REVERT: 7 99 VAL cc_start: 0.8915 (p) cc_final: 0.8631 (t) REVERT: 7 119 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7912 (tt) REVERT: 7 129 LYS cc_start: 0.8330 (mmmm) cc_final: 0.7982 (mttp) REVERT: 7 156 LYS cc_start: 0.8778 (ttpt) cc_final: 0.8425 (tttp) REVERT: 7 162 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8292 (p) REVERT: 7 228 GLU cc_start: 0.7079 (tm-30) cc_final: 0.6495 (tm-30) REVERT: 7 232 LYS cc_start: 0.8421 (ttmm) cc_final: 0.7755 (ttpp) REVERT: 7 255 GLU cc_start: 0.7468 (tp30) cc_final: 0.6918 (tp30) outliers start: 110 outliers final: 66 residues processed: 649 average time/residue: 0.1715 time to fit residues: 157.5848 Evaluate side-chains 659 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 574 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 29 MET Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 1 residue 82 ILE Chi-restraints excluded: chain 1 residue 99 VAL Chi-restraints excluded: chain 1 residue 107 LEU Chi-restraints excluded: chain 1 residue 110 THR Chi-restraints excluded: chain 1 residue 117 LYS Chi-restraints excluded: chain 1 residue 119 LEU Chi-restraints excluded: chain 1 residue 142 GLU Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 1 residue 162 THR Chi-restraints excluded: chain 1 residue 217 LEU Chi-restraints excluded: chain 1 residue 269 PHE Chi-restraints excluded: chain 1 residue 279 ASP Chi-restraints excluded: chain 1 residue 309 GLU Chi-restraints excluded: chain 2 residue 22 VAL Chi-restraints excluded: chain 2 residue 101 MET Chi-restraints excluded: chain 2 residue 192 VAL Chi-restraints excluded: chain 2 residue 208 THR Chi-restraints excluded: chain 2 residue 213 LEU Chi-restraints excluded: chain 2 residue 294 VAL Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 19 THR Chi-restraints excluded: chain 3 residue 35 LEU Chi-restraints excluded: chain 3 residue 45 MET Chi-restraints excluded: chain 3 residue 46 MET Chi-restraints excluded: chain 3 residue 65 GLN Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 99 VAL Chi-restraints excluded: chain 3 residue 115 LEU Chi-restraints excluded: chain 3 residue 142 GLU Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 193 GLU Chi-restraints excluded: chain 3 residue 220 GLU Chi-restraints excluded: chain 3 residue 269 PHE Chi-restraints excluded: chain 3 residue 270 VAL Chi-restraints excluded: chain 3 residue 312 LEU Chi-restraints excluded: chain 4 residue 46 MET Chi-restraints excluded: chain 4 residue 60 LYS Chi-restraints excluded: chain 4 residue 63 LEU Chi-restraints excluded: chain 4 residue 96 GLU Chi-restraints excluded: chain 4 residue 110 THR Chi-restraints excluded: chain 4 residue 119 LEU Chi-restraints excluded: chain 4 residue 130 LEU Chi-restraints excluded: chain 4 residue 142 GLU Chi-restraints excluded: chain 4 residue 148 LEU Chi-restraints excluded: chain 4 residue 162 THR Chi-restraints excluded: chain 4 residue 231 GLN Chi-restraints excluded: chain 4 residue 264 ILE Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 5 residue 38 LEU Chi-restraints excluded: chain 5 residue 46 MET Chi-restraints excluded: chain 5 residue 97 LEU Chi-restraints excluded: chain 5 residue 105 LEU Chi-restraints excluded: chain 5 residue 140 VAL Chi-restraints excluded: chain 5 residue 142 GLU Chi-restraints excluded: chain 5 residue 147 VAL Chi-restraints excluded: chain 5 residue 168 ILE Chi-restraints excluded: chain 5 residue 183 GLN Chi-restraints excluded: chain 5 residue 259 ASN Chi-restraints excluded: chain 5 residue 299 LEU Chi-restraints excluded: chain 6 residue 115 LEU Chi-restraints excluded: chain 6 residue 118 ARG Chi-restraints excluded: chain 6 residue 119 LEU Chi-restraints excluded: chain 6 residue 142 GLU Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 148 LEU Chi-restraints excluded: chain 6 residue 162 THR Chi-restraints excluded: chain 6 residue 259 ASN Chi-restraints excluded: chain 6 residue 263 THR Chi-restraints excluded: chain 6 residue 269 PHE Chi-restraints excluded: chain 6 residue 292 VAL Chi-restraints excluded: chain 6 residue 304 LYS Chi-restraints excluded: chain 7 residue 46 MET Chi-restraints excluded: chain 7 residue 107 LEU Chi-restraints excluded: chain 7 residue 117 LYS Chi-restraints excluded: chain 7 residue 119 LEU Chi-restraints excluded: chain 7 residue 142 GLU Chi-restraints excluded: chain 7 residue 146 ARG Chi-restraints excluded: chain 7 residue 148 LEU Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 214 ASP Chi-restraints excluded: chain 7 residue 269 PHE Chi-restraints excluded: chain 7 residue 305 ASP Chi-restraints excluded: chain 7 residue 309 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 184 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 38 optimal weight: 0.0020 chunk 206 optimal weight: 0.0980 chunk 105 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.4980 chunk 143 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 64 ASN 1 87 ASN ** 1 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 282 ASN ** 2 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 231 GLN 2 261 HIS 3 183 GLN ** 6 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 247 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.169203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.134005 restraints weight = 26237.318| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.25 r_work: 0.3550 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18773 Z= 0.130 Angle : 0.695 13.578 25612 Z= 0.338 Chirality : 0.042 0.214 2863 Planarity : 0.004 0.038 3122 Dihedral : 14.711 89.591 2878 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 5.22 % Allowed : 29.05 % Favored : 65.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.19), residues: 2163 helix: 0.91 (0.15), residues: 1204 sheet: -1.83 (0.39), residues: 224 loop : -1.90 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 4 14 TYR 0.024 0.001 TYR 6 199 PHE 0.010 0.001 PHE 6 219 TRP 0.037 0.002 TRP 6 154 HIS 0.004 0.000 HIS 1 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (18772) covalent geometry : angle 0.69514 / 0.34 (25612) hydrogen bonds : bond 0.03066 / 3.45 ( 816) hydrogen bonds : angle 3.63076 / 4.27 ( 2372) Misc. bond : bond 0.00197 / 0.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 579 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 11 ARG cc_start: 0.8200 (mtp180) cc_final: 0.7911 (mtp85) REVERT: 1 23 ARG cc_start: 0.8438 (mtm110) cc_final: 0.8149 (mtm110) REVERT: 1 37 ASP cc_start: 0.8099 (p0) cc_final: 0.7721 (p0) REVERT: 1 38 LEU cc_start: 0.7949 (mp) cc_final: 0.7644 (mt) REVERT: 1 39 GLU cc_start: 0.7092 (mp0) cc_final: 0.6652 (mp0) REVERT: 1 48 TYR cc_start: 0.8684 (m-80) cc_final: 0.8161 (m-80) REVERT: 1 60 LYS cc_start: 0.8510 (mmmt) cc_final: 0.8085 (mttp) REVERT: 1 83 GLU cc_start: 0.7277 (tt0) cc_final: 0.6990 (mt-10) REVERT: 1 100 GLU cc_start: 0.7493 (tm-30) cc_final: 0.7119 (tm-30) REVERT: 1 101 MET cc_start: 0.7880 (ttp) cc_final: 0.7561 (ttp) REVERT: 1 105 LEU cc_start: 0.7518 (pp) cc_final: 0.7212 (mp) REVERT: 1 129 LYS cc_start: 0.8516 (mtpt) cc_final: 0.8141 (mtpt) REVERT: 1 149 THR cc_start: 0.8625 (p) cc_final: 0.8298 (p) REVERT: 1 162 THR cc_start: 0.8161 (OUTLIER) cc_final: 0.7943 (t) REVERT: 1 163 LYS cc_start: 0.8224 (mptt) cc_final: 0.7974 (mmtt) REVERT: 1 228 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7367 (tm-30) REVERT: 1 269 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.7771 (m-80) REVERT: 1 274 LYS cc_start: 0.8635 (mttt) cc_final: 0.8383 (mtpp) REVERT: 1 285 LYS cc_start: 0.7635 (tppt) cc_final: 0.7326 (tppt) REVERT: 2 33 ARG cc_start: 0.8271 (ttp80) cc_final: 0.8051 (ttp-170) REVERT: 2 65 GLN cc_start: 0.7665 (pp30) cc_final: 0.7373 (pt0) REVERT: 2 96 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7394 (tm-30) REVERT: 2 116 THR cc_start: 0.7997 (m) cc_final: 0.7698 (p) REVERT: 2 117 LYS cc_start: 0.7907 (tmmt) cc_final: 0.7668 (tmmt) REVERT: 2 122 LEU cc_start: 0.8594 (tp) cc_final: 0.8146 (tp) REVERT: 2 129 LYS cc_start: 0.8412 (mmtt) cc_final: 0.8123 (mmpt) REVERT: 2 146 ARG cc_start: 0.7205 (ptm-80) cc_final: 0.6414 (ptm-80) REVERT: 2 150 GLN cc_start: 0.8085 (mt0) cc_final: 0.7733 (mt0) REVERT: 2 163 LYS cc_start: 0.8343 (mppt) cc_final: 0.8034 (mmtm) REVERT: 2 175 LYS cc_start: 0.8911 (ttmt) cc_final: 0.8614 (ttmm) REVERT: 2 211 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7308 (mp0) REVERT: 2 235 TYR cc_start: 0.8117 (t80) cc_final: 0.7707 (t80) REVERT: 3 24 LYS cc_start: 0.8723 (tttt) cc_final: 0.8233 (ttpp) REVERT: 3 27 SER cc_start: 0.8791 (m) cc_final: 0.8371 (p) REVERT: 3 39 GLU cc_start: 0.7409 (mp0) cc_final: 0.6997 (mp0) REVERT: 3 46 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7634 (tpp) REVERT: 3 61 LYS cc_start: 0.8381 (tptp) cc_final: 0.8054 (tptt) REVERT: 3 92 ASP cc_start: 0.7766 (t0) cc_final: 0.7469 (t0) REVERT: 3 96 GLU cc_start: 0.7377 (tm-30) cc_final: 0.7155 (tm-30) REVERT: 3 175 LYS cc_start: 0.8328 (ttmm) cc_final: 0.7937 (mtpp) REVERT: 3 181 ASN cc_start: 0.7711 (t0) cc_final: 0.7358 (t0) REVERT: 3 207 LYS cc_start: 0.8822 (tttt) cc_final: 0.8130 (ttmm) REVERT: 3 228 GLU cc_start: 0.6596 (tm-30) cc_final: 0.6310 (tm-30) REVERT: 3 268 ASP cc_start: 0.7540 (p0) cc_final: 0.7187 (p0) REVERT: 3 269 PHE cc_start: 0.7181 (OUTLIER) cc_final: 0.5524 (t80) REVERT: 3 300 ARG cc_start: 0.8288 (ptp90) cc_final: 0.8018 (ptp90) REVERT: 4 23 ARG cc_start: 0.7136 (mtm180) cc_final: 0.6763 (mtm110) REVERT: 4 29 MET cc_start: 0.8014 (mtt) cc_final: 0.7710 (mmp) REVERT: 4 46 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7467 (tpt) REVERT: 4 62 TYR cc_start: 0.8131 (t80) cc_final: 0.7870 (t80) REVERT: 4 63 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7326 (tp) REVERT: 4 83 GLU cc_start: 0.6737 (tt0) cc_final: 0.5916 (tt0) REVERT: 4 96 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6711 (tp30) REVERT: 4 133 ILE cc_start: 0.7910 (mt) cc_final: 0.7634 (mm) REVERT: 4 154 TRP cc_start: 0.7875 (t60) cc_final: 0.7639 (t60) REVERT: 4 155 LEU cc_start: 0.8452 (mt) cc_final: 0.8165 (mm) REVERT: 4 191 GLN cc_start: 0.7588 (mt0) cc_final: 0.7216 (mp10) REVERT: 4 193 GLU cc_start: 0.7580 (tp30) cc_final: 0.7252 (tp30) REVERT: 4 228 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7397 (tm-30) REVERT: 4 254 ILE cc_start: 0.7726 (pt) cc_final: 0.7266 (mm) REVERT: 4 255 GLU cc_start: 0.7400 (tp30) cc_final: 0.7098 (tt0) REVERT: 4 274 LYS cc_start: 0.8191 (mttt) cc_final: 0.7729 (mtmt) REVERT: 5 55 LYS cc_start: 0.7081 (mtmm) cc_final: 0.6832 (mtmm) REVERT: 5 105 LEU cc_start: 0.6827 (OUTLIER) cc_final: 0.6443 (mp) REVERT: 5 142 GLU cc_start: 0.4178 (OUTLIER) cc_final: 0.3487 (mm-30) REVERT: 5 171 MET cc_start: 0.7802 (mtp) cc_final: 0.7212 (mtp) REVERT: 5 182 SER cc_start: 0.7837 (t) cc_final: 0.7388 (m) REVERT: 6 5 ARG cc_start: 0.7097 (tpp-160) cc_final: 0.6766 (tpm170) REVERT: 6 30 ASP cc_start: 0.7383 (m-30) cc_final: 0.7056 (m-30) REVERT: 6 101 MET cc_start: 0.7407 (ttm) cc_final: 0.7199 (ttm) REVERT: 6 107 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8095 (tp) REVERT: 6 119 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8011 (tp) REVERT: 6 142 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.6288 (pm20) REVERT: 6 146 ARG cc_start: 0.7904 (ptm160) cc_final: 0.7647 (ptm160) REVERT: 6 149 THR cc_start: 0.8218 (p) cc_final: 0.7883 (p) REVERT: 6 150 GLN cc_start: 0.8348 (mt0) cc_final: 0.8024 (mt0) REVERT: 6 153 ASN cc_start: 0.8089 (m-40) cc_final: 0.7696 (m-40) REVERT: 6 162 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.8174 (p) REVERT: 6 175 LYS cc_start: 0.8294 (ttmt) cc_final: 0.7902 (ttmm) REVERT: 6 181 ASN cc_start: 0.8582 (t0) cc_final: 0.8347 (t0) REVERT: 6 231 GLN cc_start: 0.8003 (tt0) cc_final: 0.7743 (mt0) REVERT: 6 237 PHE cc_start: 0.8129 (t80) cc_final: 0.7800 (t80) REVERT: 6 255 GLU cc_start: 0.7329 (tp30) cc_final: 0.6180 (mm-30) REVERT: 6 259 ASN cc_start: 0.7237 (p0) cc_final: 0.6851 (p0) REVERT: 6 262 GLU cc_start: 0.6597 (mp0) cc_final: 0.6228 (mp0) REVERT: 6 263 THR cc_start: 0.5550 (OUTLIER) cc_final: 0.5310 (m) REVERT: 6 266 GLU cc_start: 0.7323 (tp30) cc_final: 0.6920 (tp30) REVERT: 6 270 VAL cc_start: 0.8391 (m) cc_final: 0.8094 (m) REVERT: 6 271 PHE cc_start: 0.7005 (t80) cc_final: 0.6426 (t80) REVERT: 6 275 LEU cc_start: 0.7073 (tp) cc_final: 0.6657 (mt) REVERT: 7 37 ASP cc_start: 0.7582 (p0) cc_final: 0.6040 (p0) REVERT: 7 39 GLU cc_start: 0.7708 (mp0) cc_final: 0.6909 (mp0) REVERT: 7 46 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7129 (tpp) REVERT: 7 61 LYS cc_start: 0.8332 (ttmm) cc_final: 0.8084 (ttmm) REVERT: 7 86 ASP cc_start: 0.8266 (t70) cc_final: 0.7849 (t0) REVERT: 7 99 VAL cc_start: 0.8931 (p) cc_final: 0.8653 (t) REVERT: 7 119 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7940 (tt) REVERT: 7 129 LYS cc_start: 0.8332 (mmmm) cc_final: 0.7983 (mttm) REVERT: 7 153 ASN cc_start: 0.8031 (m-40) cc_final: 0.7796 (m-40) REVERT: 7 156 LYS cc_start: 0.8774 (ttpt) cc_final: 0.8425 (tttp) REVERT: 7 162 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8285 (p) REVERT: 7 228 GLU cc_start: 0.7110 (tm-30) cc_final: 0.6538 (tm-30) REVERT: 7 232 LYS cc_start: 0.8430 (ttmm) cc_final: 0.7736 (ttpp) REVERT: 7 247 ASN cc_start: 0.8634 (m-40) cc_final: 0.8199 (m110) REVERT: 7 255 GLU cc_start: 0.7439 (tp30) cc_final: 0.6877 (tp30) outliers start: 98 outliers final: 69 residues processed: 634 average time/residue: 0.1658 time to fit residues: 150.3510 Evaluate side-chains 666 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 580 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 29 MET Chi-restraints excluded: chain 1 residue 34 ASP Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 1 residue 82 ILE Chi-restraints excluded: chain 1 residue 99 VAL Chi-restraints excluded: chain 1 residue 107 LEU Chi-restraints excluded: chain 1 residue 110 THR Chi-restraints excluded: chain 1 residue 142 GLU Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 1 residue 162 THR Chi-restraints excluded: chain 1 residue 217 LEU Chi-restraints excluded: chain 1 residue 269 PHE Chi-restraints excluded: chain 1 residue 279 ASP Chi-restraints excluded: chain 1 residue 309 GLU Chi-restraints excluded: chain 2 residue 22 VAL Chi-restraints excluded: chain 2 residue 45 MET Chi-restraints excluded: chain 2 residue 101 MET Chi-restraints excluded: chain 2 residue 192 VAL Chi-restraints excluded: chain 2 residue 208 THR Chi-restraints excluded: chain 2 residue 213 LEU Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 19 THR Chi-restraints excluded: chain 3 residue 35 LEU Chi-restraints excluded: chain 3 residue 45 MET Chi-restraints excluded: chain 3 residue 46 MET Chi-restraints excluded: chain 3 residue 65 GLN Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 115 LEU Chi-restraints excluded: chain 3 residue 142 GLU Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 193 GLU Chi-restraints excluded: chain 3 residue 269 PHE Chi-restraints excluded: chain 3 residue 270 VAL Chi-restraints excluded: chain 3 residue 312 LEU Chi-restraints excluded: chain 4 residue 46 MET Chi-restraints excluded: chain 4 residue 63 LEU Chi-restraints excluded: chain 4 residue 96 GLU Chi-restraints excluded: chain 4 residue 110 THR Chi-restraints excluded: chain 4 residue 119 LEU Chi-restraints excluded: chain 4 residue 130 LEU Chi-restraints excluded: chain 4 residue 142 GLU Chi-restraints excluded: chain 4 residue 148 LEU Chi-restraints excluded: chain 4 residue 162 THR Chi-restraints excluded: chain 4 residue 230 LEU Chi-restraints excluded: chain 4 residue 231 GLN Chi-restraints excluded: chain 4 residue 264 ILE Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 5 residue 38 LEU Chi-restraints excluded: chain 5 residue 46 MET Chi-restraints excluded: chain 5 residue 97 LEU Chi-restraints excluded: chain 5 residue 105 LEU Chi-restraints excluded: chain 5 residue 142 GLU Chi-restraints excluded: chain 5 residue 147 VAL Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 168 ILE Chi-restraints excluded: chain 5 residue 183 GLN Chi-restraints excluded: chain 5 residue 299 LEU Chi-restraints excluded: chain 6 residue 63 LEU Chi-restraints excluded: chain 6 residue 107 LEU Chi-restraints excluded: chain 6 residue 115 LEU Chi-restraints excluded: chain 6 residue 118 ARG Chi-restraints excluded: chain 6 residue 119 LEU Chi-restraints excluded: chain 6 residue 142 GLU Chi-restraints excluded: chain 6 residue 143 ARG Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 148 LEU Chi-restraints excluded: chain 6 residue 162 THR Chi-restraints excluded: chain 6 residue 178 LEU Chi-restraints excluded: chain 6 residue 263 THR Chi-restraints excluded: chain 6 residue 269 PHE Chi-restraints excluded: chain 6 residue 292 VAL Chi-restraints excluded: chain 6 residue 304 LYS Chi-restraints excluded: chain 7 residue 46 MET Chi-restraints excluded: chain 7 residue 107 LEU Chi-restraints excluded: chain 7 residue 109 GLU Chi-restraints excluded: chain 7 residue 117 LYS Chi-restraints excluded: chain 7 residue 119 LEU Chi-restraints excluded: chain 7 residue 142 GLU Chi-restraints excluded: chain 7 residue 146 ARG Chi-restraints excluded: chain 7 residue 148 LEU Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 214 ASP Chi-restraints excluded: chain 7 residue 269 PHE Chi-restraints excluded: chain 7 residue 305 ASP Chi-restraints excluded: chain 7 residue 309 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 119 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 56 optimal weight: 0.2980 chunk 128 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 64 ASN 1 145 ASN ** 1 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 282 ASN 2 191 GLN ** 2 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 261 HIS 3 183 GLN 3 261 HIS ** 6 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.164984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.130177 restraints weight = 26476.049| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.13 r_work: 0.3509 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 18773 Z= 0.228 Angle : 0.755 13.022 25612 Z= 0.372 Chirality : 0.045 0.199 2863 Planarity : 0.005 0.047 3122 Dihedral : 14.626 85.711 2876 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 4.69 % Allowed : 29.64 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.18), residues: 2163 helix: 0.68 (0.15), residues: 1204 sheet: -1.93 (0.38), residues: 224 loop : -1.97 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 1 33 TYR 0.026 0.002 TYR 6 62 PHE 0.014 0.002 PHE 7 188 TRP 0.038 0.002 TRP 6 154 HIS 0.008 0.001 HIS 1 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.23 (18772) covalent geometry : angle 0.75530 / 0.37 (25612) hydrogen bonds : bond 0.03696 / 4.11 ( 816) hydrogen bonds : angle 3.83270 / 4.49 ( 2372) Misc. bond : bond 0.00206 / 0.10 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 607 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 6 GLU cc_start: 0.7611 (pm20) cc_final: 0.7248 (pm20) REVERT: 1 23 ARG cc_start: 0.8312 (mtm110) cc_final: 0.7745 (mtm110) REVERT: 1 37 ASP cc_start: 0.8165 (p0) cc_final: 0.7217 (p0) REVERT: 1 38 LEU cc_start: 0.8070 (mp) cc_final: 0.7676 (mp) REVERT: 1 39 GLU cc_start: 0.7188 (mp0) cc_final: 0.6142 (mp0) REVERT: 1 60 LYS cc_start: 0.8594 (mmmt) cc_final: 0.8383 (mmtp) REVERT: 1 81 HIS cc_start: 0.8101 (t70) cc_final: 0.7672 (t-170) REVERT: 1 83 GLU cc_start: 0.7349 (tt0) cc_final: 0.7044 (mt-10) REVERT: 1 100 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7187 (tm-30) REVERT: 1 105 LEU cc_start: 0.7629 (pp) cc_final: 0.7289 (mp) REVERT: 1 129 LYS cc_start: 0.8579 (mtpt) cc_final: 0.8241 (mtpt) REVERT: 1 149 THR cc_start: 0.8647 (p) cc_final: 0.8170 (p) REVERT: 1 162 THR cc_start: 0.8171 (OUTLIER) cc_final: 0.7845 (p) REVERT: 1 166 ILE cc_start: 0.8217 (mt) cc_final: 0.7875 (tt) REVERT: 1 269 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7852 (m-80) REVERT: 1 274 LYS cc_start: 0.8687 (mttt) cc_final: 0.8322 (mtpp) REVERT: 1 285 LYS cc_start: 0.7900 (tppt) cc_final: 0.7563 (tppt) REVERT: 1 293 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7071 (tm-30) REVERT: 1 296 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7371 (tm-30) REVERT: 1 300 ARG cc_start: 0.8133 (mmt90) cc_final: 0.7553 (tpp80) REVERT: 2 33 ARG cc_start: 0.8391 (ttp80) cc_final: 0.8057 (ttp-170) REVERT: 2 65 GLN cc_start: 0.7689 (pp30) cc_final: 0.7386 (pt0) REVERT: 2 96 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7461 (tm-30) REVERT: 2 116 THR cc_start: 0.8024 (m) cc_final: 0.7687 (p) REVERT: 2 129 LYS cc_start: 0.8351 (mmtt) cc_final: 0.8137 (mmmt) REVERT: 2 146 ARG cc_start: 0.7398 (ptm-80) cc_final: 0.6629 (ptm-80) REVERT: 2 150 GLN cc_start: 0.8191 (mt0) cc_final: 0.7851 (mt0) REVERT: 2 163 LYS cc_start: 0.8336 (mppt) cc_final: 0.8029 (mmtm) REVERT: 2 175 LYS cc_start: 0.8980 (ttmt) cc_final: 0.8716 (ttmm) REVERT: 2 242 MET cc_start: 0.8532 (tmm) cc_final: 0.7834 (tmm) REVERT: 2 312 LEU cc_start: 0.8383 (mt) cc_final: 0.8172 (mm) REVERT: 3 24 LYS cc_start: 0.8729 (tttt) cc_final: 0.8246 (ttpp) REVERT: 3 27 SER cc_start: 0.8845 (m) cc_final: 0.8402 (p) REVERT: 3 39 GLU cc_start: 0.7322 (mp0) cc_final: 0.6663 (mp0) REVERT: 3 46 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7708 (tpp) REVERT: 3 61 LYS cc_start: 0.8621 (tptp) cc_final: 0.8222 (tptt) REVERT: 3 92 ASP cc_start: 0.7929 (t0) cc_final: 0.7627 (t0) REVERT: 3 96 GLU cc_start: 0.7360 (tm-30) cc_final: 0.7050 (tm-30) REVERT: 3 175 LYS cc_start: 0.8379 (ttmm) cc_final: 0.7932 (mtpp) REVERT: 3 181 ASN cc_start: 0.7599 (t0) cc_final: 0.7260 (t0) REVERT: 3 207 LYS cc_start: 0.8780 (tttt) cc_final: 0.8125 (ttmm) REVERT: 3 220 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6628 (pm20) REVERT: 3 228 GLU cc_start: 0.6726 (tm-30) cc_final: 0.6370 (tm-30) REVERT: 3 269 PHE cc_start: 0.7233 (OUTLIER) cc_final: 0.5607 (t80) REVERT: 4 29 MET cc_start: 0.8076 (mtt) cc_final: 0.7807 (mmp) REVERT: 4 46 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7352 (tpt) REVERT: 4 63 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7510 (tp) REVERT: 4 83 GLU cc_start: 0.6781 (tt0) cc_final: 0.5940 (tt0) REVERT: 4 96 GLU cc_start: 0.7282 (tm-30) cc_final: 0.6679 (tp30) REVERT: 4 131 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8101 (tp) REVERT: 4 133 ILE cc_start: 0.7959 (mt) cc_final: 0.7740 (mm) REVERT: 4 154 TRP cc_start: 0.8084 (t60) cc_final: 0.7696 (t60) REVERT: 4 155 LEU cc_start: 0.8511 (mt) cc_final: 0.8231 (mm) REVERT: 4 193 GLU cc_start: 0.7673 (tp30) cc_final: 0.7384 (tp30) REVERT: 4 200 GLN cc_start: 0.7324 (tm-30) cc_final: 0.7093 (tm-30) REVERT: 4 254 ILE cc_start: 0.7720 (pt) cc_final: 0.7246 (mm) REVERT: 4 255 GLU cc_start: 0.7470 (tp30) cc_final: 0.7142 (tt0) REVERT: 4 304 LYS cc_start: 0.7323 (tppt) cc_final: 0.6821 (tppt) REVERT: 5 105 LEU cc_start: 0.6814 (OUTLIER) cc_final: 0.6417 (mp) REVERT: 5 142 GLU cc_start: 0.4223 (OUTLIER) cc_final: 0.3756 (mm-30) REVERT: 5 171 MET cc_start: 0.7805 (mtp) cc_final: 0.7226 (mtp) REVERT: 5 182 SER cc_start: 0.8047 (t) cc_final: 0.7625 (m) REVERT: 5 241 ASN cc_start: 0.7421 (t0) cc_final: 0.6769 (t0) REVERT: 6 30 ASP cc_start: 0.7531 (m-30) cc_final: 0.7322 (m-30) REVERT: 6 101 MET cc_start: 0.7562 (ttm) cc_final: 0.7329 (ttm) REVERT: 6 107 LEU cc_start: 0.8550 (pt) cc_final: 0.8289 (tp) REVERT: 6 135 GLU cc_start: 0.6395 (mm-30) cc_final: 0.5737 (mm-30) REVERT: 6 142 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.6567 (pm20) REVERT: 6 149 THR cc_start: 0.8455 (p) cc_final: 0.8130 (p) REVERT: 6 150 GLN cc_start: 0.8492 (mt0) cc_final: 0.8182 (mt0) REVERT: 6 153 ASN cc_start: 0.8069 (m110) cc_final: 0.7632 (m-40) REVERT: 6 162 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8070 (p) REVERT: 6 175 LYS cc_start: 0.8277 (ttmt) cc_final: 0.7981 (ttmm) REVERT: 6 181 ASN cc_start: 0.8567 (t0) cc_final: 0.8308 (t0) REVERT: 6 185 HIS cc_start: 0.8202 (t70) cc_final: 0.7886 (t70) REVERT: 6 189 SER cc_start: 0.8574 (p) cc_final: 0.8362 (m) REVERT: 6 231 GLN cc_start: 0.7959 (tt0) cc_final: 0.7406 (mt0) REVERT: 6 255 GLU cc_start: 0.7597 (tp30) cc_final: 0.6467 (mm-30) REVERT: 6 262 GLU cc_start: 0.6590 (mp0) cc_final: 0.6208 (mp0) REVERT: 6 263 THR cc_start: 0.5593 (OUTLIER) cc_final: 0.5346 (m) REVERT: 6 266 GLU cc_start: 0.7254 (tp30) cc_final: 0.7012 (tp30) REVERT: 6 275 LEU cc_start: 0.7261 (tp) cc_final: 0.6650 (mp) REVERT: 7 5 ARG cc_start: 0.7590 (tpp80) cc_final: 0.6728 (tpt-90) REVERT: 7 14 ARG cc_start: 0.8203 (mtm-85) cc_final: 0.7973 (mtt90) REVERT: 7 37 ASP cc_start: 0.7719 (p0) cc_final: 0.6197 (p0) REVERT: 7 39 GLU cc_start: 0.7656 (mp0) cc_final: 0.6920 (mp0) REVERT: 7 46 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7250 (tpp) REVERT: 7 48 TYR cc_start: 0.8468 (m-80) cc_final: 0.7944 (m-10) REVERT: 7 61 LYS cc_start: 0.8388 (ttmm) cc_final: 0.8128 (ttmm) REVERT: 7 86 ASP cc_start: 0.8323 (t70) cc_final: 0.7892 (t0) REVERT: 7 99 VAL cc_start: 0.9057 (p) cc_final: 0.8736 (t) REVERT: 7 119 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7803 (tt) REVERT: 7 129 LYS cc_start: 0.8313 (mmmm) cc_final: 0.7985 (mttm) REVERT: 7 156 LYS cc_start: 0.8814 (ttpt) cc_final: 0.8465 (tttp) REVERT: 7 162 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8458 (p) REVERT: 7 228 GLU cc_start: 0.7102 (tm-30) cc_final: 0.6610 (tm-30) REVERT: 7 232 LYS cc_start: 0.8499 (ttmm) cc_final: 0.7812 (ttpp) REVERT: 7 247 ASN cc_start: 0.8568 (m-40) cc_final: 0.8244 (m-40) REVERT: 7 255 GLU cc_start: 0.7463 (tp30) cc_final: 0.6961 (tp30) REVERT: 7 271 PHE cc_start: 0.8285 (t80) cc_final: 0.7837 (t80) outliers start: 88 outliers final: 61 residues processed: 658 average time/residue: 0.1666 time to fit residues: 156.4628 Evaluate side-chains 671 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 594 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 26 LEU Chi-restraints excluded: chain 1 residue 29 MET Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 1 residue 99 VAL Chi-restraints excluded: chain 1 residue 107 LEU Chi-restraints excluded: chain 1 residue 110 THR Chi-restraints excluded: chain 1 residue 145 ASN Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 1 residue 162 THR Chi-restraints excluded: chain 1 residue 269 PHE Chi-restraints excluded: chain 1 residue 279 ASP Chi-restraints excluded: chain 2 residue 22 VAL Chi-restraints excluded: chain 2 residue 45 MET Chi-restraints excluded: chain 2 residue 101 MET Chi-restraints excluded: chain 2 residue 192 VAL Chi-restraints excluded: chain 2 residue 200 GLN Chi-restraints excluded: chain 2 residue 208 THR Chi-restraints excluded: chain 2 residue 213 LEU Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 19 THR Chi-restraints excluded: chain 3 residue 35 LEU Chi-restraints excluded: chain 3 residue 46 MET Chi-restraints excluded: chain 3 residue 63 LEU Chi-restraints excluded: chain 3 residue 65 GLN Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 142 GLU Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 193 GLU Chi-restraints excluded: chain 3 residue 200 GLN Chi-restraints excluded: chain 3 residue 220 GLU Chi-restraints excluded: chain 3 residue 261 HIS Chi-restraints excluded: chain 3 residue 269 PHE Chi-restraints excluded: chain 4 residue 30 ASP Chi-restraints excluded: chain 4 residue 46 MET Chi-restraints excluded: chain 4 residue 60 LYS Chi-restraints excluded: chain 4 residue 63 LEU Chi-restraints excluded: chain 4 residue 101 MET Chi-restraints excluded: chain 4 residue 110 THR Chi-restraints excluded: chain 4 residue 119 LEU Chi-restraints excluded: chain 4 residue 131 ILE Chi-restraints excluded: chain 4 residue 142 GLU Chi-restraints excluded: chain 4 residue 148 LEU Chi-restraints excluded: chain 4 residue 149 THR Chi-restraints excluded: chain 4 residue 162 THR Chi-restraints excluded: chain 4 residue 231 GLN Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 5 residue 46 MET Chi-restraints excluded: chain 5 residue 97 LEU Chi-restraints excluded: chain 5 residue 105 LEU Chi-restraints excluded: chain 5 residue 114 ARG Chi-restraints excluded: chain 5 residue 142 GLU Chi-restraints excluded: chain 5 residue 147 VAL Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 168 ILE Chi-restraints excluded: chain 5 residue 183 GLN Chi-restraints excluded: chain 6 residue 63 LEU Chi-restraints excluded: chain 6 residue 115 LEU Chi-restraints excluded: chain 6 residue 118 ARG Chi-restraints excluded: chain 6 residue 119 LEU Chi-restraints excluded: chain 6 residue 142 GLU Chi-restraints excluded: chain 6 residue 143 ARG Chi-restraints excluded: chain 6 residue 148 LEU Chi-restraints excluded: chain 6 residue 162 THR Chi-restraints excluded: chain 6 residue 178 LEU Chi-restraints excluded: chain 6 residue 263 THR Chi-restraints excluded: chain 6 residue 269 PHE Chi-restraints excluded: chain 7 residue 46 MET Chi-restraints excluded: chain 7 residue 107 LEU Chi-restraints excluded: chain 7 residue 117 LYS Chi-restraints excluded: chain 7 residue 119 LEU Chi-restraints excluded: chain 7 residue 148 LEU Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 214 ASP Chi-restraints excluded: chain 7 residue 263 THR Chi-restraints excluded: chain 7 residue 269 PHE Chi-restraints excluded: chain 7 residue 305 ASP Chi-restraints excluded: chain 7 residue 309 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 26 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 161 optimal weight: 0.8980 chunk 144 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 95 optimal weight: 0.0050 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 64 ASN 1 87 ASN ** 1 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 231 GLN 1 282 ASN 2 191 GLN ** 2 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 261 HIS 3 183 GLN 3 259 ASN 3 261 HIS 4 247 ASN 5 150 GLN ** 6 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 81 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.166742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.132172 restraints weight = 26514.441| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.13 r_work: 0.3538 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18773 Z= 0.154 Angle : 0.732 13.206 25612 Z= 0.359 Chirality : 0.043 0.190 2863 Planarity : 0.004 0.067 3122 Dihedral : 14.557 84.707 2868 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 4.42 % Allowed : 30.65 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.19), residues: 2163 helix: 0.78 (0.15), residues: 1204 sheet: -1.86 (0.38), residues: 224 loop : -1.92 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 4 14 TYR 0.023 0.002 TYR 6 199 PHE 0.012 0.001 PHE 7 188 TRP 0.037 0.002 TRP 6 154 HIS 0.012 0.001 HIS 1 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (18772) covalent geometry : angle 0.73181 / 0.36 (25612) hydrogen bonds : bond 0.03352 / 3.73 ( 816) hydrogen bonds : angle 3.74038 / 4.38 ( 2372) Misc. bond : bond 0.00239 / 0.12 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5807.42 seconds wall clock time: 99 minutes 52.22 seconds (5992.22 seconds total)