Starting phenix.real_space_refine on Tue Oct 27 12:00:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yuq_73506/10_2026/9yuq_73506.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yuq_73506/10_2026/9yuq_73506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9yuq_73506/10_2026/9yuq_73506.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yuq_73506/10_2026/9yuq_73506.map" model { file = "/net/cci-nas-00/data/ceres_data/9yuq_73506/10_2026/9yuq_73506.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yuq_73506/10_2026/9yuq_73506.cif" } resolution = 3.11 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 ------------------------------------------------------------------------------- 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= 0.003 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 32 9.91 5 Fe 64 7.16 5 S 176 5.16 5 C 15568 2.51 5 N 4080 2.21 5 O 4912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24832 Number of models: 1 Model: "" Number of chains: 32 Chain: "N" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1378 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 188} Chain: "M" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1378 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 188} Chain: "L" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1378 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 188} Chain: "K" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1378 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 188} Chain: "J" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1378 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 188} Chain: "I" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1378 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 188} Chain: "C" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1378 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 188} Chain: "D" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1378 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 188} Chain: "E" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1378 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 188} Chain: "F" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1378 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 188} Chain: "G" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1378 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 188} Chain: "P" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1378 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 188} Chain: "Q" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1378 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 188} Chain: "R" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1378 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 188} Chain: "S" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1378 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 188} Chain: "T" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1378 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 188} Chain: "N" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 217 Unusual residues: {' CA': 2, 'HEC': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "M" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 174 Unusual residues: {' CA': 2, 'HEC': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "L" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 174 Unusual residues: {' CA': 2, 'HEC': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "K" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 174 Unusual residues: {' CA': 2, 'HEC': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "J" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 174 Unusual residues: {' CA': 2, 'HEC': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "I" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 131 Unusual residues: {' CA': 2, 'HEC': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 260 Unusual residues: {' CA': 2, 'HEC': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 131 Unusual residues: {' CA': 2, 'HEC': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 174 Unusual residues: {' CA': 2, 'HEC': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "F" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 174 Unusual residues: {' CA': 2, 'HEC': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "G" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 131 Unusual residues: {' CA': 2, 'HEC': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "P" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 260 Unusual residues: {' CA': 2, 'HEC': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "Q" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 131 Unusual residues: {' CA': 2, 'HEC': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "R" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 174 Unusual residues: {' CA': 2, 'HEC': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "S" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 217 Unusual residues: {' CA': 2, 'HEC': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "T" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Unusual residues: {' CA': 2, 'HEC': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 6.76, per 1000 atoms: 0.27 Number of scatterers: 24832 At special positions: 0 Unit cell: (161.57, 103.79, 217.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 64 26.01 Ca 32 19.99 S 176 16.00 O 4912 8.00 N 4080 7.00 C 15568 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=237, symmetry=0 Number of additional bonds: simple=237, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 932.1 milliseconds 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5632 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 14 sheets defined 17.3% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'N' and resid 95 through 104 removed outlier: 3.875A pdb=" N SER N 101 " --> pdb=" O VAL N 97 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS N 102 " --> pdb=" O LEU N 98 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 156 removed outlier: 4.067A pdb=" N GLY N 156 " --> pdb=" O ALA N 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 185 through 190 removed outlier: 4.399A pdb=" N CYS N 189 " --> pdb=" O TRP N 185 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS N 190 " --> pdb=" O CYS N 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 185 through 190' Processing helix chain 'N' and resid 206 through 208 No H-bonds generated for 'chain 'N' and resid 206 through 208' Processing helix chain 'N' and resid 209 through 214 Processing helix chain 'M' and resid 95 through 104 removed outlier: 3.748A pdb=" N SER M 101 " --> pdb=" O VAL M 97 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N CYS M 102 " --> pdb=" O LEU M 98 " (cutoff:3.500A) Processing helix chain 'M' and resid 138 through 142 removed outlier: 3.694A pdb=" N ASP M 142 " --> pdb=" O MET M 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 148 through 154 Processing helix chain 'M' and resid 185 through 190 removed outlier: 4.467A pdb=" N CYS M 189 " --> pdb=" O TRP M 185 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N HIS M 190 " --> pdb=" O CYS M 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 185 through 190' Processing helix chain 'M' and resid 206 through 208 No H-bonds generated for 'chain 'M' and resid 206 through 208' Processing helix chain 'M' and resid 209 through 214 Processing helix chain 'L' and resid 95 through 104 removed outlier: 3.923A pdb=" N CYS L 102 " --> pdb=" O LEU L 98 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP L 104 " --> pdb=" O LEU L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 134 Processing helix chain 'L' and resid 138 through 142 removed outlier: 4.080A pdb=" N ASN L 141 " --> pdb=" O ASP L 138 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP L 142 " --> pdb=" O MET L 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 138 through 142' Processing helix chain 'L' and resid 148 through 155 Processing helix chain 'L' and resid 206 through 208 No H-bonds generated for 'chain 'L' and resid 206 through 208' Processing helix chain 'L' and resid 209 through 217 removed outlier: 4.136A pdb=" N CYS L 215 " --> pdb=" O LEU L 211 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 104 removed outlier: 4.269A pdb=" N CYS K 102 " --> pdb=" O LEU K 98 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP K 104 " --> pdb=" O LEU K 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 148 through 156 removed outlier: 3.709A pdb=" N GLY K 156 " --> pdb=" O ALA K 152 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 208 No H-bonds generated for 'chain 'K' and resid 206 through 208' Processing helix chain 'K' and resid 209 through 214 Processing helix chain 'J' and resid 95 through 104 removed outlier: 4.047A pdb=" N CYS J 102 " --> pdb=" O LEU J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 155 Processing helix chain 'J' and resid 185 through 189 removed outlier: 4.017A pdb=" N CYS J 189 " --> pdb=" O CYS J 186 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 208 No H-bonds generated for 'chain 'J' and resid 206 through 208' Processing helix chain 'J' and resid 209 through 217 removed outlier: 4.097A pdb=" N CYS J 215 " --> pdb=" O LEU J 211 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER J 217 " --> pdb=" O THR J 213 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 104 removed outlier: 3.889A pdb=" N SER I 101 " --> pdb=" O VAL I 97 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N CYS I 102 " --> pdb=" O LEU I 98 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP I 104 " --> pdb=" O LEU I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 142 removed outlier: 4.041A pdb=" N ASP I 142 " --> pdb=" O MET I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 148 through 156 removed outlier: 3.897A pdb=" N GLY I 156 " --> pdb=" O ALA I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 190 removed outlier: 4.476A pdb=" N CYS I 189 " --> pdb=" O TRP I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 208 No H-bonds generated for 'chain 'I' and resid 206 through 208' Processing helix chain 'I' and resid 209 through 217 removed outlier: 4.041A pdb=" N CYS I 215 " --> pdb=" O LEU I 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 100 Processing helix chain 'C' and resid 138 through 142 Processing helix chain 'C' and resid 148 through 155 Processing helix chain 'C' and resid 206 through 208 No H-bonds generated for 'chain 'C' and resid 206 through 208' Processing helix chain 'C' and resid 209 through 214 Processing helix chain 'D' and resid 95 through 104 removed outlier: 4.066A pdb=" N CYS D 102 " --> pdb=" O LEU D 98 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASP D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 155 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 209 through 214 Processing helix chain 'E' and resid 94 through 104 removed outlier: 4.484A pdb=" N LEU E 98 " --> pdb=" O THR E 94 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N CYS E 102 " --> pdb=" O LEU E 98 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP E 104 " --> pdb=" O LEU E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 134 Processing helix chain 'E' and resid 148 through 155 Processing helix chain 'E' and resid 185 through 190 removed outlier: 4.407A pdb=" N CYS E 189 " --> pdb=" O TRP E 185 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS E 190 " --> pdb=" O CYS E 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 185 through 190' Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 209 through 217 removed outlier: 3.984A pdb=" N CYS E 215 " --> pdb=" O LEU E 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 100 removed outlier: 4.515A pdb=" N LEU F 98 " --> pdb=" O THR F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 155 Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 209 through 214 Processing helix chain 'G' and resid 95 through 104 removed outlier: 3.947A pdb=" N SER G 101 " --> pdb=" O VAL G 97 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N CYS G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 155 Processing helix chain 'G' and resid 206 through 208 No H-bonds generated for 'chain 'G' and resid 206 through 208' Processing helix chain 'G' and resid 209 through 217 removed outlier: 4.003A pdb=" N CYS G 215 " --> pdb=" O LEU G 211 " (cutoff:3.500A) Processing helix chain 'P' and resid 94 through 104 removed outlier: 4.219A pdb=" N LEU P 98 " --> pdb=" O THR P 94 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N CYS P 102 " --> pdb=" O LEU P 98 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP P 104 " --> pdb=" O LEU P 100 " (cutoff:3.500A) Processing helix chain 'P' and resid 138 through 142 removed outlier: 3.505A pdb=" N ASP P 142 " --> pdb=" O MET P 139 " (cutoff:3.500A) Processing helix chain 'P' and resid 148 through 155 Processing helix chain 'P' and resid 209 through 214 Processing helix chain 'Q' and resid 95 through 104 removed outlier: 4.228A pdb=" N SER Q 101 " --> pdb=" O VAL Q 97 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N CYS Q 102 " --> pdb=" O LEU Q 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 138 through 142 Processing helix chain 'Q' and resid 148 through 156 removed outlier: 3.690A pdb=" N GLY Q 156 " --> pdb=" O ALA Q 152 " (cutoff:3.500A) Processing helix chain 'Q' and resid 206 through 208 No H-bonds generated for 'chain 'Q' and resid 206 through 208' Processing helix chain 'Q' and resid 209 through 214 Processing helix chain 'R' and resid 94 through 104 removed outlier: 4.349A pdb=" N LEU R 98 " --> pdb=" O THR R 94 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N CYS R 102 " --> pdb=" O LEU R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 142 removed outlier: 4.062A pdb=" N ASP R 142 " --> pdb=" O MET R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 154 Processing helix chain 'R' and resid 185 through 190 removed outlier: 4.281A pdb=" N CYS R 189 " --> pdb=" O TRP R 185 " (cutoff:3.500A) Processing helix chain 'R' and resid 206 through 208 No H-bonds generated for 'chain 'R' and resid 206 through 208' Processing helix chain 'R' and resid 209 through 217 removed outlier: 4.139A pdb=" N CYS R 215 " --> pdb=" O LEU R 211 " (cutoff:3.500A) Processing helix chain 'S' and resid 95 through 104 removed outlier: 3.634A pdb=" N SER S 101 " --> pdb=" O VAL S 97 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N CYS S 102 " --> pdb=" O LEU S 98 " (cutoff:3.500A) Processing helix chain 'S' and resid 130 through 134 Processing helix chain 'S' and resid 138 through 142 removed outlier: 3.850A pdb=" N ASP S 142 " --> pdb=" O MET S 139 " (cutoff:3.500A) Processing helix chain 'S' and resid 148 through 156 removed outlier: 3.933A pdb=" N GLY S 156 " --> pdb=" O ALA S 152 " (cutoff:3.500A) Processing helix chain 'S' and resid 206 through 208 No H-bonds generated for 'chain 'S' and resid 206 through 208' Processing helix chain 'S' and resid 209 through 214 Processing helix chain 'T' and resid 95 through 104 removed outlier: 4.246A pdb=" N CYS T 102 " --> pdb=" O LEU T 98 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP T 104 " --> pdb=" O LEU T 100 " (cutoff:3.500A) Processing helix chain 'T' and resid 138 through 142 Processing helix chain 'T' and resid 148 through 155 removed outlier: 3.895A pdb=" N GLY T 155 " --> pdb=" O ASP T 151 " (cutoff:3.500A) Processing helix chain 'T' and resid 185 through 189 removed outlier: 3.599A pdb=" N CYS T 189 " --> pdb=" O CYS T 186 " (cutoff:3.500A) Processing helix chain 'T' and resid 206 through 208 No H-bonds generated for 'chain 'T' and resid 206 through 208' Processing helix chain 'T' and resid 209 through 217 removed outlier: 4.072A pdb=" N CYS T 215 " --> pdb=" O LEU T 211 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER T 217 " --> pdb=" O THR T 213 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 170 through 174 removed outlier: 6.646A pdb=" N GLN N 172 " --> pdb=" O THR N 181 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N THR N 181 " --> pdb=" O GLN N 172 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU N 174 " --> pdb=" O ALA N 179 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ALA N 179 " --> pdb=" O LEU N 174 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 170 through 174 removed outlier: 5.558A pdb=" N PHE L 170 " --> pdb=" O ASP L 182 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP L 182 " --> pdb=" O PHE L 170 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY L 178 " --> pdb=" O LEU L 174 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 170 through 173 removed outlier: 6.309A pdb=" N GLN K 172 " --> pdb=" O THR K 181 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N THR K 181 " --> pdb=" O GLN K 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 170 through 173 removed outlier: 6.173A pdb=" N GLN J 172 " --> pdb=" O THR J 181 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N THR J 181 " --> pdb=" O GLN J 172 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 170 through 173 removed outlier: 6.588A pdb=" N GLN I 172 " --> pdb=" O THR I 181 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N THR I 181 " --> pdb=" O GLN I 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 170 through 174 removed outlier: 6.411A pdb=" N GLN C 172 " --> pdb=" O THR C 181 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N THR C 181 " --> pdb=" O GLN C 172 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU C 174 " --> pdb=" O ALA C 179 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ALA C 179 " --> pdb=" O LEU C 174 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 170 through 174 removed outlier: 6.181A pdb=" N PHE D 170 " --> pdb=" O ASP D 182 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP D 182 " --> pdb=" O PHE D 170 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS D 180 " --> pdb=" O GLN D 172 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 170 through 174 removed outlier: 5.501A pdb=" N PHE E 170 " --> pdb=" O ASP E 182 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP E 182 " --> pdb=" O PHE E 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 170 through 174 removed outlier: 5.967A pdb=" N PHE F 170 " --> pdb=" O ASP F 182 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP F 182 " --> pdb=" O PHE F 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 170 through 173 removed outlier: 6.326A pdb=" N GLN G 172 " --> pdb=" O THR G 181 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N THR G 181 " --> pdb=" O GLN G 172 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'P' and resid 170 through 174 removed outlier: 6.707A pdb=" N GLN P 172 " --> pdb=" O THR P 181 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N THR P 181 " --> pdb=" O GLN P 172 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU P 174 " --> pdb=" O ALA P 179 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ALA P 179 " --> pdb=" O LEU P 174 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 170 through 173 removed outlier: 6.338A pdb=" N GLN Q 172 " --> pdb=" O THR Q 181 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N THR Q 181 " --> pdb=" O GLN Q 172 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 170 through 174 removed outlier: 6.123A pdb=" N PHE S 170 " --> pdb=" O ASP S 182 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP S 182 " --> pdb=" O PHE S 170 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS S 180 " --> pdb=" O GLN S 172 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY S 178 " --> pdb=" O LEU S 174 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'T' and resid 170 through 174 removed outlier: 5.606A pdb=" N PHE T 170 " --> pdb=" O ASP T 182 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP T 182 " --> pdb=" O PHE T 170 " (cutoff:3.500A) 223 hydrogen bonds defined for protein. 576 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.92 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.37: 8683 1.37 - 1.53: 13635 1.53 - 1.69: 2850 1.69 - 1.84: 221 1.84 - 2.00: 259 Bond restraints: 25648 Sorted by residual: bond pdb=" CG HIS M 52 " pdb=" CD2 HIS M 52 " ideal model delta sigma weight residual 1.354 1.427 -0.073 1.10e-02 8.26e+03 4.46e+01 bond pdb=" CG HIS M 52 " pdb=" ND1 HIS M 52 " ideal model delta sigma weight residual 1.378 1.441 -0.063 1.10e-02 8.26e+03 3.31e+01 bond pdb=" CB HIS J 52 " pdb=" CG HIS J 52 " ideal model delta sigma weight residual 1.497 1.419 0.078 1.40e-02 5.10e+03 3.10e+01 bond pdb=" C3A HEC E 305 " pdb=" CMA HEC E 305 " ideal model delta sigma weight residual 1.544 1.648 -0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" C4C HEC L 301 " pdb=" CHD HEC L 301 " ideal model delta sigma weight residual 1.378 1.280 0.098 2.00e-02 2.50e+03 2.42e+01 ... (remaining 25643 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.38: 35608 5.38 - 10.77: 381 10.77 - 16.15: 48 16.15 - 21.54: 6 21.54 - 26.92: 5 Bond angle restraints: 36048 Sorted by residual: angle pdb=" CA HIS R 52 " pdb=" CB HIS R 52 " pdb=" CG HIS R 52 " ideal model delta sigma weight residual 113.80 99.08 14.72 1.00e+00 1.00e+00 2.17e+02 angle pdb=" N HIS J 52 " pdb=" CA HIS J 52 " pdb=" C HIS J 52 " ideal model delta sigma weight residual 108.34 126.35 -18.01 1.31e+00 5.83e-01 1.89e+02 angle pdb=" CA HIS M 52 " pdb=" CB HIS M 52 " pdb=" CG HIS M 52 " ideal model delta sigma weight residual 113.80 103.44 10.36 1.00e+00 1.00e+00 1.07e+02 angle pdb=" CA HIS Q 52 " pdb=" CB HIS Q 52 " pdb=" CG HIS Q 52 " ideal model delta sigma weight residual 113.80 106.40 7.40 1.00e+00 1.00e+00 5.47e+01 angle pdb=" N HIS Q 52 " pdb=" CA HIS Q 52 " pdb=" C HIS Q 52 " ideal model delta sigma weight residual 109.14 119.44 -10.30 1.49e+00 4.50e-01 4.78e+01 ... (remaining 36043 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 11579 17.99 - 35.98: 1454 35.98 - 53.97: 364 53.97 - 71.96: 114 71.96 - 89.96: 73 Dihedral angle restraints: 13584 sinusoidal: 4768 harmonic: 8816 Sorted by residual: dihedral pdb=" CA HIS Q 52 " pdb=" C HIS Q 52 " pdb=" N GLY Q 53 " pdb=" CA GLY Q 53 " ideal model delta harmonic sigma weight residual 180.00 124.69 55.31 0 5.00e+00 4.00e-02 1.22e+02 dihedral pdb=" CA PRO N 51 " pdb=" C PRO N 51 " pdb=" N HIS N 52 " pdb=" CA HIS N 52 " ideal model delta harmonic sigma weight residual -180.00 -132.75 -47.25 0 5.00e+00 4.00e-02 8.93e+01 dihedral pdb=" CA CYS I 189 " pdb=" C CYS I 189 " pdb=" N HIS I 190 " pdb=" CA HIS I 190 " ideal model delta harmonic sigma weight residual -180.00 -145.65 -34.35 0 5.00e+00 4.00e-02 4.72e+01 ... (remaining 13581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 3731 0.110 - 0.220: 72 0.220 - 0.330: 2 0.330 - 0.440: 2 0.440 - 0.550: 1 Chirality restraints: 3808 Sorted by residual: chirality pdb=" CA HIS J 52 " pdb=" N HIS J 52 " pdb=" C HIS J 52 " pdb=" CB HIS J 52 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.56e+00 chirality pdb=" CA HIS S 52 " pdb=" N HIS S 52 " pdb=" C HIS S 52 " pdb=" CB HIS S 52 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA HIS Q 52 " pdb=" N HIS Q 52 " pdb=" C HIS Q 52 " pdb=" CB HIS Q 52 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 3805 not shown) Planarity restraints: 4432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS R 52 " -0.034 2.00e-02 2.50e+03 6.59e-02 6.51e+01 pdb=" CG HIS R 52 " 0.113 2.00e-02 2.50e+03 pdb=" ND1 HIS R 52 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 HIS R 52 " -0.079 2.00e-02 2.50e+03 pdb=" CE1 HIS R 52 " -0.047 2.00e-02 2.50e+03 pdb=" NE2 HIS R 52 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS Q 52 " -0.080 2.00e-02 2.50e+03 6.48e-02 6.30e+01 pdb=" CG HIS Q 52 " 0.120 2.00e-02 2.50e+03 pdb=" ND1 HIS Q 52 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS Q 52 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 HIS Q 52 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS Q 52 " -0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC S 301 " -0.000 2.00e-02 2.50e+03 4.97e-02 5.55e+01 pdb=" C2C HEC S 301 " 0.079 2.00e-02 2.50e+03 pdb=" C3C HEC S 301 " 0.085 2.00e-02 2.50e+03 pdb=" C4C HEC S 301 " 0.007 2.00e-02 2.50e+03 pdb=" CAC HEC S 301 " -0.065 2.00e-02 2.50e+03 pdb=" CHC HEC S 301 " -0.012 2.00e-02 2.50e+03 pdb=" CHD HEC S 301 " -0.002 2.00e-02 2.50e+03 pdb=" CMC HEC S 301 " -0.040 2.00e-02 2.50e+03 pdb=" NC HEC S 301 " -0.052 2.00e-02 2.50e+03 ... (remaining 4429 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.33: 72 2.33 - 2.97: 13079 2.97 - 3.61: 36658 3.61 - 4.26: 58499 4.26 - 4.90: 95812 Nonbonded interactions: 204120 Sorted by model distance: nonbonded pdb=" O SER C 106 " pdb="CA CA C 304 " model vdw 1.683 2.510 nonbonded pdb=" NE2 HIS I 190 " pdb="FE HEC I 301 " model vdw 1.931 3.080 nonbonded pdb=" NE2 HIS R 190 " pdb="FE HEC R 301 " model vdw 1.965 3.080 nonbonded pdb=" NE2 HIS T 190 " pdb="FE HEC S 305 " model vdw 1.973 3.080 nonbonded pdb=" NE2 HIS Q 190 " pdb="FE HEC P 307 " model vdw 1.992 3.080 ... (remaining 204115 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 'C' and resid 21 through 301) selection = (chain 'D' and resid 21 through 301) selection = (chain 'E' and resid 21 through 301) selection = (chain 'F' and resid 21 through 301) selection = (chain 'G' and resid 21 through 301) selection = (chain 'I' and resid 21 through 301) selection = (chain 'J' and resid 21 through 301) selection = (chain 'K' and resid 21 through 301) selection = (chain 'L' and resid 21 through 301) selection = (chain 'M' and resid 21 through 301) selection = (chain 'N' and resid 21 through 301) selection = (chain 'P' and resid 21 through 301) selection = (chain 'Q' and resid 21 through 301) selection = (chain 'R' and resid 21 through 301) selection = (chain 'S' and resid 21 through 301) selection = (chain 'T' and resid 21 through 301) } 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: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 22.390 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 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 : 0.024 0.683 25885 Z= 2.050 Angle : 1.404 26.922 36048 Z= 0.549 Chirality : 0.046 0.550 3808 Planarity : 0.005 0.066 4432 Dihedral : 19.091 89.955 7952 Min Nonbonded Distance : 1.683 Molprobity Statistics. All-atom Clashscore : 20.69 Ramachandran Plot: Outliers : 0.41 % Allowed : 10.97 % Favored : 88.62 % Rotamer: Outliers : 4.03 % Allowed : 30.10 % Favored : 65.87 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.06 (0.13), residues: 3136 helix: -1.47 (0.26), residues: 320 sheet: None (None), residues: 0 loop : -2.36 (0.10), residues: 2816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 65 TYR 0.007 0.001 TYR T 149 PHE 0.012 0.001 PHE E 47 TRP 0.008 0.001 TRP Q 185 HIS 0.094 0.007 HIS R 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00987 / 0.33 (25648) covalent geometry : angle 1.40416 / 0.55 (36048) hydrogen bonds : bond 0.23154 / 15.56 ( 223) hydrogen bonds : angle 8.87871 / 6.12 ( 576) Misc. bond : bond 0.22817 / 15.63 ( 237) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 512 time to evaluate : 0.726 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 52 HIS cc_start: 0.6132 (OUTLIER) cc_final: 0.5653 (t-90) REVERT: K 65 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.8066 (mtp-110) REVERT: I 147 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7872 (pmm) REVERT: D 26 LYS cc_start: 0.8568 (mtpt) cc_final: 0.8220 (mmtp) REVERT: D 52 HIS cc_start: 0.5774 (OUTLIER) cc_final: 0.5439 (t-90) REVERT: E 129 LEU cc_start: 0.6088 (OUTLIER) cc_final: 0.5632 (mt) REVERT: Q 216 HIS cc_start: 0.6023 (m-70) cc_final: 0.5434 (m-70) REVERT: R 25 THR cc_start: 0.7351 (OUTLIER) cc_final: 0.7032 (t) REVERT: R 52 HIS cc_start: 0.5972 (OUTLIER) cc_final: 0.5550 (t-90) outliers start: 98 outliers final: 86 residues processed: 574 average time/residue: 0.1227 time to fit residues: 123.4307 Evaluate side-chains 602 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 509 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 ILE Chi-restraints excluded: chain N residue 212 CYS Chi-restraints excluded: chain N residue 215 CYS Chi-restraints excluded: chain M residue 45 CYS Chi-restraints excluded: chain M residue 52 HIS Chi-restraints excluded: chain M residue 68 ASP Chi-restraints excluded: chain M residue 99 CYS Chi-restraints excluded: chain M residue 157 ASP Chi-restraints excluded: chain M residue 199 SER Chi-restraints excluded: chain L residue 99 CYS Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 153 ILE Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 212 CYS Chi-restraints excluded: chain L residue 215 CYS Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain K residue 99 CYS Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 212 CYS Chi-restraints excluded: chain K residue 215 CYS Chi-restraints excluded: chain J residue 99 CYS Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 134 ASN Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain J residue 212 CYS Chi-restraints excluded: chain I residue 45 CYS Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 186 CYS Chi-restraints excluded: chain I residue 190 HIS Chi-restraints excluded: chain I residue 192 VAL Chi-restraints excluded: chain I residue 212 CYS Chi-restraints excluded: chain I residue 215 CYS Chi-restraints excluded: chain C residue 45 CYS Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain D residue 99 CYS Chi-restraints excluded: chain D residue 102 CYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 186 CYS Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain E residue 45 CYS Chi-restraints excluded: chain E residue 52 HIS Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain F residue 52 HIS Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 99 CYS Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 218 LYS Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 212 CYS Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 45 CYS Chi-restraints excluded: chain P residue 99 CYS Chi-restraints excluded: chain P residue 148 SER Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 52 HIS Chi-restraints excluded: chain Q residue 102 CYS Chi-restraints excluded: chain Q residue 157 ASP Chi-restraints excluded: chain Q residue 212 CYS Chi-restraints excluded: chain Q residue 215 CYS Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 52 HIS Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 99 CYS Chi-restraints excluded: chain R residue 126 THR Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 212 CYS Chi-restraints excluded: chain S residue 52 HIS Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 215 CYS Chi-restraints excluded: chain T residue 69 THR Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 98 LEU Chi-restraints excluded: chain T residue 99 CYS Chi-restraints excluded: chain T residue 111 LEU Chi-restraints excluded: chain T residue 129 LEU Chi-restraints excluded: chain T residue 199 SER Chi-restraints excluded: chain T residue 212 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.0980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.1980 chunk 298 optimal weight: 5.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 ASN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN ** G 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 ASN Q 109 ASN ** R 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 64 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.132552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.121533 restraints weight = 40771.918| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.88 r_work: 0.3519 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.519 25885 Z= 0.190 Angle : 1.050 28.077 36048 Z= 0.360 Chirality : 0.043 0.200 3808 Planarity : 0.003 0.040 4432 Dihedral : 18.033 89.992 3855 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.38 % Favored : 90.18 % Rotamer: Outliers : 5.55 % Allowed : 27.34 % Favored : 67.11 % 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: -2.94 (0.13), residues: 3136 helix: -1.22 (0.26), residues: 336 sheet: None (None), residues: 0 loop : -2.30 (0.11), residues: 2800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 65 TYR 0.011 0.001 TYR P 149 PHE 0.012 0.002 PHE R 47 TRP 0.006 0.001 TRP F 185 HIS 0.014 0.002 HIS I 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.18 (25648) covalent geometry : angle 1.05022 / 0.36 (36048) hydrogen bonds : bond 0.04481 / 3.02 ( 223) hydrogen bonds : angle 6.64994 / 4.67 ( 576) Misc. bond : bond 0.10929 / 7.25 ( 237) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 537 time to evaluate : 0.706 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 216 HIS cc_start: 0.7248 (OUTLIER) cc_final: 0.6652 (m-70) REVERT: L 200 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.8262 (m) REVERT: K 139 MET cc_start: 0.7911 (mmm) cc_final: 0.7654 (mmm) REVERT: K 216 HIS cc_start: 0.7039 (m-70) cc_final: 0.6527 (m-70) REVERT: K 218 LYS cc_start: 0.5725 (OUTLIER) cc_final: 0.4712 (pptt) REVERT: J 129 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8049 (tp) REVERT: I 182 ASP cc_start: 0.8214 (p0) cc_final: 0.7989 (p0) REVERT: C 33 ASN cc_start: 0.7828 (m-40) cc_final: 0.7526 (m-40) REVERT: D 42 ASP cc_start: 0.7964 (p0) cc_final: 0.7673 (p0) REVERT: D 151 ASP cc_start: 0.7750 (m-30) cc_final: 0.7532 (m-30) REVERT: E 116 ASN cc_start: 0.7807 (m-40) cc_final: 0.7497 (m-40) REVERT: E 129 LEU cc_start: 0.5722 (OUTLIER) cc_final: 0.5475 (mp) REVERT: P 28 ASP cc_start: 0.8273 (p0) cc_final: 0.8072 (p0) REVERT: P 104 ASP cc_start: 0.6646 (OUTLIER) cc_final: 0.6066 (p0) REVERT: P 148 SER cc_start: 0.8550 (OUTLIER) cc_final: 0.8068 (p) REVERT: Q 33 ASN cc_start: 0.7331 (t0) cc_final: 0.6808 (t0) REVERT: Q 62 LEU cc_start: 0.6407 (OUTLIER) cc_final: 0.6185 (mp) REVERT: Q 147 MET cc_start: 0.8237 (ptp) cc_final: 0.7897 (pmm) REVERT: Q 200 THR cc_start: 0.8288 (m) cc_final: 0.8088 (m) REVERT: T 27 HIS cc_start: 0.8073 (m170) cc_final: 0.7771 (m90) REVERT: T 157 ASP cc_start: 0.7223 (OUTLIER) cc_final: 0.6897 (t70) REVERT: T 190 HIS cc_start: 0.7543 (m-70) cc_final: 0.7331 (m170) outliers start: 135 outliers final: 82 residues processed: 636 average time/residue: 0.1241 time to fit residues: 138.8578 Evaluate side-chains 607 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 516 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 110 THR Chi-restraints excluded: chain N residue 151 ASP Chi-restraints excluded: chain N residue 198 VAL Chi-restraints excluded: chain N residue 215 CYS Chi-restraints excluded: chain M residue 45 CYS Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 99 CYS Chi-restraints excluded: chain M residue 147 MET Chi-restraints excluded: chain M residue 153 ILE Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 216 HIS Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 99 CYS Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain L residue 212 CYS Chi-restraints excluded: chain L residue 213 THR Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 99 CYS Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain K residue 215 CYS Chi-restraints excluded: chain K residue 218 LYS Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 52 HIS Chi-restraints excluded: chain J residue 102 CYS Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain J residue 129 LEU Chi-restraints excluded: chain J residue 134 ASN Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain I residue 26 LYS Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 186 CYS Chi-restraints excluded: chain I residue 192 VAL Chi-restraints excluded: chain I residue 212 CYS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 45 CYS Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain D residue 99 CYS Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 45 CYS Chi-restraints excluded: chain E residue 52 HIS Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 218 LYS Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 102 CYS Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain P residue 104 ASP Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 148 SER Chi-restraints excluded: chain Q residue 52 HIS Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain Q residue 99 CYS Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain Q residue 215 CYS Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 52 HIS Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain R residue 181 THR Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 215 CYS Chi-restraints excluded: chain S residue 52 HIS Chi-restraints excluded: chain S residue 183 VAL Chi-restraints excluded: chain S residue 215 CYS Chi-restraints excluded: chain T residue 64 ASN Chi-restraints excluded: chain T residue 69 THR Chi-restraints excluded: chain T residue 83 ASN Chi-restraints excluded: chain T residue 111 LEU Chi-restraints excluded: chain T residue 129 LEU Chi-restraints excluded: chain T residue 157 ASP Chi-restraints excluded: chain T residue 215 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [163, 81, 83, 34, 32, 303, 171, 237, 2, 260, 149] chunk 163 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 303 optimal weight: 0.9990 chunk 171 optimal weight: 0.6980 chunk 237 optimal weight: 6.9990 chunk 2 optimal weight: 0.0070 chunk 260 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 193 HIS ** K 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 35 ASN P 67 ASN P 77 ASN Q 113 ASN ** R 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 141 ASN ** S 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 64 ASN T 172 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.131162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.120005 restraints weight = 40598.608| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.89 r_work: 0.3493 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.365 25885 Z= 0.174 Angle : 0.929 19.123 36048 Z= 0.341 Chirality : 0.043 0.163 3808 Planarity : 0.003 0.038 4432 Dihedral : 17.641 89.573 3776 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.44 % Favored : 90.18 % Rotamer: Outliers : 6.58 % Allowed : 27.01 % Favored : 66.41 % 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: -2.84 (0.13), residues: 3136 helix: -0.97 (0.27), residues: 336 sheet: None (None), residues: 0 loop : -2.25 (0.11), residues: 2800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 65 TYR 0.009 0.001 TYR P 149 PHE 0.013 0.002 PHE K 47 TRP 0.010 0.001 TRP N 185 HIS 0.012 0.002 HIS M 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.17 (25648) covalent geometry : angle 0.92886 / 0.34 (36048) hydrogen bonds : bond 0.03761 / 2.52 ( 223) hydrogen bonds : angle 6.04795 / 4.25 ( 576) Misc. bond : bond 0.07946 / 5.35 ( 237) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 506 time to evaluate : 0.609 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: symmetry clash REVERT: N 134 ASN cc_start: 0.7621 (p0) cc_final: 0.7326 (p0) REVERT: N 176 VAL cc_start: 0.8647 (t) cc_final: 0.8445 (p) REVERT: M 216 HIS cc_start: 0.6967 (OUTLIER) cc_final: 0.6361 (m-70) REVERT: L 200 THR cc_start: 0.8473 (OUTLIER) cc_final: 0.8255 (m) REVERT: K 65 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.8039 (mtp-110) REVERT: K 139 MET cc_start: 0.7896 (mmm) cc_final: 0.7615 (mmm) REVERT: K 216 HIS cc_start: 0.6806 (m-70) cc_final: 0.6308 (m-70) REVERT: J 129 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8020 (tp) REVERT: I 182 ASP cc_start: 0.8115 (p0) cc_final: 0.7913 (p0) REVERT: C 28 ASP cc_start: 0.7990 (t0) cc_final: 0.7539 (t0) REVERT: C 33 ASN cc_start: 0.7822 (m-40) cc_final: 0.7389 (m-40) REVERT: D 42 ASP cc_start: 0.7970 (p0) cc_final: 0.7717 (p0) REVERT: D 151 ASP cc_start: 0.7795 (m-30) cc_final: 0.7559 (m-30) REVERT: E 141 ASN cc_start: 0.7927 (p0) cc_final: 0.7335 (p0) REVERT: E 147 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7528 (pmm) REVERT: F 29 LEU cc_start: 0.8095 (mp) cc_final: 0.7883 (mt) REVERT: F 101 SER cc_start: 0.8159 (m) cc_final: 0.7475 (p) REVERT: G 216 HIS cc_start: 0.6762 (OUTLIER) cc_final: 0.5806 (m-70) REVERT: P 104 ASP cc_start: 0.6502 (OUTLIER) cc_final: 0.6065 (p0) REVERT: P 141 ASN cc_start: 0.7356 (m110) cc_final: 0.7148 (t0) REVERT: Q 33 ASN cc_start: 0.7315 (t0) cc_final: 0.6645 (t0) REVERT: R 25 THR cc_start: 0.7456 (t) cc_final: 0.7131 (t) REVERT: R 182 ASP cc_start: 0.7653 (p0) cc_final: 0.7332 (p0) REVERT: R 199 SER cc_start: 0.7708 (p) cc_final: 0.7461 (t) REVERT: T 27 HIS cc_start: 0.8091 (m170) cc_final: 0.7875 (m170) REVERT: T 171 SER cc_start: 0.7674 (m) cc_final: 0.7319 (p) outliers start: 160 outliers final: 113 residues processed: 624 average time/residue: 0.1259 time to fit residues: 137.8593 Evaluate side-chains 620 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 500 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 110 THR Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 151 ASP Chi-restraints excluded: chain N residue 198 VAL Chi-restraints excluded: chain N residue 215 CYS Chi-restraints excluded: chain M residue 45 CYS Chi-restraints excluded: chain M residue 52 HIS Chi-restraints excluded: chain M residue 68 ASP Chi-restraints excluded: chain M residue 147 MET Chi-restraints excluded: chain M residue 153 ILE Chi-restraints excluded: chain M residue 157 ASP Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 199 SER Chi-restraints excluded: chain M residue 216 HIS Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 45 CYS Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 153 ILE Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain L residue 212 CYS Chi-restraints excluded: chain L residue 215 CYS Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain K residue 215 CYS Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 102 CYS Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain J residue 129 LEU Chi-restraints excluded: chain J residue 134 ASN Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain I residue 26 LYS Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 186 CYS Chi-restraints excluded: chain I residue 192 VAL Chi-restraints excluded: chain I residue 215 CYS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 45 CYS Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 45 CYS Chi-restraints excluded: chain E residue 52 HIS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 147 MET Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 218 LYS Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 216 HIS Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 103 HIS Chi-restraints excluded: chain P residue 104 ASP Chi-restraints excluded: chain P residue 107 ILE Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 148 SER Chi-restraints excluded: chain P residue 158 THR Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 52 HIS Chi-restraints excluded: chain Q residue 99 CYS Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain Q residue 157 ASP Chi-restraints excluded: chain Q residue 205 THR Chi-restraints excluded: chain Q residue 215 CYS Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 52 HIS Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 215 CYS Chi-restraints excluded: chain S residue 52 HIS Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 121 THR Chi-restraints excluded: chain S residue 171 SER Chi-restraints excluded: chain S residue 183 VAL Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 69 THR Chi-restraints excluded: chain T residue 99 CYS Chi-restraints excluded: chain T residue 199 SER Chi-restraints excluded: chain T residue 215 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [300, 145, 8, 281, 213, 277, 201, 37, 167, 38, 33] chunk 300 optimal weight: 4.9990 chunk 145 optimal weight: 0.0980 chunk 8 optimal weight: 0.8980 chunk 281 optimal weight: 3.9990 chunk 213 optimal weight: 0.9980 chunk 277 optimal weight: 3.9990 chunk 201 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 33 ASN ** N 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 ASN ** F 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 67 ASN P 77 ASN Q 109 ASN Q 113 ASN R 35 ASN R 52 HIS ** R 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 141 ASN ** S 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 64 ASN T 172 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.125254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.114245 restraints weight = 40471.237| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.85 r_work: 0.3434 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.394 25885 Z= 0.221 Angle : 0.985 19.011 36048 Z= 0.365 Chirality : 0.045 0.202 3808 Planarity : 0.003 0.043 4432 Dihedral : 17.520 89.894 3764 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.51 % Allowed : 10.11 % Favored : 89.38 % Rotamer: Outliers : 7.85 % Allowed : 26.69 % Favored : 65.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.85 (0.13), residues: 3136 helix: -0.99 (0.27), residues: 336 sheet: None (None), residues: 0 loop : -2.26 (0.11), residues: 2800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 65 TYR 0.013 0.002 TYR P 149 PHE 0.017 0.002 PHE K 47 TRP 0.010 0.001 TRP R 185 HIS 0.027 0.002 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.21 (25648) covalent geometry : angle 0.98488 / 0.37 (36048) hydrogen bonds : bond 0.03698 / 2.46 ( 223) hydrogen bonds : angle 5.88563 / 4.15 ( 576) Misc. bond : bond 0.08469 / 5.73 ( 237) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 516 time to evaluate : 0.570 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: symmetry clash revert: symmetry clash REVERT: N 52 HIS cc_start: 0.6902 (OUTLIER) cc_final: 0.6593 (t-90) REVERT: N 134 ASN cc_start: 0.7677 (p0) cc_final: 0.7413 (p0) REVERT: M 216 HIS cc_start: 0.7059 (OUTLIER) cc_final: 0.6451 (m-70) REVERT: L 200 THR cc_start: 0.8469 (OUTLIER) cc_final: 0.8244 (m) REVERT: K 65 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.8043 (mtp-110) REVERT: K 139 MET cc_start: 0.7936 (mmm) cc_final: 0.7682 (mmm) REVERT: K 216 HIS cc_start: 0.6836 (m-70) cc_final: 0.6403 (m-70) REVERT: J 33 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.8054 (t0) REVERT: J 104 ASP cc_start: 0.7681 (p0) cc_final: 0.7393 (p0) REVERT: J 129 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8045 (tp) REVERT: C 33 ASN cc_start: 0.7876 (m-40) cc_final: 0.7493 (m-40) REVERT: D 42 ASP cc_start: 0.8024 (p0) cc_final: 0.7755 (p0) REVERT: D 151 ASP cc_start: 0.7830 (m-30) cc_final: 0.7540 (m-30) REVERT: E 28 ASP cc_start: 0.7594 (t0) cc_final: 0.7192 (t0) REVERT: E 33 ASN cc_start: 0.7575 (m-40) cc_final: 0.7082 (m-40) REVERT: E 141 ASN cc_start: 0.8023 (p0) cc_final: 0.7519 (p0) REVERT: E 147 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7472 (pmm) REVERT: F 68 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7375 (p0) REVERT: F 101 SER cc_start: 0.8214 (m) cc_final: 0.7919 (m) REVERT: F 141 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.8165 (p0) REVERT: G 33 ASN cc_start: 0.6924 (m-40) cc_final: 0.6490 (m-40) REVERT: G 216 HIS cc_start: 0.6711 (OUTLIER) cc_final: 0.5859 (m-70) REVERT: P 104 ASP cc_start: 0.6445 (OUTLIER) cc_final: 0.6015 (p0) REVERT: Q 33 ASN cc_start: 0.7465 (t0) cc_final: 0.6741 (t0) REVERT: Q 62 LEU cc_start: 0.6581 (OUTLIER) cc_final: 0.6375 (mp) REVERT: R 95 ASP cc_start: 0.8160 (p0) cc_final: 0.7866 (p0) REVERT: R 182 ASP cc_start: 0.7628 (p0) cc_final: 0.7365 (p0) REVERT: R 199 SER cc_start: 0.7736 (p) cc_final: 0.7485 (t) REVERT: S 41 THR cc_start: 0.6880 (OUTLIER) cc_final: 0.6642 (p) REVERT: S 218 LYS cc_start: 0.5119 (OUTLIER) cc_final: 0.4229 (pptt) REVERT: T 171 SER cc_start: 0.7652 (m) cc_final: 0.7313 (p) outliers start: 191 outliers final: 139 residues processed: 652 average time/residue: 0.1245 time to fit residues: 142.2751 Evaluate side-chains 652 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 499 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 52 HIS Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 110 THR Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 151 ASP Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 198 VAL Chi-restraints excluded: chain M residue 68 ASP Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 147 MET Chi-restraints excluded: chain M residue 153 ILE Chi-restraints excluded: chain M residue 157 ASP Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 199 SER Chi-restraints excluded: chain M residue 216 HIS Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 45 CYS Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 153 ILE Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain L residue 212 CYS Chi-restraints excluded: chain L residue 215 CYS Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain K residue 215 CYS Chi-restraints excluded: chain K residue 218 LYS Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 33 ASN Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 102 CYS Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 129 LEU Chi-restraints excluded: chain J residue 134 ASN Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 216 HIS Chi-restraints excluded: chain I residue 26 LYS Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 99 CYS Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 186 CYS Chi-restraints excluded: chain I residue 192 VAL Chi-restraints excluded: chain I residue 212 CYS Chi-restraints excluded: chain I residue 215 CYS Chi-restraints excluded: chain I residue 216 HIS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain D residue 99 CYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 45 CYS Chi-restraints excluded: chain E residue 52 HIS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 147 MET Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 99 CYS Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 141 ASN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 218 LYS Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 216 HIS Chi-restraints excluded: chain P residue 24 ASP Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 103 HIS Chi-restraints excluded: chain P residue 104 ASP Chi-restraints excluded: chain P residue 107 ILE Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 140 SER Chi-restraints excluded: chain P residue 158 THR Chi-restraints excluded: chain P residue 175 SER Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 52 HIS Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain Q residue 99 CYS Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain Q residue 157 ASP Chi-restraints excluded: chain Q residue 169 LEU Chi-restraints excluded: chain Q residue 205 THR Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 52 HIS Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 181 THR Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 215 CYS Chi-restraints excluded: chain S residue 41 THR Chi-restraints excluded: chain S residue 52 HIS Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 121 THR Chi-restraints excluded: chain S residue 171 SER Chi-restraints excluded: chain S residue 183 VAL Chi-restraints excluded: chain S residue 185 TRP Chi-restraints excluded: chain S residue 218 LYS Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 64 ASN Chi-restraints excluded: chain T residue 69 THR Chi-restraints excluded: chain T residue 99 CYS Chi-restraints excluded: chain T residue 106 SER Chi-restraints excluded: chain T residue 111 LEU Chi-restraints excluded: chain T residue 186 CYS Chi-restraints excluded: chain T residue 199 SER Chi-restraints excluded: chain T residue 215 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [260, 85, 59, 124, 197, 29, 272, 251, 64, 154, 293] chunk 260 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 59 optimal weight: 0.3980 chunk 124 optimal weight: 0.0040 chunk 197 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 272 optimal weight: 1.9990 chunk 251 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 154 optimal weight: 0.8980 chunk 293 optimal weight: 9.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 67 ASN ** N 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 ASN ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 ASN ** F 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 ASN Q 113 ASN R 35 ASN ** R 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 141 ASN ** S 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 64 ASN T 172 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.131338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.120136 restraints weight = 40382.638| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.90 r_work: 0.3469 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.313 25885 Z= 0.145 Angle : 0.869 16.174 36048 Z= 0.331 Chirality : 0.042 0.315 3808 Planarity : 0.003 0.045 4432 Dihedral : 17.398 89.658 3759 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.12 % Favored : 90.56 % Rotamer: Outliers : 6.62 % Allowed : 27.75 % Favored : 65.62 % 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: -2.77 (0.13), residues: 3136 helix: -0.81 (0.28), residues: 336 sheet: None (None), residues: 0 loop : -2.22 (0.11), residues: 2800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 65 TYR 0.008 0.001 TYR P 149 PHE 0.012 0.001 PHE K 47 TRP 0.005 0.001 TRP C 185 HIS 0.014 0.001 HIS E 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.14 (25648) covalent geometry : angle 0.86926 / 0.33 (36048) hydrogen bonds : bond 0.03001 / 2.00 ( 223) hydrogen bonds : angle 5.66564 / 3.98 ( 576) Misc. bond : bond 0.06637 / 4.49 ( 237) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 509 time to evaluate : 0.846 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 52 HIS cc_start: 0.6819 (OUTLIER) cc_final: 0.6583 (t-90) REVERT: N 134 ASN cc_start: 0.7725 (p0) cc_final: 0.7442 (p0) REVERT: M 216 HIS cc_start: 0.6667 (OUTLIER) cc_final: 0.6136 (m-70) REVERT: L 200 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.8211 (m) REVERT: K 65 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.8029 (mtp-110) REVERT: J 33 ASN cc_start: 0.8333 (OUTLIER) cc_final: 0.8023 (t0) REVERT: J 70 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8650 (m) REVERT: J 104 ASP cc_start: 0.7600 (p0) cc_final: 0.7307 (p0) REVERT: J 129 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7988 (tp) REVERT: J 216 HIS cc_start: 0.6763 (OUTLIER) cc_final: 0.6216 (m-70) REVERT: C 33 ASN cc_start: 0.7769 (m-40) cc_final: 0.7360 (m-40) REVERT: C 214 THR cc_start: 0.8097 (t) cc_final: 0.7863 (m) REVERT: D 42 ASP cc_start: 0.7972 (p0) cc_final: 0.7722 (p0) REVERT: D 151 ASP cc_start: 0.7839 (m-30) cc_final: 0.7537 (m-30) REVERT: E 25 THR cc_start: 0.8601 (t) cc_final: 0.8362 (t) REVERT: E 147 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7583 (pmm) REVERT: F 101 SER cc_start: 0.8262 (m) cc_final: 0.7981 (m) REVERT: G 216 HIS cc_start: 0.6435 (OUTLIER) cc_final: 0.5475 (m-70) REVERT: P 104 ASP cc_start: 0.6411 (OUTLIER) cc_final: 0.6206 (p0) REVERT: P 134 ASN cc_start: 0.7959 (t0) cc_final: 0.7746 (t0) REVERT: Q 33 ASN cc_start: 0.7603 (t0) cc_final: 0.6837 (t0) REVERT: R 147 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.6928 (pmm) REVERT: R 199 SER cc_start: 0.7689 (p) cc_final: 0.7453 (t) REVERT: S 41 THR cc_start: 0.6871 (OUTLIER) cc_final: 0.6620 (p) REVERT: S 110 THR cc_start: 0.8601 (m) cc_final: 0.8290 (t) REVERT: S 218 LYS cc_start: 0.5356 (OUTLIER) cc_final: 0.4358 (pptt) REVERT: T 171 SER cc_start: 0.7684 (m) cc_final: 0.7351 (p) outliers start: 161 outliers final: 117 residues processed: 623 average time/residue: 0.1271 time to fit residues: 138.2956 Evaluate side-chains 629 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 498 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 52 HIS Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 110 THR Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 151 ASP Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 198 VAL Chi-restraints excluded: chain M residue 68 ASP Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 93 LEU Chi-restraints excluded: chain M residue 147 MET Chi-restraints excluded: chain M residue 153 ILE Chi-restraints excluded: chain M residue 157 ASP Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 216 HIS Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 45 CYS Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain L residue 212 CYS Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain K residue 215 CYS Chi-restraints excluded: chain J residue 33 ASN Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 102 CYS Chi-restraints excluded: chain J residue 129 LEU Chi-restraints excluded: chain J residue 134 ASN Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain J residue 216 HIS Chi-restraints excluded: chain I residue 26 LYS Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 99 CYS Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 186 CYS Chi-restraints excluded: chain I residue 192 VAL Chi-restraints excluded: chain I residue 216 HIS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain D residue 99 CYS Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 52 HIS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 147 MET Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 99 CYS Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 218 LYS Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 99 CYS Chi-restraints excluded: chain G residue 216 HIS Chi-restraints excluded: chain P residue 24 ASP Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 103 HIS Chi-restraints excluded: chain P residue 104 ASP Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 140 SER Chi-restraints excluded: chain P residue 158 THR Chi-restraints excluded: chain P residue 175 SER Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain Q residue 52 HIS Chi-restraints excluded: chain Q residue 99 CYS Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain Q residue 157 ASP Chi-restraints excluded: chain Q residue 218 LYS Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 52 HIS Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain R residue 99 CYS Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 147 MET Chi-restraints excluded: chain R residue 181 THR Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 215 CYS Chi-restraints excluded: chain S residue 41 THR Chi-restraints excluded: chain S residue 52 HIS Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 121 THR Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 171 SER Chi-restraints excluded: chain S residue 215 CYS Chi-restraints excluded: chain S residue 218 LYS Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 69 THR Chi-restraints excluded: chain T residue 99 CYS Chi-restraints excluded: chain T residue 215 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [157, 230, 245, 289, 1, 129, 134, 40, 124, 254, 137] chunk 157 optimal weight: 0.0040 chunk 230 optimal weight: 0.1980 chunk 245 optimal weight: 2.9990 chunk 289 optimal weight: 0.0270 chunk 1 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 40 optimal weight: 0.0980 chunk 124 optimal weight: 6.9990 chunk 254 optimal weight: 0.6980 chunk 137 optimal weight: 0.8980 overall best weight: 0.2050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 33 ASN N 67 ASN ** N 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 GLN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 ASN Q 113 ASN ** R 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 172 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.133921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.122678 restraints weight = 40682.550| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.93 r_work: 0.3510 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.269 25885 Z= 0.123 Angle : 0.810 14.599 36048 Z= 0.314 Chirality : 0.041 0.264 3808 Planarity : 0.003 0.086 4432 Dihedral : 17.209 89.966 3758 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.23 % Favored : 91.52 % Rotamer: Outliers : 5.51 % Allowed : 29.56 % Favored : 64.93 % Cbeta Deviations : 0.04 % 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: -2.67 (0.13), residues: 3136 helix: -0.62 (0.28), residues: 336 sheet: None (None), residues: 0 loop : -2.15 (0.11), residues: 2800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 65 TYR 0.006 0.001 TYR P 149 PHE 0.010 0.001 PHE I 170 TRP 0.012 0.001 TRP T 63 HIS 0.016 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.12 (25648) covalent geometry : angle 0.81048 / 0.31 (36048) hydrogen bonds : bond 0.02586 / 1.74 ( 223) hydrogen bonds : angle 5.43091 / 3.82 ( 576) Misc. bond : bond 0.05240 / 3.55 ( 237) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 525 time to evaluate : 0.739 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 43 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7754 (mt-10) REVERT: N 134 ASN cc_start: 0.7777 (p0) cc_final: 0.7563 (p0) REVERT: L 31 SER cc_start: 0.8381 (t) cc_final: 0.7877 (p) REVERT: L 200 THR cc_start: 0.8397 (OUTLIER) cc_final: 0.8166 (m) REVERT: K 26 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8027 (ttpp) REVERT: K 216 HIS cc_start: 0.6335 (m-70) cc_final: 0.5807 (m-70) REVERT: J 33 ASN cc_start: 0.8288 (OUTLIER) cc_final: 0.7969 (t0) REVERT: J 104 ASP cc_start: 0.7490 (p0) cc_final: 0.7120 (p0) REVERT: J 129 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7976 (tp) REVERT: J 147 MET cc_start: 0.8457 (pmm) cc_final: 0.7705 (pmm) REVERT: J 216 HIS cc_start: 0.6651 (OUTLIER) cc_final: 0.6054 (m-70) REVERT: C 28 ASP cc_start: 0.8030 (t0) cc_final: 0.7509 (t70) REVERT: C 33 ASN cc_start: 0.7613 (m-40) cc_final: 0.7175 (m-40) REVERT: C 62 LEU cc_start: 0.6654 (mt) cc_final: 0.6413 (mp) REVERT: D 42 ASP cc_start: 0.7927 (p0) cc_final: 0.7708 (p0) REVERT: D 151 ASP cc_start: 0.7836 (m-30) cc_final: 0.7514 (m-30) REVERT: E 25 THR cc_start: 0.8559 (t) cc_final: 0.8318 (t) REVERT: F 101 SER cc_start: 0.8151 (m) cc_final: 0.7883 (m) REVERT: G 216 HIS cc_start: 0.6258 (OUTLIER) cc_final: 0.5235 (m-70) REVERT: P 21 VAL cc_start: 0.7040 (t) cc_final: 0.6664 (m) REVERT: P 134 ASN cc_start: 0.7973 (t0) cc_final: 0.7726 (t0) REVERT: Q 33 ASN cc_start: 0.7624 (t0) cc_final: 0.6865 (t0) REVERT: Q 41 THR cc_start: 0.8506 (m) cc_final: 0.8276 (t) REVERT: Q 134 ASN cc_start: 0.8151 (t0) cc_final: 0.7824 (t0) REVERT: Q 147 MET cc_start: 0.8239 (ptp) cc_final: 0.7895 (pmm) REVERT: Q 200 THR cc_start: 0.8343 (OUTLIER) cc_final: 0.8048 (m) REVERT: R 123 LEU cc_start: 0.6297 (OUTLIER) cc_final: 0.6069 (tt) REVERT: R 199 SER cc_start: 0.7617 (p) cc_final: 0.7396 (t) REVERT: S 41 THR cc_start: 0.6837 (OUTLIER) cc_final: 0.6588 (p) REVERT: S 110 THR cc_start: 0.8432 (m) cc_final: 0.8156 (t) REVERT: S 218 LYS cc_start: 0.5326 (OUTLIER) cc_final: 0.4397 (pptt) REVERT: T 171 SER cc_start: 0.7630 (m) cc_final: 0.7362 (p) outliers start: 134 outliers final: 95 residues processed: 623 average time/residue: 0.1230 time to fit residues: 133.5356 Evaluate side-chains 617 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 512 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 33 ASN Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 151 ASP Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 198 VAL Chi-restraints excluded: chain N residue 215 CYS Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 93 LEU Chi-restraints excluded: chain M residue 147 MET Chi-restraints excluded: chain M residue 157 ASP Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 45 CYS Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain J residue 33 ASN Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 102 CYS Chi-restraints excluded: chain J residue 129 LEU Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain J residue 216 HIS Chi-restraints excluded: chain I residue 26 LYS Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 99 CYS Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 186 CYS Chi-restraints excluded: chain I residue 192 VAL Chi-restraints excluded: chain I residue 216 HIS Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain D residue 99 CYS Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 99 CYS Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 218 LYS Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 99 CYS Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 216 HIS Chi-restraints excluded: chain P residue 24 ASP Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 158 THR Chi-restraints excluded: chain P residue 175 SER Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain Q residue 35 ASN Chi-restraints excluded: chain Q residue 52 HIS Chi-restraints excluded: chain Q residue 99 CYS Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain Q residue 218 LYS Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 52 HIS Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain R residue 99 CYS Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 181 THR Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain S residue 41 THR Chi-restraints excluded: chain S residue 52 HIS Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 121 THR Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 171 SER Chi-restraints excluded: chain S residue 183 VAL Chi-restraints excluded: chain S residue 218 LYS Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 99 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [288, 289, 218, 75, 128, 18, 1, 107, 195, 271, 43] chunk 288 optimal weight: 4.9990 chunk 289 optimal weight: 0.5980 chunk 218 optimal weight: 0.3980 chunk 75 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 271 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 33 ASN N 67 ASN ** N 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 ASN Q 113 ASN R 35 ASN ** R 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 33 ASN T 172 GLN ** T 216 HIS ** 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 = 0.3662 r_free = 0.3662 target = 0.127523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.116362 restraints weight = 40274.805| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.87 r_work: 0.3415 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 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 : 0.011 0.493 25885 Z= 0.244 Angle : 1.009 19.607 36048 Z= 0.379 Chirality : 0.046 0.312 3808 Planarity : 0.004 0.057 4432 Dihedral : 17.295 89.877 3750 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.73 % Allowed : 10.33 % Favored : 88.93 % Rotamer: Outliers : 6.66 % Allowed : 28.66 % Favored : 64.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.79 (0.13), residues: 3136 helix: -0.80 (0.28), residues: 336 sheet: None (None), residues: 0 loop : -2.23 (0.11), residues: 2800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 65 TYR 0.015 0.002 TYR P 149 PHE 0.020 0.002 PHE K 47 TRP 0.012 0.002 TRP R 63 HIS 0.019 0.002 HIS E 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00633 / 0.24 (25648) covalent geometry : angle 1.00919 / 0.38 (36048) hydrogen bonds : bond 0.03843 / 2.52 ( 223) hydrogen bonds : angle 5.64726 / 3.94 ( 576) Misc. bond : bond 0.09098 / 6.08 ( 237) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 512 time to evaluate : 0.816 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: N 33 ASN cc_start: 0.7096 (t0) cc_final: 0.6891 (t0) REVERT: N 134 ASN cc_start: 0.7826 (p0) cc_final: 0.7540 (p0) REVERT: M 216 HIS cc_start: 0.6637 (OUTLIER) cc_final: 0.6138 (m-70) REVERT: L 200 THR cc_start: 0.8473 (OUTLIER) cc_final: 0.8243 (m) REVERT: K 26 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8133 (ttpp) REVERT: K 65 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8072 (mtp-110) REVERT: K 216 HIS cc_start: 0.6825 (OUTLIER) cc_final: 0.6381 (m-70) REVERT: K 218 LYS cc_start: 0.6082 (OUTLIER) cc_final: 0.5350 (pptt) REVERT: J 104 ASP cc_start: 0.7656 (p0) cc_final: 0.7284 (p0) REVERT: J 129 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7999 (tp) REVERT: I 193 HIS cc_start: 0.8025 (OUTLIER) cc_final: 0.7807 (m90) REVERT: C 33 ASN cc_start: 0.7747 (m-40) cc_final: 0.7372 (m-40) REVERT: D 42 ASP cc_start: 0.8016 (p0) cc_final: 0.7743 (p0) REVERT: D 151 ASP cc_start: 0.7775 (m-30) cc_final: 0.7443 (m-30) REVERT: E 147 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7393 (pmm) REVERT: F 101 SER cc_start: 0.8268 (m) cc_final: 0.8006 (m) REVERT: G 214 THR cc_start: 0.7862 (p) cc_final: 0.5838 (m) REVERT: G 216 HIS cc_start: 0.6396 (OUTLIER) cc_final: 0.5660 (m-70) REVERT: P 21 VAL cc_start: 0.7429 (t) cc_final: 0.7106 (m) REVERT: P 134 ASN cc_start: 0.8070 (t0) cc_final: 0.7828 (t0) REVERT: Q 33 ASN cc_start: 0.7525 (t0) cc_final: 0.6725 (t0) REVERT: Q 41 THR cc_start: 0.8549 (m) cc_final: 0.8303 (t) REVERT: Q 200 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8144 (m) REVERT: R 95 ASP cc_start: 0.8151 (p0) cc_final: 0.7913 (p0) REVERT: R 147 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.6812 (pmm) REVERT: R 182 ASP cc_start: 0.7634 (p0) cc_final: 0.7426 (p0) REVERT: S 41 THR cc_start: 0.6882 (OUTLIER) cc_final: 0.6641 (p) REVERT: S 110 THR cc_start: 0.8486 (m) cc_final: 0.8130 (t) REVERT: S 139 MET cc_start: 0.7617 (mmt) cc_final: 0.7093 (mmt) REVERT: T 34 VAL cc_start: 0.8233 (m) cc_final: 0.8019 (p) outliers start: 162 outliers final: 117 residues processed: 621 average time/residue: 0.1256 time to fit residues: 136.2774 Evaluate side-chains 633 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 503 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 110 THR Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 151 ASP Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain M residue 68 ASP Chi-restraints excluded: chain M residue 93 LEU Chi-restraints excluded: chain M residue 147 MET Chi-restraints excluded: chain M residue 153 ILE Chi-restraints excluded: chain M residue 157 ASP Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 216 HIS Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 45 CYS Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain L residue 212 CYS Chi-restraints excluded: chain L residue 215 CYS Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain K residue 216 HIS Chi-restraints excluded: chain K residue 218 LYS Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 129 LEU Chi-restraints excluded: chain J residue 134 ASN Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 216 HIS Chi-restraints excluded: chain I residue 26 LYS Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 99 CYS Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 192 VAL Chi-restraints excluded: chain I residue 193 HIS Chi-restraints excluded: chain I residue 215 CYS Chi-restraints excluded: chain I residue 216 HIS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 99 CYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 147 MET Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 99 CYS Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 218 LYS Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 216 HIS Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 99 CYS Chi-restraints excluded: chain P residue 103 HIS Chi-restraints excluded: chain P residue 140 SER Chi-restraints excluded: chain P residue 158 THR Chi-restraints excluded: chain P residue 175 SER Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 199 SER Chi-restraints excluded: chain Q residue 99 CYS Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain Q residue 157 ASP Chi-restraints excluded: chain Q residue 169 LEU Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 52 HIS Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 147 MET Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 181 THR Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 215 CYS Chi-restraints excluded: chain S residue 41 THR Chi-restraints excluded: chain S residue 52 HIS Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 153 ILE Chi-restraints excluded: chain S residue 171 SER Chi-restraints excluded: chain S residue 183 VAL Chi-restraints excluded: chain S residue 218 LYS Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 55 SER Chi-restraints excluded: chain T residue 69 THR Chi-restraints excluded: chain T residue 74 THR Chi-restraints excluded: chain T residue 99 CYS Chi-restraints excluded: chain T residue 199 SER Chi-restraints excluded: chain T residue 215 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [178, 127, 275, 40, 153, 130, 24, 27, 49, 199, 293] chunk 178 optimal weight: 0.3980 chunk 127 optimal weight: 6.9990 chunk 275 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 153 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 24 optimal weight: 0.0870 chunk 27 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 199 optimal weight: 3.9990 chunk 293 optimal weight: 2.9990 overall best weight: 1.2762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 141 ASN ** N 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 ASN Q 113 ASN R 35 ASN ** R 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 172 GLN ** T 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.123758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.113019 restraints weight = 40635.738| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.82 r_work: 0.3430 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.485 25885 Z= 0.207 Angle : 0.937 19.191 36048 Z= 0.353 Chirality : 0.045 0.294 3808 Planarity : 0.003 0.050 4432 Dihedral : 17.289 89.955 3746 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.51 % Allowed : 9.76 % Favored : 89.73 % Rotamer: Outliers : 6.04 % Allowed : 29.65 % Favored : 64.31 % 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: -2.80 (0.13), residues: 3136 helix: -0.82 (0.27), residues: 336 sheet: None (None), residues: 0 loop : -2.24 (0.10), residues: 2800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 65 TYR 0.011 0.002 TYR P 149 PHE 0.017 0.002 PHE K 47 TRP 0.007 0.001 TRP T 63 HIS 0.023 0.002 HIS L 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.20 (25648) covalent geometry : angle 0.93661 / 0.35 (36048) hydrogen bonds : bond 0.03373 / 2.23 ( 223) hydrogen bonds : angle 5.59754 / 3.91 ( 576) Misc. bond : bond 0.08756 / 5.94 ( 237) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 514 time to evaluate : 0.806 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 134 ASN cc_start: 0.7840 (p0) cc_final: 0.7574 (p0) REVERT: M 107 ILE cc_start: 0.7629 (OUTLIER) cc_final: 0.7212 (mt) REVERT: M 216 HIS cc_start: 0.6454 (OUTLIER) cc_final: 0.6035 (m-70) REVERT: L 200 THR cc_start: 0.8467 (OUTLIER) cc_final: 0.8234 (m) REVERT: L 214 THR cc_start: 0.7869 (p) cc_final: 0.7074 (t) REVERT: K 26 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8205 (ttpp) REVERT: K 65 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.8040 (mtp-110) REVERT: J 33 ASN cc_start: 0.8323 (OUTLIER) cc_final: 0.7999 (t0) REVERT: J 104 ASP cc_start: 0.7678 (p0) cc_final: 0.7348 (p0) REVERT: J 129 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7973 (tp) REVERT: J 216 HIS cc_start: 0.6859 (OUTLIER) cc_final: 0.6333 (m-70) REVERT: I 193 HIS cc_start: 0.8035 (OUTLIER) cc_final: 0.7793 (m90) REVERT: C 33 ASN cc_start: 0.7665 (m-40) cc_final: 0.7318 (m-40) REVERT: D 26 LYS cc_start: 0.8722 (mtpt) cc_final: 0.8384 (mmtp) REVERT: D 42 ASP cc_start: 0.8025 (p0) cc_final: 0.7757 (p0) REVERT: D 151 ASP cc_start: 0.7737 (m-30) cc_final: 0.7398 (m-30) REVERT: E 147 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7421 (pmm) REVERT: F 101 SER cc_start: 0.8320 (m) cc_final: 0.8103 (m) REVERT: G 82 MET cc_start: 0.7622 (tpp) cc_final: 0.7364 (mmm) REVERT: G 214 THR cc_start: 0.7854 (p) cc_final: 0.5811 (m) REVERT: G 216 HIS cc_start: 0.6361 (OUTLIER) cc_final: 0.5525 (m-70) REVERT: P 21 VAL cc_start: 0.7314 (t) cc_final: 0.7001 (m) REVERT: P 134 ASN cc_start: 0.8060 (t0) cc_final: 0.7801 (t0) REVERT: Q 33 ASN cc_start: 0.7592 (t0) cc_final: 0.6767 (t0) REVERT: Q 41 THR cc_start: 0.8546 (m) cc_final: 0.8298 (t) REVERT: Q 134 ASN cc_start: 0.8190 (t0) cc_final: 0.7877 (t0) REVERT: Q 200 THR cc_start: 0.8432 (OUTLIER) cc_final: 0.8145 (m) REVERT: R 95 ASP cc_start: 0.8170 (p0) cc_final: 0.7953 (p0) REVERT: R 147 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.6908 (pmm) REVERT: S 41 THR cc_start: 0.6835 (OUTLIER) cc_final: 0.6603 (p) REVERT: S 110 THR cc_start: 0.8455 (m) cc_final: 0.8132 (t) REVERT: S 139 MET cc_start: 0.7395 (mmt) cc_final: 0.6891 (mmt) REVERT: T 171 SER cc_start: 0.7670 (m) cc_final: 0.7305 (p) outliers start: 147 outliers final: 119 residues processed: 616 average time/residue: 0.1272 time to fit residues: 136.3988 Evaluate side-chains 633 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 500 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 110 THR Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 141 ASN Chi-restraints excluded: chain N residue 151 ASP Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain M residue 68 ASP Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 93 LEU Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain M residue 147 MET Chi-restraints excluded: chain M residue 157 ASP Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 199 SER Chi-restraints excluded: chain M residue 216 HIS Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 45 CYS Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 153 ILE Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain L residue 212 CYS Chi-restraints excluded: chain L residue 215 CYS Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain J residue 33 ASN Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 129 LEU Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 216 HIS Chi-restraints excluded: chain I residue 26 LYS Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 99 CYS Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 192 VAL Chi-restraints excluded: chain I residue 193 HIS Chi-restraints excluded: chain I residue 215 CYS Chi-restraints excluded: chain I residue 216 HIS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain D residue 99 CYS Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 147 MET Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 99 CYS Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 218 LYS Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 216 HIS Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 103 HIS Chi-restraints excluded: chain P residue 140 SER Chi-restraints excluded: chain P residue 158 THR Chi-restraints excluded: chain P residue 175 SER Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 199 SER Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 99 CYS Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain Q residue 157 ASP Chi-restraints excluded: chain Q residue 169 LEU Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain Q residue 218 LYS Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 52 HIS Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain R residue 99 CYS Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 147 MET Chi-restraints excluded: chain R residue 181 THR Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 215 CYS Chi-restraints excluded: chain S residue 41 THR Chi-restraints excluded: chain S residue 52 HIS Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 153 ILE Chi-restraints excluded: chain S residue 171 SER Chi-restraints excluded: chain S residue 183 VAL Chi-restraints excluded: chain S residue 184 VAL Chi-restraints excluded: chain S residue 185 TRP Chi-restraints excluded: chain S residue 218 LYS Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 69 THR Chi-restraints excluded: chain T residue 74 THR Chi-restraints excluded: chain T residue 99 CYS Chi-restraints excluded: chain T residue 199 SER Chi-restraints excluded: chain T residue 215 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [204, 194, 199, 157, 119, 196, 189, 197, 231, 52, 298] chunk 204 optimal weight: 0.0970 chunk 194 optimal weight: 0.6980 chunk 199 optimal weight: 0.0470 chunk 157 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 189 optimal weight: 3.9990 chunk 197 optimal weight: 6.9990 chunk 231 optimal weight: 0.0060 chunk 52 optimal weight: 0.4980 chunk 298 optimal weight: 2.9990 overall best weight: 0.2692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 141 ASN ** N 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 ASN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 ASN Q 113 ASN R 35 ASN S 109 ASN ** S 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 172 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.128029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.117272 restraints weight = 40887.709| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.85 r_work: 0.3494 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.455 25885 Z= 0.126 Angle : 0.814 12.976 36048 Z= 0.315 Chirality : 0.041 0.280 3808 Planarity : 0.003 0.039 4432 Dihedral : 17.140 89.879 3745 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.51 % Favored : 91.20 % Rotamer: Outliers : 4.52 % Allowed : 31.29 % Favored : 64.19 % 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: -2.68 (0.13), residues: 3136 helix: -0.69 (0.28), residues: 336 sheet: None (None), residues: 0 loop : -2.15 (0.11), residues: 2800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 65 TYR 0.006 0.001 TYR T 149 PHE 0.010 0.001 PHE K 47 TRP 0.011 0.001 TRP T 63 HIS 0.015 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.12 (25648) covalent geometry : angle 0.81399 / 0.31 (36048) hydrogen bonds : bond 0.02615 / 1.75 ( 223) hydrogen bonds : angle 5.36171 / 3.75 ( 576) Misc. bond : bond 0.06231 / 4.37 ( 237) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 514 time to evaluate : 0.858 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 104 ASP cc_start: 0.7673 (p0) cc_final: 0.7437 (p0) REVERT: M 107 ILE cc_start: 0.7114 (OUTLIER) cc_final: 0.6751 (mt) REVERT: L 31 SER cc_start: 0.8379 (t) cc_final: 0.7871 (p) REVERT: L 200 THR cc_start: 0.8414 (OUTLIER) cc_final: 0.8181 (m) REVERT: K 26 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8168 (ttpp) REVERT: K 65 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.8004 (mtp-110) REVERT: K 216 HIS cc_start: 0.6310 (m-70) cc_final: 0.5918 (m-70) REVERT: J 33 ASN cc_start: 0.8295 (OUTLIER) cc_final: 0.7961 (t0) REVERT: J 95 ASP cc_start: 0.8526 (p0) cc_final: 0.8300 (p0) REVERT: J 104 ASP cc_start: 0.7622 (p0) cc_final: 0.7238 (p0) REVERT: J 129 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7895 (tp) REVERT: J 147 MET cc_start: 0.8426 (pmm) cc_final: 0.7732 (pmm) REVERT: J 216 HIS cc_start: 0.6505 (OUTLIER) cc_final: 0.6150 (m-70) REVERT: D 42 ASP cc_start: 0.7963 (p0) cc_final: 0.7729 (p0) REVERT: D 151 ASP cc_start: 0.7718 (m-30) cc_final: 0.7356 (m-30) REVERT: E 147 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7598 (pmm) REVERT: F 101 SER cc_start: 0.8222 (m) cc_final: 0.8004 (m) REVERT: G 216 HIS cc_start: 0.6073 (OUTLIER) cc_final: 0.5125 (m-70) REVERT: P 21 VAL cc_start: 0.7075 (t) cc_final: 0.6745 (m) REVERT: P 134 ASN cc_start: 0.7992 (t0) cc_final: 0.7738 (t0) REVERT: Q 33 ASN cc_start: 0.7586 (t0) cc_final: 0.6797 (t0) REVERT: Q 41 THR cc_start: 0.8536 (m) cc_final: 0.8327 (t) REVERT: Q 134 ASN cc_start: 0.8126 (t0) cc_final: 0.7866 (t0) REVERT: Q 200 THR cc_start: 0.8380 (OUTLIER) cc_final: 0.8066 (m) REVERT: R 95 ASP cc_start: 0.8148 (p0) cc_final: 0.7935 (p0) REVERT: R 147 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7029 (pmm) REVERT: R 182 ASP cc_start: 0.7528 (p0) cc_final: 0.7319 (p0) REVERT: S 41 THR cc_start: 0.6761 (OUTLIER) cc_final: 0.6538 (p) REVERT: S 110 THR cc_start: 0.8430 (m) cc_final: 0.8103 (t) REVERT: S 139 MET cc_start: 0.7274 (mmt) cc_final: 0.7005 (mmp) REVERT: S 218 LYS cc_start: 0.5148 (OUTLIER) cc_final: 0.4306 (pptt) REVERT: T 147 MET cc_start: 0.8390 (pmm) cc_final: 0.7958 (pmm) REVERT: T 171 SER cc_start: 0.7566 (m) cc_final: 0.7272 (p) outliers start: 110 outliers final: 83 residues processed: 588 average time/residue: 0.1242 time to fit residues: 127.6298 Evaluate side-chains 599 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 503 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 141 ASN Chi-restraints excluded: chain N residue 151 ASP Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 93 LEU Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain M residue 147 MET Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 199 SER Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 45 CYS Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain J residue 33 ASN Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 129 LEU Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain J residue 216 HIS Chi-restraints excluded: chain I residue 26 LYS Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 99 CYS Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 192 VAL Chi-restraints excluded: chain I residue 216 HIS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 99 CYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 147 MET Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 99 CYS Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 218 LYS Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 99 CYS Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 216 HIS Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 103 HIS Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 199 SER Chi-restraints excluded: chain Q residue 99 CYS Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain Q residue 157 ASP Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain Q residue 218 LYS Chi-restraints excluded: chain R residue 52 HIS Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain R residue 99 CYS Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 147 MET Chi-restraints excluded: chain R residue 181 THR Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain S residue 41 THR Chi-restraints excluded: chain S residue 52 HIS Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 153 ILE Chi-restraints excluded: chain S residue 183 VAL Chi-restraints excluded: chain S residue 218 LYS Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 55 SER Chi-restraints excluded: chain T residue 99 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [101, 136, 221, 210, 106, 178, 255, 199, 167, 119, 147] chunk 101 optimal weight: 0.5980 chunk 136 optimal weight: 0.1980 chunk 221 optimal weight: 0.8980 chunk 210 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 178 optimal weight: 0.0370 chunk 255 optimal weight: 7.9990 chunk 199 optimal weight: 0.0570 chunk 167 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 ASN ** I 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 113 ASN ** S 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 172 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.129542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.118973 restraints weight = 40703.958| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.81 r_work: 0.3503 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.561 25885 Z= 0.131 Angle : 0.805 13.379 36048 Z= 0.313 Chirality : 0.041 0.271 3808 Planarity : 0.003 0.046 4432 Dihedral : 16.930 89.845 3743 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.26 % Favored : 91.49 % Rotamer: Outliers : 4.36 % Allowed : 31.41 % Favored : 64.23 % 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: -2.60 (0.13), residues: 3136 helix: -0.59 (0.28), residues: 336 sheet: None (None), residues: 0 loop : -2.11 (0.11), residues: 2800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 65 TYR 0.005 0.001 TYR P 149 PHE 0.011 0.001 PHE K 47 TRP 0.010 0.001 TRP C 185 HIS 0.013 0.001 HIS E 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.12 (25648) covalent geometry : angle 0.80523 / 0.31 (36048) hydrogen bonds : bond 0.02588 / 1.72 ( 223) hydrogen bonds : angle 5.26866 / 3.68 ( 576) Misc. bond : bond 0.06764 / 4.68 ( 237) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 507 time to evaluate : 0.825 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 134 ASN cc_start: 0.7779 (p0) cc_final: 0.7549 (p0) REVERT: M 104 ASP cc_start: 0.7663 (p0) cc_final: 0.7437 (p0) REVERT: M 107 ILE cc_start: 0.7021 (OUTLIER) cc_final: 0.6653 (mt) REVERT: L 31 SER cc_start: 0.8394 (t) cc_final: 0.7906 (p) REVERT: L 200 THR cc_start: 0.8412 (OUTLIER) cc_final: 0.8176 (m) REVERT: K 26 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8153 (ttpp) REVERT: K 65 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.8029 (mtp-110) REVERT: K 216 HIS cc_start: 0.6446 (m-70) cc_final: 0.6003 (m-70) REVERT: J 33 ASN cc_start: 0.8266 (OUTLIER) cc_final: 0.7894 (t0) REVERT: J 95 ASP cc_start: 0.8487 (p0) cc_final: 0.8256 (p0) REVERT: J 104 ASP cc_start: 0.7608 (p0) cc_final: 0.7211 (p0) REVERT: J 147 MET cc_start: 0.8401 (pmm) cc_final: 0.7715 (pmm) REVERT: J 216 HIS cc_start: 0.6503 (OUTLIER) cc_final: 0.5905 (m-70) REVERT: D 26 LYS cc_start: 0.8671 (mtpt) cc_final: 0.8370 (mmtp) REVERT: D 42 ASP cc_start: 0.7960 (p0) cc_final: 0.7741 (p0) REVERT: D 79 THR cc_start: 0.7901 (p) cc_final: 0.6892 (t) REVERT: D 151 ASP cc_start: 0.7703 (m-30) cc_final: 0.7357 (m-30) REVERT: E 83 ASN cc_start: 0.6345 (m110) cc_final: 0.5690 (m-40) REVERT: E 98 LEU cc_start: 0.8183 (mt) cc_final: 0.7942 (mp) REVERT: E 147 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7478 (pmm) REVERT: F 101 SER cc_start: 0.8195 (m) cc_final: 0.7954 (m) REVERT: F 107 ILE cc_start: 0.7827 (OUTLIER) cc_final: 0.7604 (mt) REVERT: G 216 HIS cc_start: 0.6081 (OUTLIER) cc_final: 0.5145 (m-70) REVERT: P 21 VAL cc_start: 0.7050 (t) cc_final: 0.6719 (m) REVERT: P 134 ASN cc_start: 0.8010 (t0) cc_final: 0.7750 (t0) REVERT: Q 33 ASN cc_start: 0.7542 (t0) cc_final: 0.6799 (t0) REVERT: Q 41 THR cc_start: 0.8596 (m) cc_final: 0.8371 (t) REVERT: Q 134 ASN cc_start: 0.8127 (t0) cc_final: 0.7867 (t0) REVERT: Q 147 MET cc_start: 0.7771 (pmm) cc_final: 0.7361 (pmm) REVERT: Q 200 THR cc_start: 0.8379 (OUTLIER) cc_final: 0.8062 (m) REVERT: R 147 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.6977 (pmm) REVERT: R 182 ASP cc_start: 0.7516 (p0) cc_final: 0.7295 (p0) REVERT: S 41 THR cc_start: 0.6706 (OUTLIER) cc_final: 0.6490 (p) REVERT: S 110 THR cc_start: 0.8360 (m) cc_final: 0.8046 (t) REVERT: S 125 VAL cc_start: 0.8527 (m) cc_final: 0.8182 (p) REVERT: S 139 MET cc_start: 0.7301 (mmt) cc_final: 0.7032 (mmp) REVERT: S 218 LYS cc_start: 0.5113 (OUTLIER) cc_final: 0.4295 (pptt) REVERT: T 147 MET cc_start: 0.8391 (pmm) cc_final: 0.7964 (pmm) REVERT: T 171 SER cc_start: 0.7568 (m) cc_final: 0.7265 (p) outliers start: 106 outliers final: 82 residues processed: 576 average time/residue: 0.1289 time to fit residues: 129.0861 Evaluate side-chains 602 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 507 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 151 ASP Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 93 LEU Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain M residue 147 MET Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 199 SER Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 45 CYS Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain J residue 33 ASN Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain J residue 216 HIS Chi-restraints excluded: chain I residue 26 LYS Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 99 CYS Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 123 LEU Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 192 VAL Chi-restraints excluded: chain I residue 216 HIS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 99 CYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 147 MET Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 99 CYS Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 218 LYS Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 99 CYS Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 216 HIS Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 103 HIS Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 199 SER Chi-restraints excluded: chain Q residue 99 CYS Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain Q residue 157 ASP Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain Q residue 218 LYS Chi-restraints excluded: chain R residue 52 HIS Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain R residue 99 CYS Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 147 MET Chi-restraints excluded: chain R residue 181 THR Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain S residue 41 THR Chi-restraints excluded: chain S residue 52 HIS Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 183 VAL Chi-restraints excluded: chain S residue 218 LYS Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 55 SER Chi-restraints excluded: chain T residue 99 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [18, 98, 196, 298, 174, 84, 22, 16, 26, 201, 214] chunk 18 optimal weight: 2.9990 chunk 98 optimal weight: 0.0270 chunk 196 optimal weight: 0.9990 chunk 298 optimal weight: 6.9990 chunk 174 optimal weight: 0.0030 chunk 84 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 chunk 214 optimal weight: 0.3980 overall best weight: 0.4852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 ASN ** J 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 ASN ** I 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 ASN Q 113 ASN ** S 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 172 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.129451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.118717 restraints weight = 40708.893| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.83 r_work: 0.3504 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.592 25885 Z= 0.133 Angle : 0.808 12.952 36048 Z= 0.312 Chirality : 0.042 0.252 3808 Planarity : 0.003 0.048 4432 Dihedral : 16.832 89.981 3743 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.39 % Favored : 91.33 % Rotamer: Outliers : 4.52 % Allowed : 31.33 % Favored : 64.14 % 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: -2.56 (0.13), residues: 3136 helix: -0.57 (0.28), residues: 336 sheet: None (None), residues: 0 loop : -2.07 (0.11), residues: 2800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 65 TYR 0.008 0.001 TYR P 149 PHE 0.011 0.001 PHE K 47 TRP 0.012 0.001 TRP C 185 HIS 0.029 0.001 HIS K 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.13 (25648) covalent geometry : angle 0.80768 / 0.31 (36048) hydrogen bonds : bond 0.02592 / 1.71 ( 223) hydrogen bonds : angle 5.22004 / 3.65 ( 576) Misc. bond : bond 0.06701 / 4.73 ( 237) =============================================================================== Job complete usr+sys time: 6809.80 seconds wall clock time: 117 minutes 2.64 seconds (7022.64 seconds total)