Starting phenix.real_space_refine on Sun Aug 9 03:38:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xbu_38229/08_2026/8xbu_38229.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xbu_38229/08_2026/8xbu_38229.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xbu_38229/08_2026/8xbu_38229.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xbu_38229/08_2026/8xbu_38229.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xbu_38229/08_2026/8xbu_38229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xbu_38229/08_2026/8xbu_38229.map" } resolution = 4.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 309 5.49 5 S 131 5.16 5 C 19432 2.51 5 N 5887 2.21 5 O 6808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 257 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32567 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 819 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 805 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 714 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 3189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3189 Classifications: {'DNA': 156} Link IDs: {'rna3p': 155} Chain: "J" Number of atoms: 3143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3143 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Chain: "K" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2163 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Chain: "L" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2163 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Chain: "M" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2163 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Chain: "N" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2163 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Chain: "O" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1698 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 216} Chain breaks: 1 Chain: "P" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1698 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 216} Chain breaks: 1 Chain: "Q" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2163 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Chain: "R" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2163 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Chain: "S" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1698 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 216} Chain breaks: 1 Chain: "T" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2163 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Time building chain proxies: 6.51, per 1000 atoms: 0.20 Number of scatterers: 32567 At special positions: 0 Unit cell: (171.72, 156.88, 167.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 131 16.00 P 309 15.00 O 6808 8.00 N 5887 7.00 C 19432 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=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.86 Conformation dependent library (CDL) restraints added in 1.2 seconds 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6218 Finding SS restraints... Secondary structure from input PDB file: 171 helices and 20 sheets defined 57.2% alpha, 14.2% beta 151 base pairs and 269 stacking pairs defined. Time for finding SS restraints: 4.29 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.698A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.595A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.579A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.738A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.486A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 123 Processing helix chain 'K' and resid 25 through 30 removed outlier: 3.751A pdb=" N GLU K 29 " --> pdb=" O ILE K 25 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN K 30 " --> pdb=" O SER K 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 25 through 30' Processing helix chain 'K' and resid 34 through 45 Processing helix chain 'K' and resid 48 through 54 Processing helix chain 'K' and resid 57 through 63 removed outlier: 3.784A pdb=" N ILE K 63 " --> pdb=" O GLU K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 82 removed outlier: 3.765A pdb=" N LYS K 80 " --> pdb=" O ALA K 76 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU K 81 " --> pdb=" O GLU K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 113 Processing helix chain 'K' and resid 132 through 144 removed outlier: 3.814A pdb=" N VAL K 142 " --> pdb=" O HIS K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 146 No H-bonds generated for 'chain 'K' and resid 145 through 146' Processing helix chain 'K' and resid 147 through 151 Processing helix chain 'K' and resid 167 through 178 Processing helix chain 'K' and resid 181 through 188 Processing helix chain 'K' and resid 196 through 214 removed outlier: 4.100A pdb=" N LEU K 204 " --> pdb=" O GLN K 200 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR K 205 " --> pdb=" O THR K 201 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN K 206 " --> pdb=" O GLN K 202 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA K 209 " --> pdb=" O TYR K 205 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL K 212 " --> pdb=" O SER K 208 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU K 213 " --> pdb=" O ALA K 209 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER K 214 " --> pdb=" O MET K 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 231 removed outlier: 3.588A pdb=" N ARG K 229 " --> pdb=" O THR K 225 " (cutoff:3.500A) Processing helix chain 'K' and resid 237 through 260 Processing helix chain 'K' and resid 290 through 296 removed outlier: 4.218A pdb=" N HIS K 294 " --> pdb=" O ASN K 290 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA K 295 " --> pdb=" O ILE K 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 30 removed outlier: 3.813A pdb=" N GLU L 29 " --> pdb=" O ILE L 25 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN L 30 " --> pdb=" O SER L 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 25 through 30' Processing helix chain 'L' and resid 34 through 45 Processing helix chain 'L' and resid 48 through 54 Processing helix chain 'L' and resid 57 through 63 removed outlier: 3.783A pdb=" N ILE L 63 " --> pdb=" O GLU L 59 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 82 removed outlier: 3.766A pdb=" N LYS L 80 " --> pdb=" O ALA L 76 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU L 81 " --> pdb=" O GLU L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 113 Processing helix chain 'L' and resid 132 through 144 removed outlier: 3.814A pdb=" N VAL L 142 " --> pdb=" O HIS L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 146 No H-bonds generated for 'chain 'L' and resid 145 through 146' Processing helix chain 'L' and resid 147 through 151 Processing helix chain 'L' and resid 167 through 178 Processing helix chain 'L' and resid 181 through 188 Processing helix chain 'L' and resid 196 through 214 removed outlier: 4.100A pdb=" N LEU L 204 " --> pdb=" O GLN L 200 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR L 205 " --> pdb=" O THR L 201 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN L 206 " --> pdb=" O GLN L 202 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA L 209 " --> pdb=" O TYR L 205 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL L 212 " --> pdb=" O SER L 208 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU L 213 " --> pdb=" O ALA L 209 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER L 214 " --> pdb=" O MET L 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 231 removed outlier: 3.589A pdb=" N ARG L 229 " --> pdb=" O THR L 225 " (cutoff:3.500A) Processing helix chain 'L' and resid 237 through 260 Processing helix chain 'L' and resid 290 through 296 removed outlier: 4.218A pdb=" N HIS L 294 " --> pdb=" O ASN L 290 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA L 295 " --> pdb=" O ILE L 291 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 30 removed outlier: 3.813A pdb=" N GLU M 29 " --> pdb=" O ILE M 25 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN M 30 " --> pdb=" O SER M 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 25 through 30' Processing helix chain 'M' and resid 34 through 45 Processing helix chain 'M' and resid 48 through 54 Processing helix chain 'M' and resid 57 through 63 removed outlier: 3.783A pdb=" N ILE M 63 " --> pdb=" O GLU M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 82 removed outlier: 3.766A pdb=" N LYS M 80 " --> pdb=" O ALA M 76 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU M 81 " --> pdb=" O GLU M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 113 Processing helix chain 'M' and resid 132 through 144 removed outlier: 3.814A pdb=" N VAL M 142 " --> pdb=" O HIS M 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 146 No H-bonds generated for 'chain 'M' and resid 145 through 146' Processing helix chain 'M' and resid 147 through 151 Processing helix chain 'M' and resid 167 through 178 Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'M' and resid 196 through 214 removed outlier: 4.100A pdb=" N LEU M 204 " --> pdb=" O GLN M 200 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR M 205 " --> pdb=" O THR M 201 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN M 206 " --> pdb=" O GLN M 202 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA M 209 " --> pdb=" O TYR M 205 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL M 212 " --> pdb=" O SER M 208 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU M 213 " --> pdb=" O ALA M 209 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER M 214 " --> pdb=" O MET M 210 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 231 removed outlier: 3.590A pdb=" N ARG M 229 " --> pdb=" O THR M 225 " (cutoff:3.500A) Processing helix chain 'M' and resid 237 through 260 Processing helix chain 'M' and resid 290 through 296 removed outlier: 4.218A pdb=" N HIS M 294 " --> pdb=" O ASN M 290 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA M 295 " --> pdb=" O ILE M 291 " (cutoff:3.500A) Processing helix chain 'N' and resid 25 through 31 removed outlier: 3.749A pdb=" N GLU N 29 " --> pdb=" O ILE N 25 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN N 30 " --> pdb=" O SER N 26 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N CYS N 31 " --> pdb=" O ARG N 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 25 through 31' Processing helix chain 'N' and resid 34 through 45 Processing helix chain 'N' and resid 48 through 54 Processing helix chain 'N' and resid 57 through 63 removed outlier: 3.784A pdb=" N ILE N 63 " --> pdb=" O GLU N 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 82 removed outlier: 3.766A pdb=" N LYS N 80 " --> pdb=" O ALA N 76 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU N 81 " --> pdb=" O GLU N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 113 Processing helix chain 'N' and resid 132 through 144 removed outlier: 3.815A pdb=" N VAL N 142 " --> pdb=" O HIS N 138 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 146 No H-bonds generated for 'chain 'N' and resid 145 through 146' Processing helix chain 'N' and resid 147 through 151 Processing helix chain 'N' and resid 167 through 178 Processing helix chain 'N' and resid 181 through 188 Processing helix chain 'N' and resid 196 through 214 removed outlier: 4.101A pdb=" N LEU N 204 " --> pdb=" O GLN N 200 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR N 205 " --> pdb=" O THR N 201 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN N 206 " --> pdb=" O GLN N 202 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA N 209 " --> pdb=" O TYR N 205 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL N 212 " --> pdb=" O SER N 208 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU N 213 " --> pdb=" O ALA N 209 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER N 214 " --> pdb=" O MET N 210 " (cutoff:3.500A) Processing helix chain 'N' and resid 225 through 231 removed outlier: 3.587A pdb=" N ARG N 229 " --> pdb=" O THR N 225 " (cutoff:3.500A) Processing helix chain 'N' and resid 237 through 260 Processing helix chain 'N' and resid 290 through 296 removed outlier: 4.219A pdb=" N HIS N 294 " --> pdb=" O ASN N 290 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA N 295 " --> pdb=" O ILE N 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 113 Processing helix chain 'O' and resid 132 through 144 removed outlier: 3.814A pdb=" N VAL O 142 " --> pdb=" O HIS O 138 " (cutoff:3.500A) Processing helix chain 'O' and resid 145 through 146 No H-bonds generated for 'chain 'O' and resid 145 through 146' Processing helix chain 'O' and resid 147 through 151 Processing helix chain 'O' and resid 167 through 178 Processing helix chain 'O' and resid 181 through 188 Processing helix chain 'O' and resid 196 through 214 removed outlier: 4.099A pdb=" N LEU O 204 " --> pdb=" O GLN O 200 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR O 205 " --> pdb=" O THR O 201 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN O 206 " --> pdb=" O GLN O 202 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA O 209 " --> pdb=" O TYR O 205 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL O 212 " --> pdb=" O SER O 208 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU O 213 " --> pdb=" O ALA O 209 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER O 214 " --> pdb=" O MET O 210 " (cutoff:3.500A) Processing helix chain 'O' and resid 225 through 231 removed outlier: 3.588A pdb=" N ARG O 229 " --> pdb=" O THR O 225 " (cutoff:3.500A) Processing helix chain 'O' and resid 237 through 260 Processing helix chain 'O' and resid 290 through 296 removed outlier: 4.218A pdb=" N HIS O 294 " --> pdb=" O ASN O 290 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA O 295 " --> pdb=" O ILE O 291 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 113 Processing helix chain 'P' and resid 132 through 144 removed outlier: 3.815A pdb=" N VAL P 142 " --> pdb=" O HIS P 138 " (cutoff:3.500A) Processing helix chain 'P' and resid 145 through 146 No H-bonds generated for 'chain 'P' and resid 145 through 146' Processing helix chain 'P' and resid 147 through 151 Processing helix chain 'P' and resid 167 through 178 Processing helix chain 'P' and resid 181 through 188 Processing helix chain 'P' and resid 196 through 214 removed outlier: 4.100A pdb=" N LEU P 204 " --> pdb=" O GLN P 200 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR P 205 " --> pdb=" O THR P 201 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN P 206 " --> pdb=" O GLN P 202 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA P 209 " --> pdb=" O TYR P 205 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL P 212 " --> pdb=" O SER P 208 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU P 213 " --> pdb=" O ALA P 209 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER P 214 " --> pdb=" O MET P 210 " (cutoff:3.500A) Processing helix chain 'P' and resid 225 through 231 removed outlier: 3.588A pdb=" N ARG P 229 " --> pdb=" O THR P 225 " (cutoff:3.500A) Processing helix chain 'P' and resid 237 through 260 Processing helix chain 'P' and resid 290 through 296 removed outlier: 4.218A pdb=" N HIS P 294 " --> pdb=" O ASN P 290 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA P 295 " --> pdb=" O ILE P 291 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 3.750A pdb=" N GLU Q 29 " --> pdb=" O ILE Q 25 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN Q 30 " --> pdb=" O SER Q 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 25 through 30' Processing helix chain 'Q' and resid 34 through 45 Processing helix chain 'Q' and resid 48 through 54 Processing helix chain 'Q' and resid 57 through 63 removed outlier: 3.785A pdb=" N ILE Q 63 " --> pdb=" O GLU Q 59 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 82 removed outlier: 3.766A pdb=" N LYS Q 80 " --> pdb=" O ALA Q 76 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU Q 81 " --> pdb=" O GLU Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 113 Processing helix chain 'Q' and resid 132 through 144 removed outlier: 3.814A pdb=" N VAL Q 142 " --> pdb=" O HIS Q 138 " (cutoff:3.500A) Processing helix chain 'Q' and resid 145 through 146 No H-bonds generated for 'chain 'Q' and resid 145 through 146' Processing helix chain 'Q' and resid 147 through 151 Processing helix chain 'Q' and resid 167 through 178 Processing helix chain 'Q' and resid 181 through 188 Processing helix chain 'Q' and resid 196 through 214 removed outlier: 4.101A pdb=" N LEU Q 204 " --> pdb=" O GLN Q 200 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR Q 205 " --> pdb=" O THR Q 201 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN Q 206 " --> pdb=" O GLN Q 202 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA Q 209 " --> pdb=" O TYR Q 205 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL Q 212 " --> pdb=" O SER Q 208 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU Q 213 " --> pdb=" O ALA Q 209 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER Q 214 " --> pdb=" O MET Q 210 " (cutoff:3.500A) Processing helix chain 'Q' and resid 225 through 231 removed outlier: 3.589A pdb=" N ARG Q 229 " --> pdb=" O THR Q 225 " (cutoff:3.500A) Processing helix chain 'Q' and resid 237 through 260 Processing helix chain 'Q' and resid 290 through 296 removed outlier: 4.218A pdb=" N HIS Q 294 " --> pdb=" O ASN Q 290 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA Q 295 " --> pdb=" O ILE Q 291 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 30 removed outlier: 3.750A pdb=" N GLU R 29 " --> pdb=" O ILE R 25 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN R 30 " --> pdb=" O SER R 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 25 through 30' Processing helix chain 'R' and resid 34 through 45 Processing helix chain 'R' and resid 48 through 54 Processing helix chain 'R' and resid 57 through 63 removed outlier: 3.785A pdb=" N ILE R 63 " --> pdb=" O GLU R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 82 removed outlier: 3.767A pdb=" N LYS R 80 " --> pdb=" O ALA R 76 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU R 81 " --> pdb=" O GLU R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 113 Processing helix chain 'R' and resid 132 through 144 removed outlier: 3.814A pdb=" N VAL R 142 " --> pdb=" O HIS R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 146 No H-bonds generated for 'chain 'R' and resid 145 through 146' Processing helix chain 'R' and resid 147 through 151 Processing helix chain 'R' and resid 167 through 178 Processing helix chain 'R' and resid 181 through 188 Processing helix chain 'R' and resid 196 through 214 removed outlier: 4.100A pdb=" N LEU R 204 " --> pdb=" O GLN R 200 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR R 205 " --> pdb=" O THR R 201 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN R 206 " --> pdb=" O GLN R 202 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA R 209 " --> pdb=" O TYR R 205 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL R 212 " --> pdb=" O SER R 208 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU R 213 " --> pdb=" O ALA R 209 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER R 214 " --> pdb=" O MET R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 231 removed outlier: 3.589A pdb=" N ARG R 229 " --> pdb=" O THR R 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 260 Processing helix chain 'R' and resid 290 through 296 removed outlier: 4.218A pdb=" N HIS R 294 " --> pdb=" O ASN R 290 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA R 295 " --> pdb=" O ILE R 291 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 113 Processing helix chain 'S' and resid 132 through 144 removed outlier: 3.813A pdb=" N VAL S 142 " --> pdb=" O HIS S 138 " (cutoff:3.500A) Processing helix chain 'S' and resid 145 through 146 No H-bonds generated for 'chain 'S' and resid 145 through 146' Processing helix chain 'S' and resid 147 through 151 Processing helix chain 'S' and resid 167 through 178 Processing helix chain 'S' and resid 181 through 188 Processing helix chain 'S' and resid 196 through 214 removed outlier: 4.100A pdb=" N LEU S 204 " --> pdb=" O GLN S 200 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR S 205 " --> pdb=" O THR S 201 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN S 206 " --> pdb=" O GLN S 202 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA S 209 " --> pdb=" O TYR S 205 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL S 212 " --> pdb=" O SER S 208 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU S 213 " --> pdb=" O ALA S 209 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER S 214 " --> pdb=" O MET S 210 " (cutoff:3.500A) Processing helix chain 'S' and resid 225 through 231 removed outlier: 3.588A pdb=" N ARG S 229 " --> pdb=" O THR S 225 " (cutoff:3.500A) Processing helix chain 'S' and resid 237 through 260 Processing helix chain 'S' and resid 290 through 296 removed outlier: 4.218A pdb=" N HIS S 294 " --> pdb=" O ASN S 290 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA S 295 " --> pdb=" O ILE S 291 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 30 removed outlier: 3.750A pdb=" N GLU T 29 " --> pdb=" O ILE T 25 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN T 30 " --> pdb=" O SER T 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 25 through 30' Processing helix chain 'T' and resid 34 through 45 Processing helix chain 'T' and resid 48 through 54 Processing helix chain 'T' and resid 57 through 63 removed outlier: 3.785A pdb=" N ILE T 63 " --> pdb=" O GLU T 59 " (cutoff:3.500A) Processing helix chain 'T' and resid 67 through 82 removed outlier: 3.766A pdb=" N LYS T 80 " --> pdb=" O ALA T 76 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU T 81 " --> pdb=" O GLU T 77 " (cutoff:3.500A) Processing helix chain 'T' and resid 106 through 113 Processing helix chain 'T' and resid 132 through 144 removed outlier: 3.814A pdb=" N VAL T 142 " --> pdb=" O HIS T 138 " (cutoff:3.500A) Processing helix chain 'T' and resid 145 through 146 No H-bonds generated for 'chain 'T' and resid 145 through 146' Processing helix chain 'T' and resid 147 through 151 Processing helix chain 'T' and resid 167 through 178 Processing helix chain 'T' and resid 181 through 188 Processing helix chain 'T' and resid 196 through 214 removed outlier: 4.101A pdb=" N LEU T 204 " --> pdb=" O GLN T 200 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR T 205 " --> pdb=" O THR T 201 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN T 206 " --> pdb=" O GLN T 202 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA T 209 " --> pdb=" O TYR T 205 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL T 212 " --> pdb=" O SER T 208 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU T 213 " --> pdb=" O ALA T 209 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER T 214 " --> pdb=" O MET T 210 " (cutoff:3.500A) Processing helix chain 'T' and resid 225 through 231 removed outlier: 3.589A pdb=" N ARG T 229 " --> pdb=" O THR T 225 " (cutoff:3.500A) Processing helix chain 'T' and resid 237 through 260 Processing helix chain 'T' and resid 290 through 296 removed outlier: 4.218A pdb=" N HIS T 294 " --> pdb=" O ASN T 290 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA T 295 " --> pdb=" O ILE T 291 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.075A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.827A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.244A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.825A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 189 through 193 removed outlier: 3.591A pdb=" N ALA K 190 " --> pdb=" O ALA K 157 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR K 159 " --> pdb=" O ALA K 190 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA K 192 " --> pdb=" O TYR K 159 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS K 156 " --> pdb=" O LEU K 218 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ILE K 220 " --> pdb=" O LYS K 156 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N MET K 158 " --> pdb=" O ILE K 220 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ASP K 222 " --> pdb=" O MET K 158 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE K 160 " --> pdb=" O ASP K 222 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA K 217 " --> pdb=" O ALA K 262 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL K 264 " --> pdb=" O ALA K 217 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU K 219 " --> pdb=" O VAL K 264 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N THR K 266 " --> pdb=" O LEU K 219 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N VAL K 221 " --> pdb=" O THR K 266 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N GLN K 268 " --> pdb=" O VAL K 221 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE K 265 " --> pdb=" O THR K 123 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N MET K 125 " --> pdb=" O ILE K 265 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN K 267 " --> pdb=" O MET K 125 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY K 127 " --> pdb=" O ASN K 267 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ILE K 122 " --> pdb=" O THR K 298 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N LEU K 300 " --> pdb=" O ILE K 122 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU K 124 " --> pdb=" O LEU K 300 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU K 302 " --> pdb=" O GLU K 124 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE K 126 " --> pdb=" O LEU K 302 " (cutoff:3.500A) removed outlier: 9.370A pdb=" N LYS K 304 " --> pdb=" O PHE K 126 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG K 299 " --> pdb=" O TYR K 315 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 189 through 193 removed outlier: 3.591A pdb=" N ALA L 190 " --> pdb=" O ALA L 157 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR L 159 " --> pdb=" O ALA L 190 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA L 192 " --> pdb=" O TYR L 159 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS L 156 " --> pdb=" O LEU L 218 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ILE L 220 " --> pdb=" O LYS L 156 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N MET L 158 " --> pdb=" O ILE L 220 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASP L 222 " --> pdb=" O MET L 158 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE L 160 " --> pdb=" O ASP L 222 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA L 217 " --> pdb=" O ALA L 262 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL L 264 " --> pdb=" O ALA L 217 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU L 219 " --> pdb=" O VAL L 264 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR L 266 " --> pdb=" O LEU L 219 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL L 221 " --> pdb=" O THR L 266 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N GLN L 268 " --> pdb=" O VAL L 221 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE L 265 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N MET L 125 " --> pdb=" O ILE L 265 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN L 267 " --> pdb=" O MET L 125 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY L 127 " --> pdb=" O ASN L 267 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE L 122 " --> pdb=" O THR L 298 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N LEU L 300 " --> pdb=" O ILE L 122 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU L 124 " --> pdb=" O LEU L 300 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU L 302 " --> pdb=" O GLU L 124 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N PHE L 126 " --> pdb=" O LEU L 302 " (cutoff:3.500A) removed outlier: 9.370A pdb=" N LYS L 304 " --> pdb=" O PHE L 126 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG L 299 " --> pdb=" O TYR L 315 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 189 through 193 removed outlier: 3.591A pdb=" N ALA M 190 " --> pdb=" O ALA M 157 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR M 159 " --> pdb=" O ALA M 190 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA M 192 " --> pdb=" O TYR M 159 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS M 156 " --> pdb=" O LEU M 218 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N ILE M 220 " --> pdb=" O LYS M 156 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N MET M 158 " --> pdb=" O ILE M 220 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ASP M 222 " --> pdb=" O MET M 158 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ILE M 160 " --> pdb=" O ASP M 222 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA M 217 " --> pdb=" O ALA M 262 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL M 264 " --> pdb=" O ALA M 217 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU M 219 " --> pdb=" O VAL M 264 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N THR M 266 " --> pdb=" O LEU M 219 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N VAL M 221 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N GLN M 268 " --> pdb=" O VAL M 221 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE M 265 " --> pdb=" O THR M 123 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET M 125 " --> pdb=" O ILE M 265 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN M 267 " --> pdb=" O MET M 125 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY M 127 " --> pdb=" O ASN M 267 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ILE M 122 " --> pdb=" O THR M 298 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N LEU M 300 " --> pdb=" O ILE M 122 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLU M 124 " --> pdb=" O LEU M 300 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU M 302 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE M 126 " --> pdb=" O LEU M 302 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N LYS M 304 " --> pdb=" O PHE M 126 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG M 299 " --> pdb=" O TYR M 315 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 189 through 193 removed outlier: 3.591A pdb=" N ALA N 190 " --> pdb=" O ALA N 157 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR N 159 " --> pdb=" O ALA N 190 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA N 192 " --> pdb=" O TYR N 159 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LYS N 156 " --> pdb=" O LEU N 218 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ILE N 220 " --> pdb=" O LYS N 156 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N MET N 158 " --> pdb=" O ILE N 220 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ASP N 222 " --> pdb=" O MET N 158 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE N 160 " --> pdb=" O ASP N 222 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA N 217 " --> pdb=" O ALA N 262 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL N 264 " --> pdb=" O ALA N 217 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU N 219 " --> pdb=" O VAL N 264 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR N 266 " --> pdb=" O LEU N 219 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL N 221 " --> pdb=" O THR N 266 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N GLN N 268 " --> pdb=" O VAL N 221 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE N 265 " --> pdb=" O THR N 123 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N MET N 125 " --> pdb=" O ILE N 265 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN N 267 " --> pdb=" O MET N 125 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY N 127 " --> pdb=" O ASN N 267 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE N 122 " --> pdb=" O THR N 298 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N LEU N 300 " --> pdb=" O ILE N 122 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU N 124 " --> pdb=" O LEU N 300 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU N 302 " --> pdb=" O GLU N 124 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N PHE N 126 " --> pdb=" O LEU N 302 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N LYS N 304 " --> pdb=" O PHE N 126 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG N 299 " --> pdb=" O TYR N 315 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 189 through 193 removed outlier: 3.591A pdb=" N ALA O 190 " --> pdb=" O ALA O 157 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR O 159 " --> pdb=" O ALA O 190 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA O 192 " --> pdb=" O TYR O 159 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS O 156 " --> pdb=" O LEU O 218 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ILE O 220 " --> pdb=" O LYS O 156 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N MET O 158 " --> pdb=" O ILE O 220 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ASP O 222 " --> pdb=" O MET O 158 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE O 160 " --> pdb=" O ASP O 222 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA O 217 " --> pdb=" O ALA O 262 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL O 264 " --> pdb=" O ALA O 217 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU O 219 " --> pdb=" O VAL O 264 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR O 266 " --> pdb=" O LEU O 219 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL O 221 " --> pdb=" O THR O 266 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N GLN O 268 " --> pdb=" O VAL O 221 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE O 265 " --> pdb=" O THR O 123 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N MET O 125 " --> pdb=" O ILE O 265 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN O 267 " --> pdb=" O MET O 125 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY O 127 " --> pdb=" O ASN O 267 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE O 122 " --> pdb=" O THR O 298 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N LEU O 300 " --> pdb=" O ILE O 122 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLU O 124 " --> pdb=" O LEU O 300 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU O 302 " --> pdb=" O GLU O 124 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N PHE O 126 " --> pdb=" O LEU O 302 " (cutoff:3.500A) removed outlier: 9.370A pdb=" N LYS O 304 " --> pdb=" O PHE O 126 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG O 299 " --> pdb=" O TYR O 315 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 189 through 193 removed outlier: 3.590A pdb=" N ALA P 190 " --> pdb=" O ALA P 157 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR P 159 " --> pdb=" O ALA P 190 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA P 192 " --> pdb=" O TYR P 159 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS P 156 " --> pdb=" O LEU P 218 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N ILE P 220 " --> pdb=" O LYS P 156 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N MET P 158 " --> pdb=" O ILE P 220 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASP P 222 " --> pdb=" O MET P 158 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE P 160 " --> pdb=" O ASP P 222 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA P 217 " --> pdb=" O ALA P 262 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL P 264 " --> pdb=" O ALA P 217 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU P 219 " --> pdb=" O VAL P 264 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N THR P 266 " --> pdb=" O LEU P 219 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL P 221 " --> pdb=" O THR P 266 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N GLN P 268 " --> pdb=" O VAL P 221 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE P 265 " --> pdb=" O THR P 123 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET P 125 " --> pdb=" O ILE P 265 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN P 267 " --> pdb=" O MET P 125 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY P 127 " --> pdb=" O ASN P 267 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE P 122 " --> pdb=" O THR P 298 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N LEU P 300 " --> pdb=" O ILE P 122 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLU P 124 " --> pdb=" O LEU P 300 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU P 302 " --> pdb=" O GLU P 124 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE P 126 " --> pdb=" O LEU P 302 " (cutoff:3.500A) removed outlier: 9.370A pdb=" N LYS P 304 " --> pdb=" O PHE P 126 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG P 299 " --> pdb=" O TYR P 315 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Q' and resid 189 through 193 removed outlier: 3.592A pdb=" N ALA Q 190 " --> pdb=" O ALA Q 157 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR Q 159 " --> pdb=" O ALA Q 190 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA Q 192 " --> pdb=" O TYR Q 159 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS Q 156 " --> pdb=" O LEU Q 218 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ILE Q 220 " --> pdb=" O LYS Q 156 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N MET Q 158 " --> pdb=" O ILE Q 220 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ASP Q 222 " --> pdb=" O MET Q 158 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE Q 160 " --> pdb=" O ASP Q 222 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA Q 217 " --> pdb=" O ALA Q 262 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL Q 264 " --> pdb=" O ALA Q 217 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU Q 219 " --> pdb=" O VAL Q 264 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR Q 266 " --> pdb=" O LEU Q 219 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL Q 221 " --> pdb=" O THR Q 266 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N GLN Q 268 " --> pdb=" O VAL Q 221 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE Q 265 " --> pdb=" O THR Q 123 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N MET Q 125 " --> pdb=" O ILE Q 265 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN Q 267 " --> pdb=" O MET Q 125 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY Q 127 " --> pdb=" O ASN Q 267 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE Q 122 " --> pdb=" O THR Q 298 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N LEU Q 300 " --> pdb=" O ILE Q 122 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU Q 124 " --> pdb=" O LEU Q 300 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU Q 302 " --> pdb=" O GLU Q 124 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE Q 126 " --> pdb=" O LEU Q 302 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N LYS Q 304 " --> pdb=" O PHE Q 126 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ARG Q 299 " --> pdb=" O TYR Q 315 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'R' and resid 189 through 193 removed outlier: 3.591A pdb=" N ALA R 190 " --> pdb=" O ALA R 157 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR R 159 " --> pdb=" O ALA R 190 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA R 192 " --> pdb=" O TYR R 159 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS R 156 " --> pdb=" O LEU R 218 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ILE R 220 " --> pdb=" O LYS R 156 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N MET R 158 " --> pdb=" O ILE R 220 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ASP R 222 " --> pdb=" O MET R 158 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE R 160 " --> pdb=" O ASP R 222 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA R 217 " --> pdb=" O ALA R 262 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL R 264 " --> pdb=" O ALA R 217 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU R 219 " --> pdb=" O VAL R 264 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR R 266 " --> pdb=" O LEU R 219 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL R 221 " --> pdb=" O THR R 266 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N GLN R 268 " --> pdb=" O VAL R 221 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE R 265 " --> pdb=" O THR R 123 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET R 125 " --> pdb=" O ILE R 265 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN R 267 " --> pdb=" O MET R 125 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY R 127 " --> pdb=" O ASN R 267 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ILE R 122 " --> pdb=" O THR R 298 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N LEU R 300 " --> pdb=" O ILE R 122 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU R 124 " --> pdb=" O LEU R 300 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU R 302 " --> pdb=" O GLU R 124 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N PHE R 126 " --> pdb=" O LEU R 302 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N LYS R 304 " --> pdb=" O PHE R 126 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG R 299 " --> pdb=" O TYR R 315 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'S' and resid 189 through 193 removed outlier: 3.590A pdb=" N ALA S 190 " --> pdb=" O ALA S 157 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR S 159 " --> pdb=" O ALA S 190 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA S 192 " --> pdb=" O TYR S 159 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS S 156 " --> pdb=" O LEU S 218 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N ILE S 220 " --> pdb=" O LYS S 156 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N MET S 158 " --> pdb=" O ILE S 220 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASP S 222 " --> pdb=" O MET S 158 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE S 160 " --> pdb=" O ASP S 222 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA S 217 " --> pdb=" O ALA S 262 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL S 264 " --> pdb=" O ALA S 217 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU S 219 " --> pdb=" O VAL S 264 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N THR S 266 " --> pdb=" O LEU S 219 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL S 221 " --> pdb=" O THR S 266 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N GLN S 268 " --> pdb=" O VAL S 221 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE S 265 " --> pdb=" O THR S 123 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET S 125 " --> pdb=" O ILE S 265 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN S 267 " --> pdb=" O MET S 125 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY S 127 " --> pdb=" O ASN S 267 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ILE S 122 " --> pdb=" O THR S 298 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N LEU S 300 " --> pdb=" O ILE S 122 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLU S 124 " --> pdb=" O LEU S 300 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU S 302 " --> pdb=" O GLU S 124 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N PHE S 126 " --> pdb=" O LEU S 302 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N LYS S 304 " --> pdb=" O PHE S 126 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ARG S 299 " --> pdb=" O TYR S 315 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'T' and resid 189 through 193 removed outlier: 3.590A pdb=" N ALA T 190 " --> pdb=" O ALA T 157 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR T 159 " --> pdb=" O ALA T 190 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA T 192 " --> pdb=" O TYR T 159 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS T 156 " --> pdb=" O LEU T 218 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ILE T 220 " --> pdb=" O LYS T 156 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N MET T 158 " --> pdb=" O ILE T 220 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASP T 222 " --> pdb=" O MET T 158 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE T 160 " --> pdb=" O ASP T 222 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA T 217 " --> pdb=" O ALA T 262 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL T 264 " --> pdb=" O ALA T 217 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU T 219 " --> pdb=" O VAL T 264 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR T 266 " --> pdb=" O LEU T 219 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL T 221 " --> pdb=" O THR T 266 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N GLN T 268 " --> pdb=" O VAL T 221 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE T 265 " --> pdb=" O THR T 123 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N MET T 125 " --> pdb=" O ILE T 265 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN T 267 " --> pdb=" O MET T 125 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY T 127 " --> pdb=" O ASN T 267 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE T 122 " --> pdb=" O THR T 298 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N LEU T 300 " --> pdb=" O ILE T 122 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU T 124 " --> pdb=" O LEU T 300 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU T 302 " --> pdb=" O GLU T 124 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N PHE T 126 " --> pdb=" O LEU T 302 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N LYS T 304 " --> pdb=" O PHE T 126 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG T 299 " --> pdb=" O TYR T 315 " (cutoff:3.500A) 1279 hydrogen bonds defined for protein. 3750 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 383 hydrogen bonds 762 hydrogen bond angles 0 basepair planarities 151 basepair parallelities 269 stacking parallelities Total time for adding SS restraints: 7.49 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.24: 3848 1.24 - 1.39: 9182 1.39 - 1.53: 17107 1.53 - 1.67: 3325 1.67 - 1.81: 211 Bond restraints: 33673 Sorted by residual: bond pdb=" CA ARG Q 167 " pdb=" CB ARG Q 167 " ideal model delta sigma weight residual 1.529 1.363 0.166 1.26e-02 6.30e+03 1.73e+02 bond pdb=" C PRO P 318 " pdb=" O PRO P 318 " ideal model delta sigma weight residual 1.238 1.102 0.136 1.24e-02 6.50e+03 1.20e+02 bond pdb=" CE1 HIS L 47 " pdb=" NE2 HIS L 47 " ideal model delta sigma weight residual 1.321 1.233 0.088 1.00e-02 1.00e+04 7.77e+01 bond pdb=" CE1 HIS M 47 " pdb=" NE2 HIS M 47 " ideal model delta sigma weight residual 1.321 1.234 0.087 1.00e-02 1.00e+04 7.66e+01 bond pdb=" CD2 HIS L 47 " pdb=" NE2 HIS L 47 " ideal model delta sigma weight residual 1.374 1.287 0.087 1.10e-02 8.26e+03 6.27e+01 ... (remaining 33668 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.88: 46316 3.88 - 7.75: 366 7.75 - 11.63: 51 11.63 - 15.51: 2 15.51 - 19.39: 3 Bond angle restraints: 46738 Sorted by residual: angle pdb=" O PRO P 318 " pdb=" C PRO P 318 " pdb=" N CYS P 319 " ideal model delta sigma weight residual 122.22 140.46 -18.24 1.29e+00 6.01e-01 2.00e+02 angle pdb=" CA PRO P 318 " pdb=" C PRO P 318 " pdb=" O PRO P 318 " ideal model delta sigma weight residual 119.55 100.16 19.39 1.52e+00 4.33e-01 1.63e+02 angle pdb=" O5' DC I 151 " pdb=" C5' DC I 151 " pdb=" C4' DC I 151 " ideal model delta sigma weight residual 109.40 117.22 -7.82 8.00e-01 1.56e+00 9.56e+01 angle pdb=" O5' DT J 8 " pdb=" C5' DT J 8 " pdb=" C4' DT J 8 " ideal model delta sigma weight residual 109.40 117.17 -7.77 8.00e-01 1.56e+00 9.42e+01 angle pdb=" O4' DC I 151 " pdb=" C1' DC I 151 " pdb=" N1 DC I 151 " ideal model delta sigma weight residual 108.00 113.51 -5.51 7.00e-01 2.04e+00 6.20e+01 ... (remaining 46733 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.42: 16468 20.42 - 40.83: 1739 40.83 - 61.25: 1288 61.25 - 81.66: 82 81.66 - 102.08: 8 Dihedral angle restraints: 19585 sinusoidal: 9877 harmonic: 9708 Sorted by residual: dihedral pdb=" CD ARG L 215 " pdb=" NE ARG L 215 " pdb=" CZ ARG L 215 " pdb=" NH1 ARG L 215 " ideal model delta sinusoidal sigma weight residual 0.00 87.74 -87.74 1 1.00e+01 1.00e-02 9.22e+01 dihedral pdb=" CD ARG M 247 " pdb=" NE ARG M 247 " pdb=" CZ ARG M 247 " pdb=" NH1 ARG M 247 " ideal model delta sinusoidal sigma weight residual 0.00 -82.75 82.75 1 1.00e+01 1.00e-02 8.39e+01 dihedral pdb=" CD ARG M 27 " pdb=" NE ARG M 27 " pdb=" CZ ARG M 27 " pdb=" NH1 ARG M 27 " ideal model delta sinusoidal sigma weight residual 0.00 59.42 -59.42 1 1.00e+01 1.00e-02 4.72e+01 ... (remaining 19582 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 5167 0.141 - 0.282: 96 0.282 - 0.422: 8 0.422 - 0.563: 41 0.563 - 0.704: 39 Chirality restraints: 5351 Sorted by residual: chirality pdb=" CG LEU M 249 " pdb=" CB LEU M 249 " pdb=" CD1 LEU M 249 " pdb=" CD2 LEU M 249 " both_signs ideal model delta sigma weight residual False -2.59 -1.89 -0.70 2.00e-01 2.50e+01 1.24e+01 chirality pdb=" CB ILE M 122 " pdb=" CA ILE M 122 " pdb=" CG1 ILE M 122 " pdb=" CG2 ILE M 122 " both_signs ideal model delta sigma weight residual False 2.64 1.95 0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" CG LEU L 255 " pdb=" CB LEU L 255 " pdb=" CD1 LEU L 255 " pdb=" CD2 LEU L 255 " both_signs ideal model delta sigma weight residual False -2.59 -1.90 -0.69 2.00e-01 2.50e+01 1.18e+01 ... (remaining 5348 not shown) Planarity restraints: 4942 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 215 " 1.106 9.50e-02 1.11e+02 4.96e-01 1.48e+02 pdb=" NE ARG L 215 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG L 215 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG L 215 " 0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG L 215 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG M 247 " -1.084 9.50e-02 1.11e+02 4.86e-01 1.42e+02 pdb=" NE ARG M 247 " 0.068 2.00e-02 2.50e+03 pdb=" CZ ARG M 247 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG M 247 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG M 247 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG M 27 " -0.949 9.50e-02 1.11e+02 4.25e-01 1.09e+02 pdb=" NE ARG M 27 " 0.056 2.00e-02 2.50e+03 pdb=" CZ ARG M 27 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG M 27 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG M 27 " -0.025 2.00e-02 2.50e+03 ... (remaining 4939 not shown) Histogram of nonbonded interaction distances: 1.12 - 1.87: 29 1.87 - 2.63: 635 2.63 - 3.39: 44970 3.39 - 4.14: 86970 4.14 - 4.90: 144465 Nonbonded interactions: 277069 Sorted by model distance: nonbonded pdb=" OG1 THR L 48 " pdb=" OE2 GLU L 258 " model vdw 1.118 3.040 nonbonded pdb=" O PRO P 318 " pdb=" CB ARG Q 167 " model vdw 1.260 3.440 nonbonded pdb=" OE2 GLU R 322 " pdb=" O ILE S 329 " model vdw 1.303 3.040 nonbonded pdb=" CB PRO P 318 " pdb=" O PHE Q 166 " model vdw 1.312 3.440 nonbonded pdb=" OP1 DC I 152 " pdb=" CG ARG R 235 " model vdw 1.329 3.440 ... (remaining 277064 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 133) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 25 through 101) } ncs_group { reference = (chain 'C' and resid 15 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 33 through 123) selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 32.860 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 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 : 0.010 0.426 33682 Z= 0.744 Angle : 0.995 19.386 46738 Z= 0.706 Chirality : 0.089 0.704 5351 Planarity : 0.015 0.496 4942 Dihedral : 20.920 102.079 13367 Min Nonbonded Distance : 1.118 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.15 % Allowed : 1.06 % Favored : 98.79 % Cbeta Deviations : 0.84 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.13), residues: 3328 helix: -0.01 (0.12), residues: 1618 sheet: 0.79 (0.20), residues: 530 loop : -0.25 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG M 250 TYR 0.023 0.003 TYR H 37 PHE 0.026 0.002 PHE E 78 HIS 0.011 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00909 / 0.62 (33673) covalent geometry : angle 0.99536 / 0.71 (46738) hydrogen bonds : bond 0.17716 / 12.09 ( 1662) hydrogen bonds : angle 6.40682 / 4.65 ( 4512) Misc. bond : bond 0.24884 / 15.20 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 472 time to evaluate : 1.110 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: A 97 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8357 (mm-30) REVERT: B 49 LEU cc_start: 0.9705 (mt) cc_final: 0.8921 (mp) REVERT: B 74 GLU cc_start: 0.9139 (tt0) cc_final: 0.8630 (tm-30) REVERT: B 92 ARG cc_start: 0.9182 (ptm-80) cc_final: 0.8869 (ttp80) REVERT: C 25 PHE cc_start: 0.8795 (m-80) cc_final: 0.8303 (m-10) REVERT: C 90 ASP cc_start: 0.9085 (t70) cc_final: 0.8786 (t0) REVERT: C 102 ILE cc_start: 0.9276 (mm) cc_final: 0.9062 (tp) REVERT: D 43 LYS cc_start: 0.9317 (mttt) cc_final: 0.9103 (mmmm) REVERT: D 80 LEU cc_start: 0.9625 (mt) cc_final: 0.9424 (tp) REVERT: E 68 GLN cc_start: 0.9321 (tt0) cc_final: 0.9076 (pp30) REVERT: E 93 GLN cc_start: 0.9425 (tt0) cc_final: 0.8682 (tp40) REVERT: E 97 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8493 (mm-30) REVERT: E 130 ILE cc_start: 0.9284 (mt) cc_final: 0.8988 (mt) REVERT: F 35 ARG cc_start: 0.9252 (ttp-110) cc_final: 0.9020 (ttm110) REVERT: F 43 VAL cc_start: 0.9523 (t) cc_final: 0.9246 (p) REVERT: F 44 LYS cc_start: 0.8819 (tttt) cc_final: 0.8427 (tppt) REVERT: F 65 VAL cc_start: 0.9667 (t) cc_final: 0.9419 (p) REVERT: G 55 LEU cc_start: 0.9651 (mt) cc_final: 0.9423 (mt) REVERT: G 56 GLU cc_start: 0.9031 (tt0) cc_final: 0.8466 (tt0) REVERT: K 198 ASP cc_start: 0.8690 (t70) cc_final: 0.8307 (m-30) REVERT: K 318 PRO cc_start: 0.5211 (Cg_exo) cc_final: 0.4669 (Cg_endo) REVERT: L 58 LYS cc_start: 0.8462 (tppt) cc_final: 0.8207 (tptp) REVERT: L 125 MET cc_start: 0.8158 (pmm) cc_final: 0.7641 (pmm) REVERT: L 158 MET cc_start: 0.6854 (mmm) cc_final: 0.6531 (mmm) REVERT: L 210 MET cc_start: 0.7650 (tmm) cc_final: 0.7388 (tmm) REVERT: L 244 HIS cc_start: 0.8948 (t70) cc_final: 0.8448 (t-90) REVERT: M 60 LEU cc_start: 0.9520 (mt) cc_final: 0.9291 (tp) REVERT: M 248 PHE cc_start: 0.9589 (t80) cc_final: 0.9188 (t80) REVERT: N 129 PHE cc_start: 0.8086 (p90) cc_final: 0.7749 (p90) REVERT: N 290 ASN cc_start: 0.7675 (m-40) cc_final: 0.7131 (p0) REVERT: N 326 MET cc_start: 0.8738 (tpt) cc_final: 0.8271 (tpp) REVERT: O 195 PHE cc_start: 0.4616 (m-10) cc_final: 0.4166 (t80) REVERT: P 326 MET cc_start: 0.1786 (tpt) cc_final: 0.0550 (mtp) REVERT: R 30 GLN cc_start: -0.2648 (mp10) cc_final: -0.2948 (mm110) REVERT: S 210 MET cc_start: 0.1480 (tmm) cc_final: 0.0541 (tpp) REVERT: S 211 MET cc_start: 0.1390 (ttm) cc_final: 0.0865 (mtt) REVERT: S 243 MET cc_start: 0.2258 (mmt) cc_final: 0.1748 (tmm) REVERT: T 63 ILE cc_start: -0.0783 (mt) cc_final: -0.1100 (mm) REVERT: T 210 MET cc_start: 0.2232 (tmm) cc_final: 0.1183 (ttt) REVERT: T 251 MET cc_start: -0.0819 (mtp) cc_final: -0.1353 (mmm) outliers start: 4 outliers final: 0 residues processed: 473 average time/residue: 0.2355 time to fit residues: 172.7172 Evaluate side-chains 222 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 197 optimal weight: 30.0000 chunk 215 optimal weight: 50.0000 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 40.0000 chunk 183 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 67.9558 > 50:) chunk 298 optimal weight: 20.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN D 84 ASN E 68 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN ** L 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 47 HIS N 47 HIS N 294 HIS O 294 HIS ** P 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 HIS R 23 GLN R 294 HIS T 23 GLN ** T 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.090971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.064278 restraints weight = 299805.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.065228 restraints weight = 139602.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.065288 restraints weight = 88906.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.065676 restraints weight = 67894.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.065724 restraints weight = 56935.109| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 33682 Z= 0.221 Angle : 0.725 12.864 46738 Z= 0.404 Chirality : 0.047 0.277 5351 Planarity : 0.006 0.096 4942 Dihedral : 25.582 91.042 7123 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.11 % Allowed : 2.48 % Favored : 97.41 % 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: 0.45 (0.14), residues: 3328 helix: 0.95 (0.12), residues: 1707 sheet: 0.53 (0.21), residues: 528 loop : -0.73 (0.17), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 241 TYR 0.045 0.003 TYR Q 54 PHE 0.035 0.002 PHE C 25 HIS 0.036 0.002 HIS L 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.22 (33673) covalent geometry : angle 0.72488 / 0.40 (46738) hydrogen bonds : bond 0.06776 / 4.61 ( 1662) hydrogen bonds : angle 5.18433 / 3.81 ( 4512) Misc. bond : bond 0.01079 / 0.52 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 284 time to evaluate : 1.224 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: A 50 GLU cc_start: 0.8927 (tp30) cc_final: 0.8508 (tp30) REVERT: A 120 MET cc_start: 0.8835 (mmp) cc_final: 0.8548 (mmm) REVERT: B 37 LEU cc_start: 0.9752 (mm) cc_final: 0.9537 (mm) REVERT: B 49 LEU cc_start: 0.9408 (mt) cc_final: 0.8876 (mm) REVERT: B 60 VAL cc_start: 0.9744 (t) cc_final: 0.9434 (p) REVERT: B 74 GLU cc_start: 0.9046 (tt0) cc_final: 0.8494 (tm-30) REVERT: B 84 MET cc_start: 0.8905 (mmp) cc_final: 0.8685 (tpp) REVERT: C 90 ASP cc_start: 0.8961 (t70) cc_final: 0.8685 (t0) REVERT: C 102 ILE cc_start: 0.9443 (mm) cc_final: 0.9227 (tp) REVERT: D 93 GLU cc_start: 0.9159 (mp0) cc_final: 0.8875 (mp0) REVERT: E 57 SER cc_start: 0.9243 (p) cc_final: 0.8811 (p) REVERT: E 68 GLN cc_start: 0.9396 (tt0) cc_final: 0.9124 (pp30) REVERT: E 93 GLN cc_start: 0.9223 (tt0) cc_final: 0.8831 (tp40) REVERT: E 105 GLU cc_start: 0.7622 (pp20) cc_final: 0.7248 (pp20) REVERT: E 106 ASP cc_start: 0.8357 (m-30) cc_final: 0.8130 (m-30) REVERT: E 119 ILE cc_start: 0.9320 (pt) cc_final: 0.8866 (pt) REVERT: F 44 LYS cc_start: 0.8815 (tttt) cc_final: 0.8566 (tppt) REVERT: F 79 LYS cc_start: 0.9413 (mppt) cc_final: 0.9114 (mmtm) REVERT: F 85 ASP cc_start: 0.8217 (m-30) cc_final: 0.7979 (m-30) REVERT: G 56 GLU cc_start: 0.8898 (tt0) cc_final: 0.8331 (tt0) REVERT: H 64 SER cc_start: 0.9238 (m) cc_final: 0.8571 (t) REVERT: K 46 PHE cc_start: 0.8775 (m-80) cc_final: 0.8212 (m-80) REVERT: K 68 GLU cc_start: 0.9728 (pm20) cc_final: 0.9452 (pm20) REVERT: K 198 ASP cc_start: 0.8654 (t70) cc_final: 0.8164 (m-30) REVERT: L 125 MET cc_start: 0.8152 (pmm) cc_final: 0.7836 (pmm) REVERT: L 158 MET cc_start: 0.6378 (mmm) cc_final: 0.6086 (mmm) REVERT: L 244 HIS cc_start: 0.8768 (t70) cc_final: 0.8501 (t-90) REVERT: L 251 MET cc_start: 0.9284 (mtm) cc_final: 0.8524 (mmm) REVERT: M 248 PHE cc_start: 0.9643 (t80) cc_final: 0.9358 (t80) REVERT: M 251 MET cc_start: 0.9552 (tpt) cc_final: 0.9260 (tpp) REVERT: N 52 VAL cc_start: -0.0359 (m) cc_final: -0.1124 (t) REVERT: N 290 ASN cc_start: 0.7634 (m-40) cc_final: 0.7257 (p0) REVERT: N 326 MET cc_start: 0.8617 (tpt) cc_final: 0.8281 (tpp) REVERT: P 210 MET cc_start: 0.0865 (ppp) cc_final: 0.0190 (ppp) REVERT: P 326 MET cc_start: 0.1234 (tpt) cc_final: 0.0258 (mtt) REVERT: R 211 MET cc_start: 0.0312 (tpp) cc_final: -0.0421 (tpp) REVERT: R 251 MET cc_start: 0.7061 (mtp) cc_final: 0.6817 (mtp) REVERT: S 210 MET cc_start: 0.0879 (tmm) cc_final: 0.0582 (tmm) REVERT: S 211 MET cc_start: -0.0980 (ttm) cc_final: -0.1431 (mtt) REVERT: S 243 MET cc_start: 0.2136 (mmt) cc_final: 0.1651 (tmm) REVERT: T 158 MET cc_start: -0.3406 (mtm) cc_final: -0.3756 (mtm) REVERT: T 191 TYR cc_start: 0.7331 (p90) cc_final: 0.7083 (t80) REVERT: T 210 MET cc_start: -0.0612 (tmm) cc_final: -0.1076 (ttt) REVERT: T 251 MET cc_start: -0.2168 (mtp) cc_final: -0.2963 (mmm) outliers start: 3 outliers final: 1 residues processed: 287 average time/residue: 0.2007 time to fit residues: 93.9139 Evaluate side-chains 201 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 200 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 32 optimal weight: 3.9990 chunk 120 optimal weight: 0.0070 chunk 63 optimal weight: 4.9990 chunk 267 optimal weight: 30.0000 chunk 8 optimal weight: 1.9990 chunk 310 optimal weight: 6.9990 chunk 83 optimal weight: 30.0000 chunk 305 optimal weight: 9.9990 chunk 306 optimal weight: 50.0000 chunk 143 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN P 114 GLN ** T 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.091349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.064543 restraints weight = 295373.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.064578 restraints weight = 121460.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.065151 restraints weight = 67247.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.065638 restraints weight = 47791.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.065775 restraints weight = 40692.160| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 33682 Z= 0.149 Angle : 0.614 11.553 46738 Z= 0.345 Chirality : 0.044 0.253 5351 Planarity : 0.004 0.057 4942 Dihedral : 25.415 91.629 7123 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 0.04 % Allowed : 2.34 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.14), residues: 3328 helix: 1.14 (0.13), residues: 1717 sheet: 0.96 (0.23), residues: 455 loop : -0.81 (0.16), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 306 TYR 0.032 0.002 TYR Q 54 PHE 0.026 0.002 PHE K 195 HIS 0.035 0.002 HIS L 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (33673) covalent geometry : angle 0.61396 / 0.34 (46738) hydrogen bonds : bond 0.05617 / 3.80 ( 1662) hydrogen bonds : angle 4.66710 / 3.43 ( 4512) Misc. bond : bond 0.00670 / 0.32 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 264 time to evaluate : 1.147 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: A 50 GLU cc_start: 0.8900 (tp30) cc_final: 0.8690 (tp30) REVERT: A 106 ASP cc_start: 0.8779 (t70) cc_final: 0.8443 (t70) REVERT: B 49 LEU cc_start: 0.9357 (mt) cc_final: 0.9134 (mt) REVERT: B 60 VAL cc_start: 0.9751 (t) cc_final: 0.9468 (p) REVERT: B 63 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8756 (mt-10) REVERT: B 68 ASP cc_start: 0.8713 (m-30) cc_final: 0.8511 (m-30) REVERT: C 72 ASP cc_start: 0.8309 (m-30) cc_final: 0.8086 (m-30) REVERT: C 102 ILE cc_start: 0.9472 (mm) cc_final: 0.9219 (tp) REVERT: D 93 GLU cc_start: 0.9035 (mp0) cc_final: 0.8737 (mp0) REVERT: E 93 GLN cc_start: 0.9124 (tt0) cc_final: 0.8853 (tp40) REVERT: E 105 GLU cc_start: 0.8046 (pp20) cc_final: 0.7437 (pp20) REVERT: E 106 ASP cc_start: 0.8497 (m-30) cc_final: 0.8210 (m-30) REVERT: E 119 ILE cc_start: 0.9319 (pt) cc_final: 0.9058 (pt) REVERT: E 120 MET cc_start: 0.8772 (mmp) cc_final: 0.8072 (mmm) REVERT: F 44 LYS cc_start: 0.8817 (tttt) cc_final: 0.8571 (tppt) REVERT: F 63 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8519 (tm-30) REVERT: F 79 LYS cc_start: 0.9377 (mppt) cc_final: 0.9099 (mmtm) REVERT: G 56 GLU cc_start: 0.8831 (tt0) cc_final: 0.8236 (mt-10) REVERT: H 59 MET cc_start: 0.8785 (tpp) cc_final: 0.8546 (tpp) REVERT: H 100 LEU cc_start: 0.9185 (tp) cc_final: 0.8923 (tt) REVERT: K 46 PHE cc_start: 0.8772 (m-80) cc_final: 0.8215 (m-80) REVERT: K 68 GLU cc_start: 0.9709 (pm20) cc_final: 0.9454 (pm20) REVERT: K 158 MET cc_start: 0.5924 (tpp) cc_final: 0.5598 (tpp) REVERT: K 198 ASP cc_start: 0.8545 (t70) cc_final: 0.8167 (m-30) REVERT: K 211 MET cc_start: 0.5729 (tpt) cc_final: 0.5366 (mmm) REVERT: L 125 MET cc_start: 0.8077 (pmm) cc_final: 0.7714 (pmm) REVERT: L 210 MET cc_start: 0.7195 (ppp) cc_final: 0.6957 (ppp) REVERT: L 244 HIS cc_start: 0.8791 (t70) cc_final: 0.8473 (t-90) REVERT: L 251 MET cc_start: 0.9226 (mtm) cc_final: 0.8325 (mmm) REVERT: M 248 PHE cc_start: 0.9557 (t80) cc_final: 0.9323 (t80) REVERT: M 251 MET cc_start: 0.9547 (tpt) cc_final: 0.9195 (tpp) REVERT: N 52 VAL cc_start: -0.1330 (m) cc_final: -0.2327 (t) REVERT: N 158 MET cc_start: 0.9061 (tmm) cc_final: 0.8767 (tmm) REVERT: N 290 ASN cc_start: 0.7653 (m-40) cc_final: 0.7344 (p0) REVERT: N 326 MET cc_start: 0.8490 (tpt) cc_final: 0.8152 (tpp) REVERT: O 211 MET cc_start: 0.0664 (ttm) cc_final: 0.0264 (ttm) REVERT: P 158 MET cc_start: -0.1845 (ptp) cc_final: -0.2407 (ptp) REVERT: P 210 MET cc_start: 0.0016 (ppp) cc_final: -0.0400 (ppp) REVERT: P 326 MET cc_start: 0.0712 (tpt) cc_final: 0.0005 (mtt) REVERT: R 243 MET cc_start: 0.3831 (mmt) cc_final: 0.3386 (ppp) REVERT: S 210 MET cc_start: 0.0510 (tmm) cc_final: 0.0264 (tmm) REVERT: S 211 MET cc_start: 0.2100 (ttm) cc_final: 0.1343 (mtt) REVERT: S 243 MET cc_start: 0.2362 (mmt) cc_final: 0.1798 (tmm) REVERT: T 158 MET cc_start: -0.3278 (mtm) cc_final: -0.3588 (mtm) REVERT: T 210 MET cc_start: -0.0143 (tmm) cc_final: -0.0393 (ttt) REVERT: T 251 MET cc_start: -0.1665 (mtp) cc_final: -0.2323 (tpp) outliers start: 1 outliers final: 1 residues processed: 265 average time/residue: 0.1973 time to fit residues: 86.9188 Evaluate side-chains 190 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 341 optimal weight: 40.0000 chunk 343 optimal weight: 50.0000 chunk 2 optimal weight: 5.9990 chunk 160 optimal weight: 0.9980 chunk 122 optimal weight: 20.0000 chunk 158 optimal weight: 9.9990 chunk 295 optimal weight: 8.9990 chunk 273 optimal weight: 9.9990 chunk 73 optimal weight: 50.0000 chunk 282 optimal weight: 6.9990 chunk 337 optimal weight: 8.9990 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 49 HIS ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN K 23 GLN K 47 HIS ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 GLN ** T 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 294 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.089179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.062120 restraints weight = 295689.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.061954 restraints weight = 124720.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.062512 restraints weight = 69720.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.062924 restraints weight = 50221.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.063039 restraints weight = 42297.687| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 33682 Z= 0.219 Angle : 0.667 13.574 46738 Z= 0.367 Chirality : 0.044 0.263 5351 Planarity : 0.004 0.058 4942 Dihedral : 25.363 90.841 7123 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.14), residues: 3328 helix: 1.07 (0.12), residues: 1719 sheet: 0.90 (0.23), residues: 462 loop : -0.75 (0.17), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 99 TYR 0.040 0.002 TYR F 88 PHE 0.051 0.002 PHE T 248 HIS 0.037 0.003 HIS L 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.22 (33673) covalent geometry : angle 0.66693 / 0.37 (46738) hydrogen bonds : bond 0.06430 / 4.38 ( 1662) hydrogen bonds : angle 4.68284 / 3.45 ( 4512) Misc. bond : bond 0.00864 / 0.41 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.935 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: A 50 GLU cc_start: 0.8971 (tp30) cc_final: 0.8532 (tp30) REVERT: B 49 LEU cc_start: 0.9283 (mt) cc_final: 0.8184 (mm) REVERT: B 60 VAL cc_start: 0.9732 (t) cc_final: 0.9413 (p) REVERT: B 85 ASP cc_start: 0.8441 (m-30) cc_final: 0.8215 (m-30) REVERT: C 72 ASP cc_start: 0.8245 (m-30) cc_final: 0.8030 (m-30) REVERT: D 93 GLU cc_start: 0.9030 (mp0) cc_final: 0.8747 (mp0) REVERT: E 68 GLN cc_start: 0.9415 (tt0) cc_final: 0.9138 (pp30) REVERT: E 93 GLN cc_start: 0.9222 (tt0) cc_final: 0.8819 (tp40) REVERT: E 120 MET cc_start: 0.8953 (mmp) cc_final: 0.8346 (mmm) REVERT: F 43 VAL cc_start: 0.9556 (t) cc_final: 0.9347 (p) REVERT: F 79 LYS cc_start: 0.9406 (mppt) cc_final: 0.9099 (mmtm) REVERT: F 88 TYR cc_start: 0.9086 (m-80) cc_final: 0.8884 (m-10) REVERT: G 56 GLU cc_start: 0.8856 (tt0) cc_final: 0.8341 (mt-10) REVERT: H 93 GLU cc_start: 0.9389 (mp0) cc_final: 0.9161 (mp0) REVERT: K 46 PHE cc_start: 0.8762 (m-80) cc_final: 0.8254 (m-80) REVERT: K 68 GLU cc_start: 0.9680 (pm20) cc_final: 0.9418 (pm20) REVERT: K 198 ASP cc_start: 0.8667 (t70) cc_final: 0.8306 (m-30) REVERT: L 125 MET cc_start: 0.8074 (pmm) cc_final: 0.7766 (pmm) REVERT: L 137 CYS cc_start: 0.8475 (m) cc_final: 0.8262 (m) REVERT: L 158 MET cc_start: 0.7080 (mmp) cc_final: 0.6718 (mmm) REVERT: L 244 HIS cc_start: 0.8841 (t70) cc_final: 0.8501 (t-90) REVERT: M 251 MET cc_start: 0.9548 (tpt) cc_final: 0.9196 (tpp) REVERT: N 52 VAL cc_start: -0.0857 (m) cc_final: -0.1870 (t) REVERT: N 158 MET cc_start: 0.9279 (tmm) cc_final: 0.8753 (tmm) REVERT: N 290 ASN cc_start: 0.7627 (m-40) cc_final: 0.7301 (p0) REVERT: N 326 MET cc_start: 0.8247 (tpt) cc_final: 0.7907 (tpp) REVERT: O 211 MET cc_start: 0.0849 (ttm) cc_final: 0.0472 (ttm) REVERT: P 158 MET cc_start: -0.2771 (ptp) cc_final: -0.2988 (ptp) REVERT: P 210 MET cc_start: 0.0066 (ppp) cc_final: -0.0183 (ppp) REVERT: P 326 MET cc_start: 0.0348 (tpt) cc_final: -0.0197 (mtt) REVERT: S 211 MET cc_start: 0.1919 (ttm) cc_final: 0.1262 (mtt) REVERT: S 243 MET cc_start: 0.2428 (mmt) cc_final: 0.1886 (tmm) REVERT: T 251 MET cc_start: -0.1327 (mtp) cc_final: -0.1968 (tpp) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1829 time to fit residues: 70.3955 Evaluate side-chains 176 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 197 optimal weight: 10.0000 chunk 257 optimal weight: 40.0000 chunk 82 optimal weight: 20.0000 chunk 64 optimal weight: 0.9990 chunk 263 optimal weight: 50.0000 chunk 278 optimal weight: 30.0000 chunk 223 optimal weight: 50.0000 chunk 33 optimal weight: 0.8980 chunk 267 optimal weight: 10.0000 chunk 108 optimal weight: 30.0000 chunk 350 optimal weight: 7.9990 overall best weight: 5.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.077770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.048439 restraints weight = 267270.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.050066 restraints weight = 119220.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.050938 restraints weight = 71561.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.051371 restraints weight = 53131.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.051561 restraints weight = 45157.971| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 33682 Z= 0.199 Angle : 0.631 13.649 46738 Z= 0.350 Chirality : 0.044 0.281 5351 Planarity : 0.004 0.043 4942 Dihedral : 25.358 92.094 7123 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.04 % Allowed : 1.64 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.14), residues: 3328 helix: 1.04 (0.12), residues: 1725 sheet: 0.92 (0.23), residues: 469 loop : -0.70 (0.17), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG N 193 TYR 0.028 0.002 TYR F 88 PHE 0.036 0.002 PHE T 248 HIS 0.036 0.002 HIS T 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.20 (33673) covalent geometry : angle 0.63150 / 0.35 (46738) hydrogen bonds : bond 0.05638 / 3.83 ( 1662) hydrogen bonds : angle 4.47317 / 3.28 ( 4512) Misc. bond : bond 0.00659 / 0.32 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 225 time to evaluate : 1.216 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: A 50 GLU cc_start: 0.9034 (tp30) cc_final: 0.8587 (tp30) REVERT: B 49 LEU cc_start: 0.9251 (mt) cc_final: 0.8640 (mm) REVERT: B 60 VAL cc_start: 0.9737 (t) cc_final: 0.9416 (p) REVERT: B 85 ASP cc_start: 0.8541 (m-30) cc_final: 0.8280 (m-30) REVERT: C 72 ASP cc_start: 0.8319 (m-30) cc_final: 0.8079 (m-30) REVERT: C 90 ASP cc_start: 0.8924 (t0) cc_final: 0.8705 (t0) REVERT: E 68 GLN cc_start: 0.9333 (tt0) cc_final: 0.9093 (pp30) REVERT: E 93 GLN cc_start: 0.9192 (tt0) cc_final: 0.8872 (tp40) REVERT: E 106 ASP cc_start: 0.8790 (t70) cc_final: 0.8564 (t70) REVERT: E 119 ILE cc_start: 0.9382 (pt) cc_final: 0.9145 (pt) REVERT: E 120 MET cc_start: 0.8953 (mmp) cc_final: 0.8220 (mmm) REVERT: F 79 LYS cc_start: 0.9378 (mppt) cc_final: 0.9023 (mmtm) REVERT: H 59 MET cc_start: 0.9040 (tpp) cc_final: 0.8703 (tpp) REVERT: K 46 PHE cc_start: 0.8613 (m-80) cc_final: 0.7887 (m-80) REVERT: K 68 GLU cc_start: 0.9668 (pm20) cc_final: 0.9400 (pm20) REVERT: K 198 ASP cc_start: 0.8524 (t70) cc_final: 0.8132 (m-30) REVERT: K 211 MET cc_start: 0.6171 (tpt) cc_final: 0.5794 (mmm) REVERT: L 125 MET cc_start: 0.8037 (pmm) cc_final: 0.7732 (pmm) REVERT: L 158 MET cc_start: 0.6975 (mmp) cc_final: 0.6605 (mmm) REVERT: L 210 MET cc_start: 0.7088 (ppp) cc_final: 0.6878 (ppp) REVERT: M 251 MET cc_start: 0.9537 (tpt) cc_final: 0.9126 (tpp) REVERT: N 52 VAL cc_start: 0.2994 (m) cc_final: 0.2778 (t) REVERT: N 158 MET cc_start: 0.9226 (tmm) cc_final: 0.8674 (tmm) REVERT: N 290 ASN cc_start: 0.7383 (m-40) cc_final: 0.6917 (p0) REVERT: N 326 MET cc_start: 0.8134 (tpt) cc_final: 0.7861 (tpp) REVERT: O 251 MET cc_start: -0.1342 (ttm) cc_final: -0.1543 (ttm) REVERT: P 158 MET cc_start: -0.2886 (ptp) cc_final: -0.3227 (ptp) REVERT: P 326 MET cc_start: -0.0115 (tpt) cc_final: -0.0593 (mtt) REVERT: S 210 MET cc_start: -0.1028 (tmm) cc_final: -0.1379 (tmm) REVERT: S 211 MET cc_start: 0.0296 (ttm) cc_final: -0.0516 (mtt) REVERT: S 243 MET cc_start: 0.2198 (mmt) cc_final: 0.1516 (tmm) REVERT: T 251 MET cc_start: -0.2329 (mtp) cc_final: -0.3101 (mmm) outliers start: 1 outliers final: 1 residues processed: 226 average time/residue: 0.1901 time to fit residues: 71.9743 Evaluate side-chains 168 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 36 optimal weight: 0.9980 chunk 136 optimal weight: 6.9990 chunk 173 optimal weight: 10.0000 chunk 89 optimal weight: 30.0000 chunk 351 optimal weight: 6.9990 chunk 319 optimal weight: 7.9990 chunk 110 optimal weight: 50.0000 chunk 267 optimal weight: 9.9990 chunk 157 optimal weight: 0.0570 chunk 347 optimal weight: 50.0000 chunk 253 optimal weight: 50.0000 overall best weight: 4.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 HIS ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 47 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.088692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.061775 restraints weight = 299265.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.061669 restraints weight = 125187.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.062310 restraints weight = 70102.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.062596 restraints weight = 49973.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.062827 restraints weight = 42295.166| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 33682 Z= 0.173 Angle : 0.611 14.345 46738 Z= 0.341 Chirality : 0.044 0.275 5351 Planarity : 0.004 0.042 4942 Dihedral : 25.300 93.595 7123 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.14), residues: 3328 helix: 1.18 (0.12), residues: 1726 sheet: 0.92 (0.23), residues: 469 loop : -0.64 (0.17), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 193 TYR 0.041 0.002 TYR F 88 PHE 0.020 0.002 PHE T 248 HIS 0.020 0.002 HIS T 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.17 (33673) covalent geometry : angle 0.61141 / 0.34 (46738) hydrogen bonds : bond 0.05424 / 3.69 ( 1662) hydrogen bonds : angle 4.25302 / 3.11 ( 4512) Misc. bond : bond 0.00931 / 0.46 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 1.114 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: A 50 GLU cc_start: 0.8966 (tp30) cc_final: 0.8575 (tp30) REVERT: A 106 ASP cc_start: 0.8707 (t70) cc_final: 0.8331 (t70) REVERT: B 49 LEU cc_start: 0.9189 (mt) cc_final: 0.8435 (mm) REVERT: B 60 VAL cc_start: 0.9726 (t) cc_final: 0.9339 (p) REVERT: B 63 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8691 (mt-10) REVERT: C 72 ASP cc_start: 0.8277 (m-30) cc_final: 0.8033 (m-30) REVERT: E 68 GLN cc_start: 0.9378 (tt0) cc_final: 0.9142 (pp30) REVERT: E 93 GLN cc_start: 0.9188 (tt0) cc_final: 0.8806 (tp40) REVERT: E 119 ILE cc_start: 0.9470 (pt) cc_final: 0.9140 (pt) REVERT: E 120 MET cc_start: 0.8875 (mmp) cc_final: 0.8176 (mmm) REVERT: F 79 LYS cc_start: 0.9370 (mppt) cc_final: 0.8994 (mmtm) REVERT: G 56 GLU cc_start: 0.8848 (tt0) cc_final: 0.8211 (mt-10) REVERT: K 46 PHE cc_start: 0.8549 (m-80) cc_final: 0.7915 (m-80) REVERT: K 198 ASP cc_start: 0.8560 (t70) cc_final: 0.8168 (m-30) REVERT: K 211 MET cc_start: 0.6426 (tpt) cc_final: 0.5809 (mmm) REVERT: L 125 MET cc_start: 0.8289 (pmm) cc_final: 0.7979 (pmm) REVERT: L 158 MET cc_start: 0.6997 (mmp) cc_final: 0.6648 (mmm) REVERT: L 210 MET cc_start: 0.7063 (ppp) cc_final: 0.6819 (ppp) REVERT: M 251 MET cc_start: 0.9545 (tpt) cc_final: 0.9180 (tpp) REVERT: N 52 VAL cc_start: 0.0406 (m) cc_final: -0.0714 (t) REVERT: N 290 ASN cc_start: 0.7393 (m-40) cc_final: 0.6945 (p0) REVERT: N 326 MET cc_start: 0.8203 (tpt) cc_final: 0.8002 (tpp) REVERT: O 211 MET cc_start: -0.0281 (ttm) cc_final: -0.0544 (ttm) REVERT: P 158 MET cc_start: -0.2777 (ptp) cc_final: -0.3126 (ptp) REVERT: P 326 MET cc_start: -0.0169 (tpt) cc_final: -0.0586 (mtt) REVERT: Q 338 LYS cc_start: 0.5366 (mmtt) cc_final: 0.4461 (mptt) REVERT: R 72 ASP cc_start: 0.6514 (p0) cc_final: 0.6237 (t70) REVERT: S 211 MET cc_start: 0.1368 (ttm) cc_final: 0.0680 (mtt) REVERT: S 243 MET cc_start: 0.2163 (mmt) cc_final: 0.1562 (tmm) REVERT: S 251 MET cc_start: 0.4314 (ptt) cc_final: 0.4078 (ptt) REVERT: T 251 MET cc_start: -0.1550 (mtp) cc_final: -0.2087 (tpp) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.1878 time to fit residues: 72.2434 Evaluate side-chains 172 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 29 optimal weight: 2.9990 chunk 98 optimal weight: 40.0000 chunk 305 optimal weight: 5.9990 chunk 360 optimal weight: 40.0000 chunk 289 optimal weight: 2.9990 chunk 229 optimal weight: 9.9990 chunk 261 optimal weight: 30.0000 chunk 113 optimal weight: 40.0000 chunk 43 optimal weight: 2.9990 chunk 81 optimal weight: 40.0000 chunk 164 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 206 GLN N 47 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.088327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.061522 restraints weight = 300209.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.061350 restraints weight = 128260.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.061985 restraints weight = 71174.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.062300 restraints weight = 50143.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.062516 restraints weight = 41995.962| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 33682 Z= 0.170 Angle : 0.604 14.673 46738 Z= 0.336 Chirality : 0.044 0.259 5351 Planarity : 0.004 0.083 4942 Dihedral : 25.247 95.284 7123 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.14), residues: 3328 helix: 1.21 (0.12), residues: 1742 sheet: 0.92 (0.24), residues: 462 loop : -0.60 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 229 TYR 0.026 0.002 TYR L 54 PHE 0.027 0.002 PHE K 195 HIS 0.025 0.002 HIS N 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.17 (33673) covalent geometry : angle 0.60380 / 0.34 (46738) hydrogen bonds : bond 0.05248 / 3.56 ( 1662) hydrogen bonds : angle 4.12924 / 3.00 ( 4512) Misc. bond : bond 0.00592 / 0.29 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 1.231 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: A 50 GLU cc_start: 0.9002 (tp30) cc_final: 0.8574 (tp30) REVERT: A 106 ASP cc_start: 0.8748 (t70) cc_final: 0.8260 (t70) REVERT: B 49 LEU cc_start: 0.9164 (mt) cc_final: 0.8379 (mm) REVERT: B 60 VAL cc_start: 0.9715 (t) cc_final: 0.9244 (p) REVERT: B 63 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8698 (mt-10) REVERT: E 68 GLN cc_start: 0.9374 (tt0) cc_final: 0.9122 (pp30) REVERT: E 93 GLN cc_start: 0.9203 (tt0) cc_final: 0.8875 (tp40) REVERT: E 119 ILE cc_start: 0.9446 (pt) cc_final: 0.9007 (pt) REVERT: E 120 MET cc_start: 0.8984 (mmp) cc_final: 0.8350 (mmm) REVERT: F 79 LYS cc_start: 0.9369 (mppt) cc_final: 0.8961 (mmtm) REVERT: K 46 PHE cc_start: 0.8555 (m-80) cc_final: 0.7922 (m-80) REVERT: K 198 ASP cc_start: 0.8570 (t70) cc_final: 0.8171 (m-30) REVERT: K 211 MET cc_start: 0.6359 (tpt) cc_final: 0.5674 (mmm) REVERT: L 125 MET cc_start: 0.8451 (pmm) cc_final: 0.8209 (pmm) REVERT: L 158 MET cc_start: 0.7137 (mmp) cc_final: 0.6801 (mmm) REVERT: L 210 MET cc_start: 0.7174 (ppp) cc_final: 0.6941 (ppp) REVERT: M 251 MET cc_start: 0.9543 (tpt) cc_final: 0.9203 (tpp) REVERT: N 290 ASN cc_start: 0.7326 (m-40) cc_final: 0.6871 (p0) REVERT: O 176 GLU cc_start: 0.8615 (pp20) cc_final: 0.8353 (pt0) REVERT: O 211 MET cc_start: -0.0370 (ttm) cc_final: -0.0633 (ttm) REVERT: O 251 MET cc_start: -0.1545 (ttm) cc_final: -0.1750 (ttm) REVERT: P 125 MET cc_start: 0.3038 (pmm) cc_final: 0.2760 (pmm) REVERT: P 158 MET cc_start: -0.3022 (ptp) cc_final: -0.3449 (ptp) REVERT: P 326 MET cc_start: -0.0242 (tpt) cc_final: -0.0652 (mtt) REVERT: Q 338 LYS cc_start: 0.5001 (mmtt) cc_final: 0.4106 (mptt) REVERT: R 72 ASP cc_start: 0.6705 (p0) cc_final: 0.6454 (t70) REVERT: R 243 MET cc_start: 0.5744 (mpp) cc_final: 0.5303 (ppp) REVERT: S 210 MET cc_start: -0.0723 (tmm) cc_final: -0.1016 (tmm) REVERT: S 211 MET cc_start: 0.1345 (ttm) cc_final: 0.0502 (mtt) REVERT: S 243 MET cc_start: 0.2121 (mmt) cc_final: 0.1510 (tmm) REVERT: S 251 MET cc_start: 0.4179 (ptt) cc_final: 0.3944 (ptt) REVERT: T 251 MET cc_start: -0.1657 (mtp) cc_final: -0.2681 (tpp) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.1988 time to fit residues: 73.2519 Evaluate side-chains 165 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 173 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 71 optimal weight: 40.0000 chunk 219 optimal weight: 4.9990 chunk 94 optimal weight: 30.0000 chunk 194 optimal weight: 8.9990 chunk 277 optimal weight: 4.9990 chunk 253 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 chunk 280 optimal weight: 10.0000 chunk 185 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 114 GLN ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 GLN S 206 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.076049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.047376 restraints weight = 275522.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.048846 restraints weight = 123236.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.049656 restraints weight = 74054.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.050045 restraints weight = 54881.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.050297 restraints weight = 46930.096| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 33682 Z= 0.217 Angle : 0.669 15.103 46738 Z= 0.366 Chirality : 0.045 0.247 5351 Planarity : 0.005 0.159 4942 Dihedral : 25.253 98.048 7123 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.04 % Allowed : 0.69 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.14), residues: 3328 helix: 1.03 (0.12), residues: 1737 sheet: 0.95 (0.24), residues: 458 loop : -0.58 (0.17), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 52 TYR 0.054 0.002 TYR F 88 PHE 0.023 0.002 PHE N 259 HIS 0.025 0.002 HIS N 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.22 (33673) covalent geometry : angle 0.66946 / 0.37 (46738) hydrogen bonds : bond 0.06143 / 4.19 ( 1662) hydrogen bonds : angle 4.32585 / 3.15 ( 4512) Misc. bond : bond 0.00777 / 0.38 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 1.033 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: A 50 GLU cc_start: 0.9033 (tp30) cc_final: 0.8633 (tp30) REVERT: A 106 ASP cc_start: 0.8868 (t70) cc_final: 0.8592 (t70) REVERT: B 49 LEU cc_start: 0.9119 (mt) cc_final: 0.8245 (mm) REVERT: B 85 ASP cc_start: 0.8540 (m-30) cc_final: 0.8294 (m-30) REVERT: C 72 ASP cc_start: 0.8405 (m-30) cc_final: 0.8201 (m-30) REVERT: E 57 SER cc_start: 0.9497 (m) cc_final: 0.9041 (p) REVERT: E 93 GLN cc_start: 0.9236 (tt0) cc_final: 0.8945 (tp40) REVERT: E 119 ILE cc_start: 0.9444 (pt) cc_final: 0.8983 (pt) REVERT: E 120 MET cc_start: 0.9024 (mmp) cc_final: 0.8408 (mmm) REVERT: K 198 ASP cc_start: 0.8542 (t70) cc_final: 0.8125 (m-30) REVERT: K 326 MET cc_start: 0.9168 (pmm) cc_final: 0.8437 (tpp) REVERT: L 125 MET cc_start: 0.8399 (pmm) cc_final: 0.8177 (pmm) REVERT: L 158 MET cc_start: 0.7058 (mmp) cc_final: 0.6638 (mmm) REVERT: L 210 MET cc_start: 0.7376 (ppp) cc_final: 0.7078 (ppp) REVERT: M 251 MET cc_start: 0.9514 (tpt) cc_final: 0.9183 (tpp) REVERT: N 290 ASN cc_start: 0.7428 (m-40) cc_final: 0.6978 (p0) REVERT: O 176 GLU cc_start: 0.8692 (pp20) cc_final: 0.8408 (pt0) REVERT: P 125 MET cc_start: 0.2816 (pmm) cc_final: 0.2512 (pmm) REVERT: P 326 MET cc_start: -0.0065 (tpt) cc_final: -0.0460 (mtt) REVERT: Q 338 LYS cc_start: 0.4489 (mmtt) cc_final: 0.3628 (mptt) REVERT: R 72 ASP cc_start: 0.6734 (p0) cc_final: 0.6448 (t70) REVERT: R 243 MET cc_start: 0.5534 (mpp) cc_final: 0.5026 (ppp) REVERT: S 211 MET cc_start: 0.0426 (ttm) cc_final: -0.0382 (mtt) REVERT: S 243 MET cc_start: 0.1898 (mmt) cc_final: 0.1263 (tmm) REVERT: S 251 MET cc_start: 0.3366 (ptt) cc_final: 0.3108 (ptt) REVERT: T 211 MET cc_start: -0.5694 (tmm) cc_final: -0.5934 (tmm) REVERT: T 251 MET cc_start: -0.2306 (mtp) cc_final: -0.3279 (tpp) outliers start: 1 outliers final: 0 residues processed: 209 average time/residue: 0.1878 time to fit residues: 66.9309 Evaluate side-chains 161 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 217 optimal weight: 6.9990 chunk 75 optimal weight: 20.0000 chunk 271 optimal weight: 8.9990 chunk 231 optimal weight: 8.9990 chunk 83 optimal weight: 30.0000 chunk 286 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 157 optimal weight: 0.0980 chunk 191 optimal weight: 20.0000 chunk 324 optimal weight: 10.0000 chunk 156 optimal weight: 20.0000 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 242 GLN ** L 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 23 GLN ** N 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.087684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.061058 restraints weight = 298143.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.060929 restraints weight = 122764.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.061527 restraints weight = 69153.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.061806 restraints weight = 49515.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.061905 restraints weight = 41774.341| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 33682 Z= 0.159 Angle : 0.595 14.261 46738 Z= 0.332 Chirality : 0.043 0.238 5351 Planarity : 0.004 0.076 4942 Dihedral : 25.208 98.953 7123 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.14), residues: 3328 helix: 1.21 (0.12), residues: 1738 sheet: 0.80 (0.24), residues: 488 loop : -0.42 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 310 TYR 0.023 0.002 TYR L 54 PHE 0.022 0.002 PHE T 248 HIS 0.039 0.002 HIS L 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.16 (33673) covalent geometry : angle 0.59470 / 0.33 (46738) hydrogen bonds : bond 0.04927 / 3.33 ( 1662) hydrogen bonds : angle 4.08642 / 2.96 ( 4512) Misc. bond : bond 0.00637 / 0.31 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 1.112 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: A 50 GLU cc_start: 0.9005 (tp30) cc_final: 0.8559 (tp30) REVERT: A 106 ASP cc_start: 0.8761 (t70) cc_final: 0.8435 (t70) REVERT: B 49 LEU cc_start: 0.9159 (mt) cc_final: 0.8205 (mm) REVERT: B 60 VAL cc_start: 0.9700 (t) cc_final: 0.9207 (p) REVERT: B 63 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8643 (mt-10) REVERT: C 72 ASP cc_start: 0.8359 (m-30) cc_final: 0.8149 (m-30) REVERT: E 57 SER cc_start: 0.9444 (m) cc_final: 0.8966 (p) REVERT: E 93 GLN cc_start: 0.9205 (tt0) cc_final: 0.8944 (tp40) REVERT: E 103 LEU cc_start: 0.9536 (tp) cc_final: 0.9334 (tp) REVERT: E 119 ILE cc_start: 0.9419 (pt) cc_final: 0.8924 (pt) REVERT: E 120 MET cc_start: 0.9044 (mmp) cc_final: 0.8432 (mmm) REVERT: K 46 PHE cc_start: 0.8584 (m-80) cc_final: 0.7937 (m-80) REVERT: K 198 ASP cc_start: 0.8553 (t70) cc_final: 0.8138 (m-30) REVERT: K 326 MET cc_start: 0.9121 (pmm) cc_final: 0.8520 (tpp) REVERT: L 158 MET cc_start: 0.6715 (mmp) cc_final: 0.6330 (mmm) REVERT: L 210 MET cc_start: 0.7341 (ppp) cc_final: 0.7050 (ppp) REVERT: M 251 MET cc_start: 0.9541 (tpt) cc_final: 0.9234 (tpp) REVERT: N 290 ASN cc_start: 0.7411 (m-40) cc_final: 0.7046 (p0) REVERT: N 326 MET cc_start: 0.8179 (tpt) cc_final: 0.7909 (tpp) REVERT: O 176 GLU cc_start: 0.8600 (pp20) cc_final: 0.8335 (pt0) REVERT: P 125 MET cc_start: 0.3752 (pmm) cc_final: 0.3506 (pmm) REVERT: P 158 MET cc_start: -0.2752 (ptp) cc_final: -0.3305 (ptp) REVERT: P 326 MET cc_start: -0.0226 (tpt) cc_final: -0.0506 (mtt) REVERT: Q 338 LYS cc_start: 0.4451 (mmtt) cc_final: 0.3572 (mptt) REVERT: R 72 ASP cc_start: 0.6843 (p0) cc_final: 0.6595 (t70) REVERT: R 178 TYR cc_start: 0.6914 (m-80) cc_final: 0.6545 (m-80) REVERT: R 211 MET cc_start: 0.3387 (tpp) cc_final: 0.3185 (tpp) REVERT: R 243 MET cc_start: 0.5534 (mpp) cc_final: 0.5047 (ppp) REVERT: S 211 MET cc_start: 0.1539 (ttm) cc_final: 0.0807 (mtt) REVERT: S 243 MET cc_start: 0.1984 (mmt) cc_final: 0.1396 (tmm) REVERT: S 251 MET cc_start: 0.3972 (ptt) cc_final: 0.3708 (ptt) REVERT: T 211 MET cc_start: -0.3643 (tmm) cc_final: -0.3865 (tmm) REVERT: T 251 MET cc_start: -0.1640 (mtp) cc_final: -0.2660 (tpp) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1927 time to fit residues: 69.9845 Evaluate side-chains 168 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 2 optimal weight: 6.9990 chunk 96 optimal weight: 20.0000 chunk 150 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 304 optimal weight: 0.0670 chunk 246 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 chunk 230 optimal weight: 40.0000 chunk 59 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 334 optimal weight: 50.0000 overall best weight: 3.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.087528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.061382 restraints weight = 300273.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.062666 restraints weight = 137779.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.062229 restraints weight = 78025.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.062497 restraints weight = 65401.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.062443 restraints weight = 50629.026| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 33682 Z= 0.157 Angle : 0.604 14.664 46738 Z= 0.333 Chirality : 0.043 0.238 5351 Planarity : 0.004 0.071 4942 Dihedral : 25.167 100.103 7123 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.14), residues: 3328 helix: 1.26 (0.12), residues: 1744 sheet: 0.89 (0.24), residues: 470 loop : -0.48 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 36 TYR 0.031 0.001 TYR Q 159 PHE 0.021 0.002 PHE K 195 HIS 0.027 0.002 HIS T 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 (33673) covalent geometry : angle 0.60353 / 0.33 (46738) hydrogen bonds : bond 0.05046 / 3.42 ( 1662) hydrogen bonds : angle 4.01770 / 2.90 ( 4512) Misc. bond : bond 0.00516 / 0.25 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 1.162 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: A 50 GLU cc_start: 0.9078 (tp30) cc_final: 0.8583 (tp30) REVERT: A 106 ASP cc_start: 0.8739 (t70) cc_final: 0.8430 (t70) REVERT: B 49 LEU cc_start: 0.9140 (mt) cc_final: 0.8404 (mm) REVERT: B 60 VAL cc_start: 0.9697 (t) cc_final: 0.9251 (p) REVERT: B 63 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8660 (mt-10) REVERT: C 72 ASP cc_start: 0.8398 (m-30) cc_final: 0.8188 (m-30) REVERT: E 57 SER cc_start: 0.9472 (m) cc_final: 0.9014 (p) REVERT: E 93 GLN cc_start: 0.9163 (tt0) cc_final: 0.8908 (tp40) REVERT: E 119 ILE cc_start: 0.9446 (pt) cc_final: 0.8965 (pt) REVERT: E 120 MET cc_start: 0.9101 (mmp) cc_final: 0.8487 (mmm) REVERT: K 46 PHE cc_start: 0.8657 (m-80) cc_final: 0.8037 (m-80) REVERT: K 198 ASP cc_start: 0.8619 (t70) cc_final: 0.8199 (m-30) REVERT: K 211 MET cc_start: 0.5740 (mmm) cc_final: 0.5280 (mmm) REVERT: L 158 MET cc_start: 0.6774 (mmp) cc_final: 0.6379 (mmm) REVERT: L 210 MET cc_start: 0.7373 (ppp) cc_final: 0.7100 (ppp) REVERT: L 243 MET cc_start: 0.9648 (mmp) cc_final: 0.9287 (tpt) REVERT: M 251 MET cc_start: 0.9575 (tpt) cc_final: 0.9257 (tpp) REVERT: N 290 ASN cc_start: 0.7428 (m-40) cc_final: 0.7079 (p0) REVERT: N 326 MET cc_start: 0.8284 (tpt) cc_final: 0.8000 (tpp) REVERT: O 176 GLU cc_start: 0.8630 (pp20) cc_final: 0.8357 (pt0) REVERT: O 251 MET cc_start: -0.0755 (ttp) cc_final: -0.0968 (ttm) REVERT: P 125 MET cc_start: 0.3979 (pmm) cc_final: 0.3728 (pmm) REVERT: P 158 MET cc_start: -0.2891 (ptp) cc_final: -0.3212 (ptp) REVERT: Q 338 LYS cc_start: 0.4476 (mmtt) cc_final: 0.3465 (mptt) REVERT: R 72 ASP cc_start: 0.6852 (p0) cc_final: 0.6572 (t70) REVERT: R 178 TYR cc_start: 0.7059 (m-80) cc_final: 0.6713 (m-80) REVERT: R 243 MET cc_start: 0.5545 (mpp) cc_final: 0.4961 (ppp) REVERT: S 125 MET cc_start: -0.5947 (mtt) cc_final: -0.6210 (ttp) REVERT: S 211 MET cc_start: -0.0519 (ttm) cc_final: -0.1204 (mtt) REVERT: S 243 MET cc_start: 0.1847 (mmt) cc_final: 0.1223 (tmm) REVERT: S 251 MET cc_start: 0.3124 (ptt) cc_final: 0.2872 (ptt) REVERT: T 251 MET cc_start: -0.2059 (mtp) cc_final: -0.3035 (tpp) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1959 time to fit residues: 70.8360 Evaluate side-chains 169 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 322 optimal weight: 10.0000 chunk 233 optimal weight: 20.0000 chunk 251 optimal weight: 20.0000 chunk 188 optimal weight: 40.0000 chunk 359 optimal weight: 8.9990 chunk 285 optimal weight: 0.0980 chunk 241 optimal weight: 5.9990 chunk 288 optimal weight: 8.9990 chunk 224 optimal weight: 6.9990 chunk 214 optimal weight: 20.0000 chunk 194 optimal weight: 0.7980 overall best weight: 4.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.087129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.060677 restraints weight = 300595.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.060471 restraints weight = 124844.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.061081 restraints weight = 69892.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.061364 restraints weight = 49165.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.061442 restraints weight = 41944.801| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 33682 Z= 0.166 Angle : 0.605 13.664 46738 Z= 0.335 Chirality : 0.043 0.251 5351 Planarity : 0.004 0.078 4942 Dihedral : 25.161 100.775 7123 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.14), residues: 3328 helix: 1.26 (0.12), residues: 1747 sheet: 0.80 (0.24), residues: 470 loop : -0.45 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG N 193 TYR 0.023 0.001 TYR Q 54 PHE 0.019 0.002 PHE Q 166 HIS 0.027 0.002 HIS T 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.17 (33673) covalent geometry : angle 0.60465 / 0.33 (46738) hydrogen bonds : bond 0.05060 / 3.43 ( 1662) hydrogen bonds : angle 4.04188 / 2.92 ( 4512) Misc. bond : bond 0.00725 / 0.36 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9418.11 seconds wall clock time: 161 minutes 46.51 seconds (9706.51 seconds total)