Starting phenix.real_space_refine on Thu May 29 17:51:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xbu_38229/05_2025/8xbu_38229.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xbu_38229/05_2025/8xbu_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8xbu_38229/05_2025/8xbu_38229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xbu_38229/05_2025/8xbu_38229.map" model { file = "/net/cci-nas-00/data/ceres_data/8xbu_38229/05_2025/8xbu_38229.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xbu_38229/05_2025/8xbu_38229.cif" } resolution = 4.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 18.75, per 1000 atoms: 0.58 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: 8.98 Conformation dependent library (CDL) restraints added in 3.4 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: 14.80 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: 14.59 Time building geometry restraints manager: 10.05 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: 46349 3.88 - 7.75: 335 7.75 - 11.63: 49 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=" CA ARG Q 167 " pdb=" CB ARG Q 167 " pdb=" CG ARG Q 167 " ideal model delta sigma weight residual 114.10 127.96 -13.86 2.00e+00 2.50e-01 4.80e+01 angle pdb=" C VAL L 52 " pdb=" N ALA L 53 " pdb=" CA ALA L 53 " ideal model delta sigma weight residual 120.65 129.68 -9.03 1.32e+00 5.74e-01 4.68e+01 angle pdb=" C VAL M 52 " pdb=" N ALA M 53 " pdb=" CA ALA M 53 " ideal model delta sigma weight residual 120.65 129.65 -9.00 1.32e+00 5.74e-01 4.65e+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: 5208 0.141 - 0.282: 55 0.282 - 0.422: 8 0.422 - 0.563: 48 0.563 - 0.704: 32 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: 1.400 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: 0.040 Extract box with map and model: 1.370 Check model and map are aligned: 0.250 Set scattering table: 0.300 Process input model: 83.430 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 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= 0.614 Angle : 0.952 19.386 46738 Z= 0.576 Chirality : 0.086 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (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 HIS 0.011 0.001 HIS A 39 PHE 0.026 0.002 PHE E 78 TYR 0.023 0.003 TYR H 37 ARG 0.013 0.002 ARG M 250 Details of bonding type rmsd hydrogen bonds : bond 0.17716 ( 1662) hydrogen bonds : angle 6.40682 ( 4512) covalent geometry : bond 0.00887 (33673) covalent geometry : angle 0.95155 (46738) Misc. bond : bond 0.24884 ( 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 : 3.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8356 (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: 0.8632 (tm-30) REVERT: B 92 ARG cc_start: 0.9182 (ptm-80) cc_final: 0.8867 (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: 0.9058 (tp) REVERT: D 43 LYS cc_start: 0.9317 (mttt) cc_final: 0.9104 (mmmm) REVERT: E 93 GLN cc_start: 0.9425 (tt0) cc_final: 0.8690 (tp40) REVERT: E 97 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8494 (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: 0.9245 (p) REVERT: F 44 LYS cc_start: 0.8819 (tttt) cc_final: 0.8425 (tppt) REVERT: F 65 VAL cc_start: 0.9667 (t) cc_final: 0.9417 (p) REVERT: G 55 LEU cc_start: 0.9651 (mt) cc_final: 0.9420 (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: 0.8306 (m-30) REVERT: K 318 PRO cc_start: 0.5211 (Cg_exo) cc_final: 0.4671 (Cg_endo) REVERT: L 58 LYS cc_start: 0.8462 (tppt) cc_final: 0.8208 (tptp) REVERT: L 125 MET cc_start: 0.8158 (pmm) cc_final: 0.7639 (pmm) REVERT: L 158 MET cc_start: 0.6854 (mmm) cc_final: 0.6530 (mmm) REVERT: L 210 MET cc_start: 0.7650 (tmm) cc_final: 0.7386 (tmm) REVERT: L 244 HIS cc_start: 0.8948 (t70) cc_final: 0.8450 (t-90) REVERT: M 60 LEU cc_start: 0.9520 (mt) cc_final: 0.9292 (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: 0.7746 (p90) REVERT: N 290 ASN cc_start: 0.7675 (m-40) cc_final: 0.7129 (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: 0.4163 (t80) REVERT: O 251 MET cc_start: -0.1556 (mtp) cc_final: -0.1836 (ttm) REVERT: P 326 MET cc_start: 0.1786 (tpt) cc_final: 0.0543 (mtp) REVERT: R 30 GLN cc_start: -0.2648 (mp10) cc_final: -0.2951 (mm110) REVERT: R 72 ASP cc_start: 0.6994 (m-30) cc_final: 0.6787 (t70) REVERT: S 210 MET cc_start: 0.1480 (tmm) cc_final: 0.0549 (tpp) REVERT: S 211 MET cc_start: 0.1390 (ttm) cc_final: 0.0855 (mtt) REVERT: S 243 MET cc_start: 0.2258 (mmt) cc_final: 0.1747 (tmm) REVERT: T 63 ILE cc_start: -0.0783 (mt) cc_final: -0.1091 (mm) REVERT: T 210 MET cc_start: 0.2232 (tmm) cc_final: 0.1191 (ttt) REVERT: T 251 MET cc_start: -0.0819 (mtp) cc_final: -0.1358 (mmm) outliers start: 4 outliers final: 0 residues processed: 473 average time/residue: 0.4898 time to fit residues: 355.6112 Evaluate side-chains 223 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 3.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 306 optimal weight: 50.0000 chunk 275 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 185 optimal weight: 0.9990 chunk 146 optimal weight: 9.9990 chunk 284 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 173 optimal weight: 7.9990 chunk 211 optimal weight: 0.5980 chunk 329 optimal weight: 50.0000 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 K 23 GLN L 47 HIS ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 GLN N 47 HIS N 242 GLN N 244 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.090782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.063877 restraints weight = 298998.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.063936 restraints weight = 124491.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.064540 restraints weight = 68707.944| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 33682 Z= 0.195 Angle : 0.603 13.979 46738 Z= 0.344 Chirality : 0.040 0.184 5351 Planarity : 0.004 0.075 4942 Dihedral : 25.164 89.768 7123 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.18 % Allowed : 1.90 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.14), residues: 3328 helix: 1.25 (0.12), residues: 1710 sheet: 0.63 (0.21), residues: 508 loop : -0.62 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS L 294 PHE 0.024 0.002 PHE S 195 TYR 0.041 0.002 TYR Q 54 ARG 0.010 0.001 ARG R 254 Details of bonding type rmsd hydrogen bonds : bond 0.05273 ( 1662) hydrogen bonds : angle 4.51869 ( 4512) covalent geometry : bond 0.00413 (33673) covalent geometry : angle 0.60255 (46738) Misc. bond : bond 0.00728 ( 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 292 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 287 time to evaluate : 3.375 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: B 49 LEU cc_start: 0.9323 (mt) cc_final: 0.8378 (mt) REVERT: B 60 VAL cc_start: 0.9740 (t) cc_final: 0.9374 (p) REVERT: B 63 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8731 (mt-10) REVERT: B 85 ASP cc_start: 0.8228 (m-30) cc_final: 0.7973 (m-30) REVERT: C 38 ASN cc_start: 0.8131 (t0) cc_final: 0.7873 (t0) REVERT: C 72 ASP cc_start: 0.8254 (m-30) cc_final: 0.8026 (m-30) REVERT: C 90 ASP cc_start: 0.8985 (t70) cc_final: 0.8749 (t0) REVERT: C 102 ILE cc_start: 0.9463 (mm) cc_final: 0.9181 (tp) REVERT: D 93 GLU cc_start: 0.9032 (mp0) cc_final: 0.8684 (mp0) REVERT: E 68 GLN cc_start: 0.9435 (tt0) cc_final: 0.9179 (pp30) REVERT: E 93 GLN cc_start: 0.9185 (tt0) cc_final: 0.8814 (tp40) REVERT: E 105 GLU cc_start: 0.7938 (pp20) cc_final: 0.7512 (pp20) REVERT: E 106 ASP cc_start: 0.8428 (m-30) cc_final: 0.8180 (m-30) REVERT: E 119 ILE cc_start: 0.9243 (pt) cc_final: 0.8854 (pt) REVERT: F 35 ARG cc_start: 0.9317 (ttp-110) cc_final: 0.8990 (ttm110) REVERT: F 44 LYS cc_start: 0.8855 (tttt) cc_final: 0.8644 (tppt) REVERT: F 68 ASP cc_start: 0.9126 (m-30) cc_final: 0.8916 (m-30) REVERT: F 79 LYS cc_start: 0.9386 (mppt) cc_final: 0.9092 (mmtm) REVERT: G 51 LEU cc_start: 0.9687 (tt) cc_final: 0.9443 (mt) REVERT: G 56 GLU cc_start: 0.8907 (tt0) cc_final: 0.8284 (mt-10) REVERT: H 64 SER cc_start: 0.9222 (m) cc_final: 0.8970 (p) REVERT: K 46 PHE cc_start: 0.8495 (m-80) cc_final: 0.7834 (m-80) REVERT: K 68 GLU cc_start: 0.9682 (pm20) cc_final: 0.9457 (mp0) REVERT: K 158 MET cc_start: 0.5977 (tpp) cc_final: 0.5709 (tpp) REVERT: K 198 ASP cc_start: 0.8608 (t70) cc_final: 0.8093 (m-30) REVERT: K 211 MET cc_start: 0.6212 (tpt) cc_final: 0.6005 (tpt) REVERT: L 125 MET cc_start: 0.8131 (pmm) cc_final: 0.7776 (pmm) REVERT: L 244 HIS cc_start: 0.8855 (t70) cc_final: 0.8500 (t-90) REVERT: L 251 MET cc_start: 0.9243 (mtm) cc_final: 0.8336 (mmm) REVERT: M 248 PHE cc_start: 0.9587 (t80) cc_final: 0.9376 (t80) REVERT: M 251 MET cc_start: 0.9556 (tpt) cc_final: 0.9177 (tpp) REVERT: N 52 VAL cc_start: -0.0574 (m) cc_final: -0.1309 (t) REVERT: N 290 ASN cc_start: 0.7556 (m-40) cc_final: 0.7155 (p0) REVERT: O 176 GLU cc_start: 0.8564 (pp20) cc_final: 0.8302 (pt0) REVERT: O 211 MET cc_start: -0.0575 (ttm) cc_final: -0.0919 (ttm) REVERT: O 251 MET cc_start: -0.1664 (mtp) cc_final: -0.1929 (ttm) REVERT: P 210 MET cc_start: 0.0814 (ppp) cc_final: 0.0259 (ppp) REVERT: P 309 THR cc_start: 0.4118 (OUTLIER) cc_final: 0.3750 (t) REVERT: P 326 MET cc_start: 0.1420 (tpt) cc_final: 0.0779 (mtt) REVERT: R 72 ASP cc_start: 0.6953 (m-30) cc_final: 0.6642 (t70) REVERT: S 210 MET cc_start: 0.0545 (tmm) cc_final: 0.0153 (tmm) REVERT: S 211 MET cc_start: 0.0858 (ttm) cc_final: 0.0075 (mtt) REVERT: S 243 MET cc_start: 0.2291 (mmt) cc_final: 0.1711 (tmm) REVERT: T 158 MET cc_start: -0.2668 (mtm) cc_final: -0.2900 (mtm) REVERT: T 210 MET cc_start: -0.0360 (tmm) cc_final: -0.0756 (ttt) REVERT: T 251 MET cc_start: -0.2242 (mtp) cc_final: -0.2954 (tpp) outliers start: 5 outliers final: 1 residues processed: 292 average time/residue: 0.4669 time to fit residues: 221.6754 Evaluate side-chains 200 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 198 time to evaluate : 3.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 43 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 330 optimal weight: 20.0000 chunk 281 optimal weight: 7.9990 chunk 169 optimal weight: 20.0000 chunk 17 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 360 optimal weight: 30.0000 chunk 286 optimal weight: 30.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 47 HIS ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 242 GLN L 244 HIS ** L 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 47 HIS N 202 GLN P 114 GLN ** P 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 244 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.087559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.060600 restraints weight = 301829.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.060448 restraints weight = 123777.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.061115 restraints weight = 69961.201| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 33682 Z= 0.234 Angle : 0.622 18.913 46738 Z= 0.347 Chirality : 0.041 0.235 5351 Planarity : 0.004 0.050 4942 Dihedral : 24.976 93.731 7123 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.07 % Allowed : 2.45 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.14), residues: 3328 helix: 1.20 (0.12), residues: 1729 sheet: 0.94 (0.23), residues: 455 loop : -0.57 (0.17), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.020 0.002 HIS L 294 PHE 0.027 0.002 PHE T 248 TYR 0.036 0.002 TYR F 88 ARG 0.013 0.001 ARG C 29 Details of bonding type rmsd hydrogen bonds : bond 0.05778 ( 1662) hydrogen bonds : angle 4.32346 ( 4512) covalent geometry : bond 0.00498 (33673) covalent geometry : angle 0.62163 (46738) Misc. bond : bond 0.00526 ( 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 240 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 238 time to evaluate : 3.514 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: 0.8814 (tp30) cc_final: 0.8259 (tp30) REVERT: A 106 ASP cc_start: 0.8827 (t70) cc_final: 0.8566 (t70) REVERT: B 49 LEU cc_start: 0.9031 (mt) cc_final: 0.8638 (mm) REVERT: B 60 VAL cc_start: 0.9716 (t) cc_final: 0.9194 (p) REVERT: B 85 ASP cc_start: 0.8559 (m-30) cc_final: 0.8273 (m-30) REVERT: C 38 ASN cc_start: 0.8357 (t0) cc_final: 0.8014 (t0) REVERT: C 90 ASP cc_start: 0.8957 (t70) cc_final: 0.8750 (t0) REVERT: D 71 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8563 (tm-30) REVERT: D 93 GLU cc_start: 0.8969 (mp0) cc_final: 0.8760 (mp0) REVERT: E 57 SER cc_start: 0.9393 (m) cc_final: 0.9124 (m) REVERT: E 93 GLN cc_start: 0.9157 (tt0) cc_final: 0.8884 (tp40) REVERT: E 105 GLU cc_start: 0.8256 (pp20) cc_final: 0.8023 (pp20) REVERT: E 119 ILE cc_start: 0.9388 (pt) cc_final: 0.8953 (pt) REVERT: E 120 MET cc_start: 0.8943 (mmp) cc_final: 0.8158 (mmm) REVERT: F 88 TYR cc_start: 0.9147 (m-80) cc_final: 0.8944 (m-10) REVERT: H 64 SER cc_start: 0.9312 (m) cc_final: 0.9067 (p) REVERT: K 46 PHE cc_start: 0.8750 (m-80) cc_final: 0.8048 (m-80) REVERT: K 68 GLU cc_start: 0.9683 (pm20) cc_final: 0.9482 (mp0) REVERT: K 198 ASP cc_start: 0.8542 (t70) cc_final: 0.8082 (m-30) REVERT: K 211 MET cc_start: 0.6436 (tpt) cc_final: 0.6133 (tpt) REVERT: K 232 TYR cc_start: 0.8061 (m-10) cc_final: 0.7781 (m-10) REVERT: L 125 MET cc_start: 0.8304 (pmm) cc_final: 0.7961 (pmm) REVERT: L 158 MET cc_start: 0.7549 (mmp) cc_final: 0.6912 (mmm) REVERT: L 210 MET cc_start: 0.6927 (ppp) cc_final: 0.6702 (ppp) REVERT: L 251 MET cc_start: 0.9379 (mtm) cc_final: 0.8531 (mmm) REVERT: M 248 PHE cc_start: 0.9569 (t80) cc_final: 0.9343 (t80) REVERT: M 251 MET cc_start: 0.9516 (tpt) cc_final: 0.9173 (tpp) REVERT: N 52 VAL cc_start: -0.0811 (m) cc_final: -0.1741 (t) REVERT: N 290 ASN cc_start: 0.7264 (m-40) cc_final: 0.6825 (p0) REVERT: N 326 MET cc_start: 0.8452 (tpt) cc_final: 0.8138 (tpp) REVERT: O 176 GLU cc_start: 0.8581 (pp20) cc_final: 0.8306 (pt0) REVERT: O 211 MET cc_start: 0.1936 (ttm) cc_final: 0.1558 (ttm) REVERT: O 251 MET cc_start: -0.1654 (mtp) cc_final: -0.1961 (ttm) REVERT: P 158 MET cc_start: -0.1557 (ptp) cc_final: -0.1966 (ptp) REVERT: P 326 MET cc_start: -0.0201 (tpt) cc_final: -0.0532 (mtt) REVERT: Q 210 MET cc_start: 0.4337 (tmm) cc_final: 0.4064 (tmm) REVERT: Q 211 MET cc_start: 0.3400 (mmt) cc_final: 0.3035 (mmt) REVERT: R 72 ASP cc_start: 0.6959 (m-30) cc_final: 0.6611 (t70) REVERT: S 210 MET cc_start: 0.0582 (tmm) cc_final: 0.0185 (tmm) REVERT: S 211 MET cc_start: 0.1811 (ttm) cc_final: 0.1234 (mtt) REVERT: S 243 MET cc_start: 0.2164 (mmt) cc_final: 0.1570 (tmm) REVERT: T 158 MET cc_start: -0.2997 (mtm) cc_final: -0.3213 (mtm) REVERT: T 210 MET cc_start: -0.0371 (tmm) cc_final: -0.0710 (ttt) REVERT: T 251 MET cc_start: -0.2021 (mtp) cc_final: -0.3056 (tpp) outliers start: 2 outliers final: 1 residues processed: 240 average time/residue: 0.4241 time to fit residues: 166.5020 Evaluate side-chains 172 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 171 time to evaluate : 3.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 128 optimal weight: 0.4980 chunk 106 optimal weight: 20.0000 chunk 209 optimal weight: 0.9980 chunk 182 optimal weight: 3.9990 chunk 224 optimal weight: 50.0000 chunk 64 optimal weight: 5.9990 chunk 274 optimal weight: 0.1980 chunk 264 optimal weight: 7.9990 chunk 190 optimal weight: 40.0000 chunk 94 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** 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** N 202 GLN T 47 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.089482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.063268 restraints weight = 299406.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.063189 restraints weight = 122037.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.063764 restraints weight = 67571.367| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 33682 Z= 0.129 Angle : 0.517 12.008 46738 Z= 0.297 Chirality : 0.038 0.151 5351 Planarity : 0.003 0.050 4942 Dihedral : 24.812 95.069 7123 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.14), residues: 3328 helix: 1.54 (0.13), residues: 1727 sheet: 1.06 (0.23), residues: 474 loop : -0.44 (0.17), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.019 0.001 HIS L 294 PHE 0.018 0.001 PHE S 195 TYR 0.028 0.001 TYR Q 54 ARG 0.004 0.000 ARG H 99 Details of bonding type rmsd hydrogen bonds : bond 0.03914 ( 1662) hydrogen bonds : angle 3.72059 ( 4512) covalent geometry : bond 0.00268 (33673) covalent geometry : angle 0.51725 (46738) Misc. bond : bond 0.00435 ( 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 242 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 3.134 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: 0.8835 (tp30) cc_final: 0.8208 (tp30) REVERT: A 106 ASP cc_start: 0.8783 (t70) cc_final: 0.8282 (t70) REVERT: B 49 LEU cc_start: 0.8920 (mt) cc_final: 0.8215 (tp) REVERT: B 60 VAL cc_start: 0.9699 (t) cc_final: 0.9231 (p) REVERT: B 63 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8657 (mt-10) REVERT: B 85 ASP cc_start: 0.8540 (m-30) cc_final: 0.8305 (m-30) REVERT: C 38 ASN cc_start: 0.8354 (t0) cc_final: 0.7948 (t0) REVERT: E 57 SER cc_start: 0.9352 (m) cc_final: 0.8743 (p) REVERT: E 93 GLN cc_start: 0.9091 (tt0) cc_final: 0.8870 (tp40) REVERT: E 106 ASP cc_start: 0.8575 (m-30) cc_final: 0.8357 (m-30) REVERT: E 119 ILE cc_start: 0.9291 (pt) cc_final: 0.8805 (pt) REVERT: E 120 MET cc_start: 0.9073 (mmp) cc_final: 0.8308 (mmm) REVERT: F 35 ARG cc_start: 0.9307 (ttp-110) cc_final: 0.8951 (ttm110) REVERT: F 88 TYR cc_start: 0.9214 (m-80) cc_final: 0.8637 (m-80) REVERT: G 56 GLU cc_start: 0.8859 (tt0) cc_final: 0.8241 (mt-10) REVERT: H 64 SER cc_start: 0.9293 (m) cc_final: 0.9064 (p) REVERT: K 46 PHE cc_start: 0.8489 (m-80) cc_final: 0.7923 (m-80) REVERT: K 198 ASP cc_start: 0.8367 (t70) cc_final: 0.7898 (m-30) REVERT: K 211 MET cc_start: 0.6400 (tpt) cc_final: 0.6056 (mmm) REVERT: K 232 TYR cc_start: 0.7894 (m-10) cc_final: 0.7642 (m-10) REVERT: L 125 MET cc_start: 0.8689 (pmm) cc_final: 0.8443 (pmm) REVERT: L 158 MET cc_start: 0.7183 (mmp) cc_final: 0.6508 (mmm) REVERT: L 210 MET cc_start: 0.7107 (ppp) cc_final: 0.6707 (ppp) REVERT: L 243 MET cc_start: 0.9599 (mmp) cc_final: 0.9272 (tpt) REVERT: L 251 MET cc_start: 0.9319 (mtp) cc_final: 0.8505 (mmm) REVERT: L 267 ASN cc_start: 0.9347 (m-40) cc_final: 0.9144 (m110) REVERT: M 251 MET cc_start: 0.9505 (tpt) cc_final: 0.9190 (tpp) REVERT: N 290 ASN cc_start: 0.7317 (m-40) cc_final: 0.6841 (p0) REVERT: O 176 GLU cc_start: 0.8527 (pp20) cc_final: 0.8253 (pt0) REVERT: O 211 MET cc_start: 0.1039 (ttm) cc_final: 0.0571 (ttm) REVERT: O 251 MET cc_start: -0.1651 (mtp) cc_final: -0.1904 (ttm) REVERT: P 125 MET cc_start: 0.3780 (pmm) cc_final: 0.3546 (pmm) REVERT: P 158 MET cc_start: -0.1717 (ptp) cc_final: -0.2440 (ptp) REVERT: R 72 ASP cc_start: 0.7061 (m-30) cc_final: 0.6748 (t70) REVERT: R 178 TYR cc_start: 0.6845 (m-10) cc_final: 0.6539 (m-80) REVERT: R 243 MET cc_start: 0.6305 (ppp) cc_final: 0.5674 (mmt) REVERT: S 210 MET cc_start: 0.0017 (tmm) cc_final: -0.0307 (tmm) REVERT: S 211 MET cc_start: 0.1500 (ttm) cc_final: 0.0746 (mtt) REVERT: S 243 MET cc_start: 0.2117 (mmt) cc_final: 0.1542 (tmm) REVERT: T 210 MET cc_start: -0.0908 (tmm) cc_final: -0.1227 (ttt) REVERT: T 251 MET cc_start: -0.2047 (mtp) cc_final: -0.2562 (tpp) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.4270 time to fit residues: 169.2085 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 : 3.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 88 optimal weight: 8.9990 chunk 232 optimal weight: 40.0000 chunk 311 optimal weight: 2.9990 chunk 331 optimal weight: 20.0000 chunk 295 optimal weight: 10.0000 chunk 258 optimal weight: 0.7980 chunk 186 optimal weight: 10.0000 chunk 337 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 162 optimal weight: 20.0000 chunk 158 optimal weight: 6.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN L 114 GLN ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 206 GLN ** N 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 202 GLN S 206 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.076046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.047647 restraints weight = 275814.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.049136 restraints weight = 121661.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.050021 restraints weight = 72768.327| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 33682 Z= 0.199 Angle : 0.566 15.341 46738 Z= 0.319 Chirality : 0.039 0.144 5351 Planarity : 0.004 0.053 4942 Dihedral : 24.781 96.677 7123 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.04 % Allowed : 1.13 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.14), residues: 3328 helix: 1.41 (0.13), residues: 1751 sheet: 1.09 (0.23), residues: 482 loop : -0.48 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.018 0.002 HIS L 294 PHE 0.016 0.001 PHE S 195 TYR 0.026 0.001 TYR Q 54 ARG 0.009 0.001 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.05165 ( 1662) hydrogen bonds : angle 3.91958 ( 4512) covalent geometry : bond 0.00428 (33673) covalent geometry : angle 0.56554 (46738) Misc. bond : bond 0.00334 ( 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 215 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 214 time to evaluate : 3.589 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: 0.9146 (mm-30) cc_final: 0.8758 (tp30) REVERT: A 106 ASP cc_start: 0.8844 (t70) cc_final: 0.8464 (t70) REVERT: B 49 LEU cc_start: 0.8671 (mt) cc_final: 0.8032 (mm) REVERT: B 60 VAL cc_start: 0.9681 (t) cc_final: 0.9224 (p) REVERT: B 63 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8670 (mt-10) REVERT: B 85 ASP cc_start: 0.8608 (m-30) cc_final: 0.8394 (m-30) REVERT: C 38 ASN cc_start: 0.8545 (t0) cc_final: 0.8178 (t0) REVERT: C 72 ASP cc_start: 0.8423 (m-30) cc_final: 0.8207 (m-30) REVERT: E 57 SER cc_start: 0.9423 (m) cc_final: 0.8748 (p) REVERT: E 93 GLN cc_start: 0.9121 (tt0) cc_final: 0.8819 (tp40) REVERT: E 120 MET cc_start: 0.9036 (mmp) cc_final: 0.8420 (mmm) REVERT: H 64 SER cc_start: 0.9360 (m) cc_final: 0.9141 (p) REVERT: K 46 PHE cc_start: 0.8333 (m-80) cc_final: 0.7723 (m-80) REVERT: K 68 GLU cc_start: 0.9648 (mp0) cc_final: 0.9412 (mp0) REVERT: K 198 ASP cc_start: 0.8470 (t70) cc_final: 0.7979 (m-30) REVERT: K 211 MET cc_start: 0.6712 (tpt) cc_final: 0.5940 (mmm) REVERT: K 326 MET cc_start: 0.9123 (pmm) cc_final: 0.8876 (pmm) REVERT: L 158 MET cc_start: 0.7505 (mmp) cc_final: 0.6664 (mmp) REVERT: L 210 MET cc_start: 0.7390 (ppp) cc_final: 0.7073 (ppp) REVERT: L 243 MET cc_start: 0.9585 (mmp) cc_final: 0.9289 (tpt) REVERT: L 251 MET cc_start: 0.9307 (mtp) cc_final: 0.8911 (mtp) REVERT: M 248 PHE cc_start: 0.9402 (t80) cc_final: 0.9199 (t80) REVERT: M 251 MET cc_start: 0.9486 (tpt) cc_final: 0.9176 (tpp) REVERT: N 290 ASN cc_start: 0.7398 (m-40) cc_final: 0.6943 (p0) REVERT: O 176 GLU cc_start: 0.8633 (pp20) cc_final: 0.8345 (pt0) REVERT: O 211 MET cc_start: -0.2579 (ttm) cc_final: -0.2810 (ttm) REVERT: P 125 MET cc_start: 0.4027 (pmm) cc_final: 0.3782 (pmm) REVERT: P 158 MET cc_start: -0.1780 (ptp) cc_final: -0.2140 (ptp) REVERT: P 294 HIS cc_start: 0.0200 (p-80) cc_final: -0.0308 (m-70) REVERT: Q 338 LYS cc_start: 0.4599 (mmtt) cc_final: 0.3614 (mptt) REVERT: R 72 ASP cc_start: 0.7058 (m-30) cc_final: 0.6715 (t70) REVERT: R 178 TYR cc_start: 0.6840 (m-10) cc_final: 0.6465 (m-80) REVERT: S 210 MET cc_start: -0.0585 (tmm) cc_final: -0.0834 (tmm) REVERT: S 211 MET cc_start: 0.0874 (ttm) cc_final: -0.0011 (mtt) REVERT: S 243 MET cc_start: 0.2065 (mmt) cc_final: 0.1367 (tmm) REVERT: T 210 MET cc_start: -0.1478 (tmm) cc_final: -0.1984 (ttt) REVERT: T 251 MET cc_start: -0.2598 (mtp) cc_final: -0.2979 (tpp) outliers start: 1 outliers final: 0 residues processed: 215 average time/residue: 0.4271 time to fit residues: 153.3632 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 : 3.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 15 optimal weight: 0.9980 chunk 333 optimal weight: 9.9990 chunk 330 optimal weight: 7.9990 chunk 176 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 248 optimal weight: 20.0000 chunk 314 optimal weight: 9.9990 chunk 341 optimal weight: 30.0000 chunk 307 optimal weight: 50.0000 chunk 24 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS D 84 ASN E 68 GLN ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 202 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.076880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.048566 restraints weight = 275394.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.050090 restraints weight = 121600.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.050860 restraints weight = 71945.310| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33682 Z= 0.144 Angle : 0.518 12.822 46738 Z= 0.296 Chirality : 0.038 0.158 5351 Planarity : 0.003 0.053 4942 Dihedral : 24.699 98.334 7123 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.15), residues: 3328 helix: 1.54 (0.13), residues: 1756 sheet: 1.30 (0.24), residues: 454 loop : -0.50 (0.17), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.001 HIS L 294 PHE 0.020 0.001 PHE Q 195 TYR 0.025 0.001 TYR F 88 ARG 0.007 0.000 ARG M 235 Details of bonding type rmsd hydrogen bonds : bond 0.03959 ( 1662) hydrogen bonds : angle 3.65987 ( 4512) covalent geometry : bond 0.00305 (33673) covalent geometry : angle 0.51801 (46738) Misc. bond : bond 0.00513 ( 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 224 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 4.029 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: 0.9140 (mm-30) cc_final: 0.8706 (tp30) REVERT: A 106 ASP cc_start: 0.8767 (t70) cc_final: 0.8446 (t70) REVERT: B 43 VAL cc_start: 0.9702 (t) cc_final: 0.9437 (p) REVERT: B 49 LEU cc_start: 0.8672 (mt) cc_final: 0.8038 (mm) REVERT: B 60 VAL cc_start: 0.9684 (t) cc_final: 0.9193 (p) REVERT: B 63 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8605 (mt-10) REVERT: C 38 ASN cc_start: 0.8425 (t0) cc_final: 0.8082 (t0) REVERT: C 72 ASP cc_start: 0.8404 (m-30) cc_final: 0.8186 (m-30) REVERT: C 102 ILE cc_start: 0.9230 (mm) cc_final: 0.9030 (mm) REVERT: E 57 SER cc_start: 0.9439 (m) cc_final: 0.8836 (p) REVERT: E 81 ASP cc_start: 0.8518 (m-30) cc_final: 0.8292 (t0) REVERT: E 106 ASP cc_start: 0.8768 (m-30) cc_final: 0.8564 (m-30) REVERT: E 120 MET cc_start: 0.9065 (mmp) cc_final: 0.8511 (mmm) REVERT: F 35 ARG cc_start: 0.9293 (ttp-110) cc_final: 0.8953 (ttm110) REVERT: H 59 MET cc_start: 0.8877 (tpp) cc_final: 0.8565 (tpp) REVERT: K 46 PHE cc_start: 0.8408 (m-80) cc_final: 0.7793 (m-80) REVERT: K 198 ASP cc_start: 0.8383 (t70) cc_final: 0.7919 (m-30) REVERT: K 211 MET cc_start: 0.6591 (tpt) cc_final: 0.6007 (mmm) REVERT: K 232 TYR cc_start: 0.7871 (m-80) cc_final: 0.7439 (m-10) REVERT: K 326 MET cc_start: 0.9042 (pmm) cc_final: 0.8776 (pmm) REVERT: L 137 CYS cc_start: 0.8625 (m) cc_final: 0.8078 (p) REVERT: L 158 MET cc_start: 0.7417 (mmp) cc_final: 0.6730 (mmm) REVERT: L 210 MET cc_start: 0.7302 (ppp) cc_final: 0.6871 (ppp) REVERT: L 243 MET cc_start: 0.9599 (mmp) cc_final: 0.9335 (tpt) REVERT: L 251 MET cc_start: 0.9335 (mtp) cc_final: 0.8874 (mtp) REVERT: M 248 PHE cc_start: 0.9342 (t80) cc_final: 0.9121 (t80) REVERT: M 251 MET cc_start: 0.9492 (tpt) cc_final: 0.9170 (tpp) REVERT: N 290 ASN cc_start: 0.7296 (m-40) cc_final: 0.6882 (p0) REVERT: N 326 MET cc_start: 0.8120 (tpt) cc_final: 0.7894 (tpp) REVERT: O 176 GLU cc_start: 0.8568 (pp20) cc_final: 0.8288 (pt0) REVERT: O 211 MET cc_start: -0.2172 (ttm) cc_final: -0.2479 (ttm) REVERT: O 251 MET cc_start: -0.1072 (mtp) cc_final: -0.1299 (ttm) REVERT: P 125 MET cc_start: 0.4566 (pmm) cc_final: 0.4362 (pmm) REVERT: P 158 MET cc_start: -0.1842 (ptp) cc_final: -0.2055 (ptp) REVERT: P 294 HIS cc_start: 0.0415 (p-80) cc_final: 0.0083 (m170) REVERT: Q 338 LYS cc_start: 0.4450 (mmtt) cc_final: 0.3481 (mptt) REVERT: R 72 ASP cc_start: 0.6914 (m-30) cc_final: 0.6587 (t70) REVERT: R 178 TYR cc_start: 0.6673 (m-10) cc_final: 0.6400 (m-80) REVERT: R 251 MET cc_start: 0.8617 (mpp) cc_final: 0.8337 (mtm) REVERT: S 211 MET cc_start: 0.1165 (ttm) cc_final: 0.0277 (mtt) REVERT: S 243 MET cc_start: 0.2195 (mmt) cc_final: 0.1535 (tmm) REVERT: T 251 MET cc_start: -0.2495 (mtp) cc_final: -0.2865 (tpp) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.4151 time to fit residues: 154.9375 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 : 3.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 256 optimal weight: 40.0000 chunk 212 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 221 optimal weight: 8.9990 chunk 351 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 331 optimal weight: 8.9990 chunk 68 optimal weight: 0.7980 chunk 190 optimal weight: 50.0000 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 125 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 267 ASN ** L 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 202 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.075004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.046899 restraints weight = 277164.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.048290 restraints weight = 124045.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.049087 restraints weight = 74826.855| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.5765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 33682 Z= 0.209 Angle : 0.577 18.015 46738 Z= 0.324 Chirality : 0.039 0.143 5351 Planarity : 0.004 0.055 4942 Dihedral : 24.800 100.241 7123 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.14), residues: 3328 helix: 1.41 (0.13), residues: 1743 sheet: 1.29 (0.24), residues: 467 loop : -0.41 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.001 HIS L 294 PHE 0.022 0.002 PHE Q 195 TYR 0.024 0.001 TYR Q 54 ARG 0.011 0.000 ARG D 33 Details of bonding type rmsd hydrogen bonds : bond 0.05206 ( 1662) hydrogen bonds : angle 3.97563 ( 4512) covalent geometry : bond 0.00449 (33673) covalent geometry : angle 0.57723 (46738) Misc. bond : bond 0.00329 ( 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 212 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 3.271 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: 0.9158 (mm-30) cc_final: 0.8776 (tp30) REVERT: A 106 ASP cc_start: 0.8858 (t70) cc_final: 0.8606 (t70) REVERT: A 123 ASP cc_start: 0.8958 (m-30) cc_final: 0.8615 (m-30) REVERT: B 49 LEU cc_start: 0.8597 (mt) cc_final: 0.8050 (mm) REVERT: B 60 VAL cc_start: 0.9691 (t) cc_final: 0.9241 (p) REVERT: B 85 ASP cc_start: 0.8636 (m-30) cc_final: 0.8433 (m-30) REVERT: C 38 ASN cc_start: 0.8579 (t0) cc_final: 0.8231 (t0) REVERT: C 72 ASP cc_start: 0.8403 (m-30) cc_final: 0.8203 (m-30) REVERT: E 57 SER cc_start: 0.9458 (m) cc_final: 0.8945 (p) REVERT: E 81 ASP cc_start: 0.8592 (m-30) cc_final: 0.8299 (t0) REVERT: E 120 MET cc_start: 0.9061 (mmp) cc_final: 0.8591 (mmm) REVERT: H 59 MET cc_start: 0.8970 (tpp) cc_final: 0.8719 (tpp) REVERT: K 46 PHE cc_start: 0.8534 (m-80) cc_final: 0.7918 (m-80) REVERT: K 198 ASP cc_start: 0.8515 (t70) cc_final: 0.8019 (m-30) REVERT: K 211 MET cc_start: 0.6459 (tpt) cc_final: 0.5722 (tpp) REVERT: K 232 TYR cc_start: 0.7895 (m-80) cc_final: 0.7494 (m-10) REVERT: K 326 MET cc_start: 0.9135 (pmm) cc_final: 0.8890 (pmm) REVERT: L 137 CYS cc_start: 0.8861 (m) cc_final: 0.8281 (p) REVERT: L 158 MET cc_start: 0.7553 (mmp) cc_final: 0.6916 (mmm) REVERT: L 210 MET cc_start: 0.7296 (ppp) cc_final: 0.7079 (ppp) REVERT: L 243 MET cc_start: 0.9588 (mmp) cc_final: 0.9342 (tpt) REVERT: L 251 MET cc_start: 0.9334 (mtp) cc_final: 0.8974 (mtp) REVERT: M 251 MET cc_start: 0.9499 (tpt) cc_final: 0.9184 (tpp) REVERT: N 290 ASN cc_start: 0.7402 (m-40) cc_final: 0.7046 (p0) REVERT: N 326 MET cc_start: 0.8110 (tpt) cc_final: 0.7873 (tpp) REVERT: O 176 GLU cc_start: 0.8752 (pp20) cc_final: 0.8488 (pt0) REVERT: O 211 MET cc_start: -0.2221 (ttm) cc_final: -0.2520 (ttm) REVERT: O 251 MET cc_start: -0.0968 (mtp) cc_final: -0.1241 (ttm) REVERT: P 125 MET cc_start: 0.5019 (pmm) cc_final: 0.4802 (pmm) REVERT: P 158 MET cc_start: -0.1853 (ptp) cc_final: -0.2152 (ptp) REVERT: P 294 HIS cc_start: 0.0187 (p-80) cc_final: -0.0251 (m170) REVERT: R 72 ASP cc_start: 0.6946 (m-30) cc_final: 0.6621 (t70) REVERT: S 125 MET cc_start: -0.3631 (ttp) cc_final: -0.4014 (mtt) REVERT: S 210 MET cc_start: -0.1181 (tmm) cc_final: -0.1422 (tmm) REVERT: S 211 MET cc_start: 0.0766 (ttm) cc_final: -0.0029 (mtt) REVERT: S 243 MET cc_start: 0.1999 (mmt) cc_final: 0.1352 (tmm) REVERT: T 251 MET cc_start: -0.2454 (mtp) cc_final: -0.3451 (mmm) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.4317 time to fit residues: 153.0969 Evaluate side-chains 164 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 3.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 268 optimal weight: 30.0000 chunk 121 optimal weight: 30.0000 chunk 89 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 chunk 359 optimal weight: 30.0000 chunk 35 optimal weight: 6.9990 chunk 303 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 165 optimal weight: 20.0000 chunk 6 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 202 GLN T 23 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.075787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.047747 restraints weight = 276601.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.049020 restraints weight = 122487.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.049826 restraints weight = 73559.875| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.5982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 33682 Z= 0.155 Angle : 0.528 14.007 46738 Z= 0.300 Chirality : 0.038 0.140 5351 Planarity : 0.003 0.055 4942 Dihedral : 24.746 101.080 7123 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.15), residues: 3328 helix: 1.52 (0.13), residues: 1748 sheet: 1.23 (0.23), residues: 474 loop : -0.32 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.018 0.001 HIS L 294 PHE 0.020 0.001 PHE T 248 TYR 0.023 0.001 TYR Q 54 ARG 0.007 0.000 ARG D 33 Details of bonding type rmsd hydrogen bonds : bond 0.04143 ( 1662) hydrogen bonds : angle 3.74396 ( 4512) covalent geometry : bond 0.00331 (33673) covalent geometry : angle 0.52829 (46738) Misc. bond : bond 0.00269 ( 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 213 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 3.168 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: A 50 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8736 (tp30) REVERT: A 106 ASP cc_start: 0.8788 (t70) cc_final: 0.8468 (t70) REVERT: A 123 ASP cc_start: 0.8915 (m-30) cc_final: 0.8597 (m-30) REVERT: B 43 VAL cc_start: 0.9683 (t) cc_final: 0.9436 (p) REVERT: B 49 LEU cc_start: 0.8579 (mt) cc_final: 0.7979 (mm) REVERT: B 60 VAL cc_start: 0.9674 (t) cc_final: 0.9225 (p) REVERT: B 63 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8614 (mt-10) REVERT: B 85 ASP cc_start: 0.8617 (m-30) cc_final: 0.8415 (m-30) REVERT: B 98 TYR cc_start: 0.8976 (m-10) cc_final: 0.8741 (m-80) REVERT: C 38 ASN cc_start: 0.8569 (t0) cc_final: 0.8241 (t0) REVERT: C 72 ASP cc_start: 0.8401 (m-30) cc_final: 0.8201 (m-30) REVERT: E 37 LYS cc_start: 0.8399 (tmtt) cc_final: 0.8149 (tmtt) REVERT: E 57 SER cc_start: 0.9439 (m) cc_final: 0.8960 (p) REVERT: E 81 ASP cc_start: 0.8530 (m-30) cc_final: 0.8135 (t0) REVERT: E 119 ILE cc_start: 0.9336 (pt) cc_final: 0.8925 (pt) REVERT: E 120 MET cc_start: 0.9091 (mmp) cc_final: 0.8576 (mmm) REVERT: K 46 PHE cc_start: 0.8477 (m-80) cc_final: 0.7835 (m-80) REVERT: K 198 ASP cc_start: 0.8530 (t70) cc_final: 0.8052 (m-30) REVERT: K 211 MET cc_start: 0.6369 (tpt) cc_final: 0.5791 (mmm) REVERT: K 232 TYR cc_start: 0.7856 (m-80) cc_final: 0.7425 (m-80) REVERT: K 326 MET cc_start: 0.9163 (pmm) cc_final: 0.8911 (pmm) REVERT: L 137 CYS cc_start: 0.8857 (m) cc_final: 0.8271 (p) REVERT: L 158 MET cc_start: 0.7539 (mmp) cc_final: 0.6899 (mmm) REVERT: M 251 MET cc_start: 0.9499 (tpt) cc_final: 0.9173 (tpp) REVERT: N 290 ASN cc_start: 0.7378 (m-40) cc_final: 0.7028 (p0) REVERT: N 326 MET cc_start: 0.8085 (tpt) cc_final: 0.7778 (tpp) REVERT: O 176 GLU cc_start: 0.8649 (pp20) cc_final: 0.8381 (pt0) REVERT: O 210 MET cc_start: -0.0168 (ptp) cc_final: -0.0372 (ptt) REVERT: O 211 MET cc_start: -0.1272 (ttm) cc_final: -0.1713 (ttm) REVERT: O 251 MET cc_start: -0.1126 (mtp) cc_final: -0.1420 (ttm) REVERT: P 125 MET cc_start: 0.5292 (pmm) cc_final: 0.5076 (pmm) REVERT: P 158 MET cc_start: -0.1707 (ptp) cc_final: -0.1972 (ptp) REVERT: P 294 HIS cc_start: 0.0307 (p-80) cc_final: -0.0088 (m170) REVERT: Q 210 MET cc_start: 0.4427 (ppp) cc_final: 0.3986 (ppp) REVERT: R 72 ASP cc_start: 0.6888 (m-30) cc_final: 0.6580 (t70) REVERT: R 251 MET cc_start: 0.8575 (mpp) cc_final: 0.8309 (mtm) REVERT: S 125 MET cc_start: -0.3743 (ttp) cc_final: -0.4114 (mtt) REVERT: S 211 MET cc_start: 0.1484 (ttm) cc_final: 0.0733 (mtt) REVERT: S 243 MET cc_start: 0.2055 (mmt) cc_final: 0.1421 (tmm) REVERT: T 251 MET cc_start: -0.2274 (mtp) cc_final: -0.3342 (mmm) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.4028 time to fit residues: 144.6296 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 : 3.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 89 optimal weight: 10.0000 chunk 255 optimal weight: 40.0000 chunk 167 optimal weight: 8.9990 chunk 194 optimal weight: 6.9990 chunk 213 optimal weight: 7.9990 chunk 131 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 249 optimal weight: 50.0000 chunk 244 optimal weight: 40.0000 chunk 173 optimal weight: 5.9990 chunk 217 optimal weight: 6.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 244 HIS ** N 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 200 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.073609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.045751 restraints weight = 277644.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.047146 restraints weight = 126160.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.047941 restraints weight = 76662.107| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.6603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 33682 Z= 0.233 Angle : 0.620 20.326 46738 Z= 0.344 Chirality : 0.041 0.202 5351 Planarity : 0.004 0.054 4942 Dihedral : 24.977 103.360 7123 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.14), residues: 3328 helix: 1.18 (0.12), residues: 1745 sheet: 1.20 (0.24), residues: 470 loop : -0.40 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.022 0.002 HIS L 294 PHE 0.025 0.002 PHE N 259 TYR 0.025 0.002 TYR E 54 ARG 0.005 0.001 ARG D 33 Details of bonding type rmsd hydrogen bonds : bond 0.05709 ( 1662) hydrogen bonds : angle 4.19574 ( 4512) covalent geometry : bond 0.00500 (33673) covalent geometry : angle 0.61964 (46738) Misc. bond : bond 0.00263 ( 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 196 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 3.439 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: A 50 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8759 (tp30) REVERT: A 106 ASP cc_start: 0.8846 (t70) cc_final: 0.8552 (t70) REVERT: A 123 ASP cc_start: 0.8882 (m-30) cc_final: 0.8507 (m-30) REVERT: B 49 LEU cc_start: 0.8674 (mt) cc_final: 0.8252 (mm) REVERT: B 60 VAL cc_start: 0.9685 (t) cc_final: 0.9194 (p) REVERT: B 85 ASP cc_start: 0.8742 (m-30) cc_final: 0.8516 (m-30) REVERT: C 38 ASN cc_start: 0.8635 (t0) cc_final: 0.8296 (t0) REVERT: E 57 SER cc_start: 0.9435 (m) cc_final: 0.8902 (p) REVERT: E 81 ASP cc_start: 0.8584 (m-30) cc_final: 0.8155 (t0) REVERT: E 120 MET cc_start: 0.9057 (mmp) cc_final: 0.8598 (mmm) REVERT: H 59 MET cc_start: 0.9015 (tpp) cc_final: 0.8807 (tpp) REVERT: K 158 MET cc_start: 0.6862 (tpt) cc_final: 0.6650 (tpt) REVERT: K 198 ASP cc_start: 0.8501 (t70) cc_final: 0.7943 (m-30) REVERT: K 211 MET cc_start: 0.6565 (tpt) cc_final: 0.5838 (mmm) REVERT: K 232 TYR cc_start: 0.7766 (m-80) cc_final: 0.7321 (m-80) REVERT: L 158 MET cc_start: 0.7045 (mmp) cc_final: 0.6478 (mmm) REVERT: M 251 MET cc_start: 0.9423 (tpt) cc_final: 0.9121 (tpp) REVERT: N 290 ASN cc_start: 0.7110 (m-40) cc_final: 0.6742 (p0) REVERT: N 326 MET cc_start: 0.8099 (tpt) cc_final: 0.7745 (tpp) REVERT: O 211 MET cc_start: -0.1669 (ttm) cc_final: -0.1911 (ttm) REVERT: O 251 MET cc_start: -0.0723 (mtp) cc_final: -0.1020 (ttm) REVERT: P 125 MET cc_start: 0.5631 (pmm) cc_final: 0.5402 (pmm) REVERT: P 294 HIS cc_start: 0.0412 (p-80) cc_final: -0.0081 (m170) REVERT: Q 210 MET cc_start: 0.4288 (ppp) cc_final: 0.4006 (ptt) REVERT: R 72 ASP cc_start: 0.6788 (m-30) cc_final: 0.6402 (t70) REVERT: R 251 MET cc_start: 0.8691 (mpp) cc_final: 0.8445 (mtm) REVERT: S 125 MET cc_start: -0.3324 (ttp) cc_final: -0.3726 (mtt) REVERT: S 158 MET cc_start: 0.2799 (mtt) cc_final: 0.2586 (mtp) REVERT: S 211 MET cc_start: 0.0686 (ttm) cc_final: -0.0085 (mtt) REVERT: S 243 MET cc_start: 0.1705 (mmt) cc_final: 0.1010 (tmm) REVERT: T 251 MET cc_start: -0.2374 (mtp) cc_final: -0.3401 (mmm) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.4034 time to fit residues: 133.5820 Evaluate side-chains 154 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 3.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 349 optimal weight: 20.0000 chunk 278 optimal weight: 6.9990 chunk 144 optimal weight: 8.9990 chunk 151 optimal weight: 20.0000 chunk 23 optimal weight: 1.9990 chunk 219 optimal weight: 7.9990 chunk 112 optimal weight: 20.0000 chunk 272 optimal weight: 6.9990 chunk 340 optimal weight: 20.0000 chunk 339 optimal weight: 10.0000 chunk 157 optimal weight: 0.0870 overall best weight: 4.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 23 GLN ** N 202 GLN ** 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 = 0.3978 r_free = 0.3978 target = 0.074181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.046599 restraints weight = 276495.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.047965 restraints weight = 125364.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.048750 restraints weight = 75816.172| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.6854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 33682 Z= 0.194 Angle : 0.575 16.486 46738 Z= 0.322 Chirality : 0.039 0.169 5351 Planarity : 0.003 0.053 4942 Dihedral : 24.982 103.975 7123 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.14), residues: 3328 helix: 1.32 (0.13), residues: 1738 sheet: 1.15 (0.24), residues: 475 loop : -0.33 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.001 HIS L 294 PHE 0.019 0.002 PHE A 104 TYR 0.023 0.001 TYR Q 54 ARG 0.004 0.000 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.04674 ( 1662) hydrogen bonds : angle 3.98704 ( 4512) covalent geometry : bond 0.00417 (33673) covalent geometry : angle 0.57472 (46738) Misc. bond : bond 0.00247 ( 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 201 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 3.086 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: A 50 GLU cc_start: 0.9138 (mm-30) cc_final: 0.8701 (tp30) REVERT: A 106 ASP cc_start: 0.8860 (t70) cc_final: 0.8537 (t70) REVERT: A 123 ASP cc_start: 0.8946 (m-30) cc_final: 0.8658 (m-30) REVERT: A 125 GLN cc_start: 0.9257 (mt0) cc_final: 0.8981 (mp10) REVERT: B 49 LEU cc_start: 0.8718 (mt) cc_final: 0.8345 (mm) REVERT: B 60 VAL cc_start: 0.9671 (t) cc_final: 0.9192 (p) REVERT: B 63 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8628 (mt-10) REVERT: B 85 ASP cc_start: 0.8704 (m-30) cc_final: 0.8497 (m-30) REVERT: C 38 ASN cc_start: 0.8653 (t0) cc_final: 0.8328 (t0) REVERT: E 57 SER cc_start: 0.9446 (m) cc_final: 0.9018 (p) REVERT: E 81 ASP cc_start: 0.8537 (m-30) cc_final: 0.8215 (t0) REVERT: E 120 MET cc_start: 0.9077 (mmp) cc_final: 0.8560 (mmm) REVERT: K 158 MET cc_start: 0.6689 (tpt) cc_final: 0.6479 (tpt) REVERT: K 198 ASP cc_start: 0.8393 (t70) cc_final: 0.7761 (m-30) REVERT: K 211 MET cc_start: 0.6515 (tpt) cc_final: 0.5847 (tpp) REVERT: K 232 TYR cc_start: 0.7686 (m-80) cc_final: 0.7189 (m-80) REVERT: K 326 MET cc_start: 0.9181 (pmm) cc_final: 0.8955 (pmm) REVERT: L 158 MET cc_start: 0.6943 (mmp) cc_final: 0.6509 (mmm) REVERT: M 211 MET cc_start: 0.8121 (mmm) cc_final: 0.7754 (mmm) REVERT: M 251 MET cc_start: 0.9402 (tpt) cc_final: 0.9065 (tpp) REVERT: N 290 ASN cc_start: 0.7212 (m-40) cc_final: 0.6924 (p0) REVERT: N 326 MET cc_start: 0.7942 (tpt) cc_final: 0.7570 (tpp) REVERT: O 251 MET cc_start: -0.0426 (mtp) cc_final: -0.0655 (ttm) REVERT: P 125 MET cc_start: 0.5816 (pmm) cc_final: 0.5615 (pmm) REVERT: P 294 HIS cc_start: 0.0276 (p-80) cc_final: -0.0191 (m170) REVERT: Q 210 MET cc_start: 0.4211 (ppp) cc_final: 0.3915 (ptt) REVERT: R 72 ASP cc_start: 0.6817 (m-30) cc_final: 0.6418 (t70) REVERT: R 251 MET cc_start: 0.8748 (mpp) cc_final: 0.8539 (mtm) REVERT: S 211 MET cc_start: 0.0341 (ttm) cc_final: -0.0268 (mtt) REVERT: S 243 MET cc_start: 0.2063 (mmt) cc_final: 0.1368 (tmm) REVERT: T 251 MET cc_start: -0.2237 (mtp) cc_final: -0.3243 (mmm) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.3965 time to fit residues: 134.6298 Evaluate side-chains 160 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 3.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 241 optimal weight: 1.9990 chunk 327 optimal weight: 30.0000 chunk 6 optimal weight: 0.7980 chunk 235 optimal weight: 6.9990 chunk 229 optimal weight: 40.0000 chunk 286 optimal weight: 20.0000 chunk 3 optimal weight: 4.9990 chunk 312 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 chunk 290 optimal weight: 20.0000 chunk 239 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 47 HIS N 202 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.074405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.048908 restraints weight = 274885.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.049095 restraints weight = 156426.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.048718 restraints weight = 104721.492| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.7023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 33682 Z= 0.164 Angle : 0.554 14.180 46738 Z= 0.310 Chirality : 0.038 0.159 5351 Planarity : 0.003 0.054 4942 Dihedral : 24.864 103.791 7123 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.15), residues: 3328 helix: 1.42 (0.13), residues: 1737 sheet: 1.26 (0.24), residues: 444 loop : -0.28 (0.18), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.023 0.001 HIS L 294 PHE 0.016 0.001 PHE L 129 TYR 0.023 0.001 TYR Q 54 ARG 0.006 0.000 ARG M 130 Details of bonding type rmsd hydrogen bonds : bond 0.04366 ( 1662) hydrogen bonds : angle 3.85145 ( 4512) covalent geometry : bond 0.00353 (33673) covalent geometry : angle 0.55432 (46738) Misc. bond : bond 0.00308 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14842.47 seconds wall clock time: 258 minutes 3.00 seconds (15483.00 seconds total)