Starting phenix.real_space_refine on Tue Aug 26 01:40:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xbu_38229/08_2025/8xbu_38229.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xbu_38229/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xbu_38229/08_2025/8xbu_38229.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xbu_38229/08_2025/8xbu_38229.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xbu_38229/08_2025/8xbu_38229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xbu_38229/08_2025/8xbu_38229.map" } resolution = 4.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 309 5.49 5 S 131 5.16 5 C 19432 2.51 5 N 5887 2.21 5 O 6808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 257 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32567 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 819 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 805 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 714 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 3189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3189 Classifications: {'DNA': 156} Link IDs: {'rna3p': 155} Chain: "J" Number of atoms: 3143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3143 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Chain: "K" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2163 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Chain: "L" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2163 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Chain: "M" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2163 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Chain: "N" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2163 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Chain: "O" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1698 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 216} Chain breaks: 1 Chain: "P" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1698 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 216} Chain breaks: 1 Chain: "Q" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2163 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Chain: "R" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2163 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Chain: "S" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1698 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 216} Chain breaks: 1 Chain: "T" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2163 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Time building chain proxies: 6.99, per 1000 atoms: 0.21 Number of scatterers: 32567 At special positions: 0 Unit cell: (171.72, 156.88, 167.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 131 16.00 P 309 15.00 O 6808 8.00 N 5887 7.00 C 19432 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6218 Finding SS restraints... Secondary structure from input PDB file: 171 helices and 20 sheets defined 57.2% alpha, 14.2% beta 151 base pairs and 269 stacking pairs defined. Time for finding SS restraints: 4.52 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.698A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.595A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.579A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.738A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.486A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 123 Processing helix chain 'K' and resid 25 through 30 removed outlier: 3.751A pdb=" N GLU K 29 " --> pdb=" O ILE K 25 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN K 30 " --> pdb=" O SER K 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 25 through 30' Processing helix chain 'K' and resid 34 through 45 Processing helix chain 'K' and resid 48 through 54 Processing helix chain 'K' and resid 57 through 63 removed outlier: 3.784A pdb=" N ILE K 63 " --> pdb=" O GLU K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 82 removed outlier: 3.765A pdb=" N LYS K 80 " --> pdb=" O ALA K 76 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU K 81 " --> pdb=" O GLU K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 113 Processing helix chain 'K' and resid 132 through 144 removed outlier: 3.814A pdb=" N VAL K 142 " --> pdb=" O HIS K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 146 No H-bonds generated for 'chain 'K' and resid 145 through 146' Processing helix chain 'K' and resid 147 through 151 Processing helix chain 'K' and resid 167 through 178 Processing helix chain 'K' and resid 181 through 188 Processing helix chain 'K' and resid 196 through 214 removed outlier: 4.100A pdb=" N LEU K 204 " --> pdb=" O GLN K 200 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR K 205 " --> pdb=" O THR K 201 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN K 206 " --> pdb=" O GLN K 202 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA K 209 " --> pdb=" O TYR K 205 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL K 212 " --> pdb=" O SER K 208 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU K 213 " --> pdb=" O ALA K 209 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER K 214 " --> pdb=" O MET K 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 231 removed outlier: 3.588A pdb=" N ARG K 229 " --> pdb=" O THR K 225 " (cutoff:3.500A) Processing helix chain 'K' and resid 237 through 260 Processing helix chain 'K' and resid 290 through 296 removed outlier: 4.218A pdb=" N HIS K 294 " --> pdb=" O ASN K 290 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA K 295 " --> pdb=" O ILE K 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 30 removed outlier: 3.813A pdb=" N GLU L 29 " --> pdb=" O ILE L 25 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN L 30 " --> pdb=" O SER L 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 25 through 30' Processing helix chain 'L' and resid 34 through 45 Processing helix chain 'L' and resid 48 through 54 Processing helix chain 'L' and resid 57 through 63 removed outlier: 3.783A pdb=" N ILE L 63 " --> pdb=" O GLU L 59 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 82 removed outlier: 3.766A pdb=" N LYS L 80 " --> pdb=" O ALA L 76 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU L 81 " --> pdb=" O GLU L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 113 Processing helix chain 'L' and resid 132 through 144 removed outlier: 3.814A pdb=" N VAL L 142 " --> pdb=" O HIS L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 146 No H-bonds generated for 'chain 'L' and resid 145 through 146' Processing helix chain 'L' and resid 147 through 151 Processing helix chain 'L' and resid 167 through 178 Processing helix chain 'L' and resid 181 through 188 Processing helix chain 'L' and resid 196 through 214 removed outlier: 4.100A pdb=" N LEU L 204 " --> pdb=" O GLN L 200 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR L 205 " --> pdb=" O THR L 201 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN L 206 " --> pdb=" O GLN L 202 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA L 209 " --> pdb=" O TYR L 205 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL L 212 " --> pdb=" O SER L 208 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU L 213 " --> pdb=" O ALA L 209 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER L 214 " --> pdb=" O MET L 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 231 removed outlier: 3.589A pdb=" N ARG L 229 " --> pdb=" O THR L 225 " (cutoff:3.500A) Processing helix chain 'L' and resid 237 through 260 Processing helix chain 'L' and resid 290 through 296 removed outlier: 4.218A pdb=" N HIS L 294 " --> pdb=" O ASN L 290 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA L 295 " --> pdb=" O ILE L 291 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 30 removed outlier: 3.813A pdb=" N GLU M 29 " --> pdb=" O ILE M 25 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN M 30 " --> pdb=" O SER M 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 25 through 30' Processing helix chain 'M' and resid 34 through 45 Processing helix chain 'M' and resid 48 through 54 Processing helix chain 'M' and resid 57 through 63 removed outlier: 3.783A pdb=" N ILE M 63 " --> pdb=" O GLU M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 82 removed outlier: 3.766A pdb=" N LYS M 80 " --> pdb=" O ALA M 76 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU M 81 " --> pdb=" O GLU M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 113 Processing helix chain 'M' and resid 132 through 144 removed outlier: 3.814A pdb=" N VAL M 142 " --> pdb=" O HIS M 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 146 No H-bonds generated for 'chain 'M' and resid 145 through 146' Processing helix chain 'M' and resid 147 through 151 Processing helix chain 'M' and resid 167 through 178 Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'M' and resid 196 through 214 removed outlier: 4.100A pdb=" N LEU M 204 " --> pdb=" O GLN M 200 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR M 205 " --> pdb=" O THR M 201 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN M 206 " --> pdb=" O GLN M 202 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA M 209 " --> pdb=" O TYR M 205 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL M 212 " --> pdb=" O SER M 208 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU M 213 " --> pdb=" O ALA M 209 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER M 214 " --> pdb=" O MET M 210 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 231 removed outlier: 3.590A pdb=" N ARG M 229 " --> pdb=" O THR M 225 " (cutoff:3.500A) Processing helix chain 'M' and resid 237 through 260 Processing helix chain 'M' and resid 290 through 296 removed outlier: 4.218A pdb=" N HIS M 294 " --> pdb=" O ASN M 290 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA M 295 " --> pdb=" O ILE M 291 " (cutoff:3.500A) Processing helix chain 'N' and resid 25 through 31 removed outlier: 3.749A pdb=" N GLU N 29 " --> pdb=" O ILE N 25 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN N 30 " --> pdb=" O SER N 26 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N CYS N 31 " --> pdb=" O ARG N 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 25 through 31' Processing helix chain 'N' and resid 34 through 45 Processing helix chain 'N' and resid 48 through 54 Processing helix chain 'N' and resid 57 through 63 removed outlier: 3.784A pdb=" N ILE N 63 " --> pdb=" O GLU N 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 82 removed outlier: 3.766A pdb=" N LYS N 80 " --> pdb=" O ALA N 76 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU N 81 " --> pdb=" O GLU N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 113 Processing helix chain 'N' and resid 132 through 144 removed outlier: 3.815A pdb=" N VAL N 142 " --> pdb=" O HIS N 138 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 146 No H-bonds generated for 'chain 'N' and resid 145 through 146' Processing helix chain 'N' and resid 147 through 151 Processing helix chain 'N' and resid 167 through 178 Processing helix chain 'N' and resid 181 through 188 Processing helix chain 'N' and resid 196 through 214 removed outlier: 4.101A pdb=" N LEU N 204 " --> pdb=" O GLN N 200 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR N 205 " --> pdb=" O THR N 201 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN N 206 " --> pdb=" O GLN N 202 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA N 209 " --> pdb=" O TYR N 205 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL N 212 " --> pdb=" O SER N 208 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU N 213 " --> pdb=" O ALA N 209 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER N 214 " --> pdb=" O MET N 210 " (cutoff:3.500A) Processing helix chain 'N' and resid 225 through 231 removed outlier: 3.587A pdb=" N ARG N 229 " --> pdb=" O THR N 225 " (cutoff:3.500A) Processing helix chain 'N' and resid 237 through 260 Processing helix chain 'N' and resid 290 through 296 removed outlier: 4.219A pdb=" N HIS N 294 " --> pdb=" O ASN N 290 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA N 295 " --> pdb=" O ILE N 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 113 Processing helix chain 'O' and resid 132 through 144 removed outlier: 3.814A pdb=" N VAL O 142 " --> pdb=" O HIS O 138 " (cutoff:3.500A) Processing helix chain 'O' and resid 145 through 146 No H-bonds generated for 'chain 'O' and resid 145 through 146' Processing helix chain 'O' and resid 147 through 151 Processing helix chain 'O' and resid 167 through 178 Processing helix chain 'O' and resid 181 through 188 Processing helix chain 'O' and resid 196 through 214 removed outlier: 4.099A pdb=" N LEU O 204 " --> pdb=" O GLN O 200 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR O 205 " --> pdb=" O THR O 201 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN O 206 " --> pdb=" O GLN O 202 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA O 209 " --> pdb=" O TYR O 205 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL O 212 " --> pdb=" O SER O 208 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU O 213 " --> pdb=" O ALA O 209 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER O 214 " --> pdb=" O MET O 210 " (cutoff:3.500A) Processing helix chain 'O' and resid 225 through 231 removed outlier: 3.588A pdb=" N ARG O 229 " --> pdb=" O THR O 225 " (cutoff:3.500A) Processing helix chain 'O' and resid 237 through 260 Processing helix chain 'O' and resid 290 through 296 removed outlier: 4.218A pdb=" N HIS O 294 " --> pdb=" O ASN O 290 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA O 295 " --> pdb=" O ILE O 291 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 113 Processing helix chain 'P' and resid 132 through 144 removed outlier: 3.815A pdb=" N VAL P 142 " --> pdb=" O HIS P 138 " (cutoff:3.500A) Processing helix chain 'P' and resid 145 through 146 No H-bonds generated for 'chain 'P' and resid 145 through 146' Processing helix chain 'P' and resid 147 through 151 Processing helix chain 'P' and resid 167 through 178 Processing helix chain 'P' and resid 181 through 188 Processing helix chain 'P' and resid 196 through 214 removed outlier: 4.100A pdb=" N LEU P 204 " --> pdb=" O GLN P 200 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR P 205 " --> pdb=" O THR P 201 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN P 206 " --> pdb=" O GLN P 202 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA P 209 " --> pdb=" O TYR P 205 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL P 212 " --> pdb=" O SER P 208 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU P 213 " --> pdb=" O ALA P 209 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER P 214 " --> pdb=" O MET P 210 " (cutoff:3.500A) Processing helix chain 'P' and resid 225 through 231 removed outlier: 3.588A pdb=" N ARG P 229 " --> pdb=" O THR P 225 " (cutoff:3.500A) Processing helix chain 'P' and resid 237 through 260 Processing helix chain 'P' and resid 290 through 296 removed outlier: 4.218A pdb=" N HIS P 294 " --> pdb=" O ASN P 290 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA P 295 " --> pdb=" O ILE P 291 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 3.750A pdb=" N GLU Q 29 " --> pdb=" O ILE Q 25 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN Q 30 " --> pdb=" O SER Q 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 25 through 30' Processing helix chain 'Q' and resid 34 through 45 Processing helix chain 'Q' and resid 48 through 54 Processing helix chain 'Q' and resid 57 through 63 removed outlier: 3.785A pdb=" N ILE Q 63 " --> pdb=" O GLU Q 59 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 82 removed outlier: 3.766A pdb=" N LYS Q 80 " --> pdb=" O ALA Q 76 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU Q 81 " --> pdb=" O GLU Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 113 Processing helix chain 'Q' and resid 132 through 144 removed outlier: 3.814A pdb=" N VAL Q 142 " --> pdb=" O HIS Q 138 " (cutoff:3.500A) Processing helix chain 'Q' and resid 145 through 146 No H-bonds generated for 'chain 'Q' and resid 145 through 146' Processing helix chain 'Q' and resid 147 through 151 Processing helix chain 'Q' and resid 167 through 178 Processing helix chain 'Q' and resid 181 through 188 Processing helix chain 'Q' and resid 196 through 214 removed outlier: 4.101A pdb=" N LEU Q 204 " --> pdb=" O GLN Q 200 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR Q 205 " --> pdb=" O THR Q 201 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN Q 206 " --> pdb=" O GLN Q 202 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA Q 209 " --> pdb=" O TYR Q 205 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL Q 212 " --> pdb=" O SER Q 208 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU Q 213 " --> pdb=" O ALA Q 209 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER Q 214 " --> pdb=" O MET Q 210 " (cutoff:3.500A) Processing helix chain 'Q' and resid 225 through 231 removed outlier: 3.589A pdb=" N ARG Q 229 " --> pdb=" O THR Q 225 " (cutoff:3.500A) Processing helix chain 'Q' and resid 237 through 260 Processing helix chain 'Q' and resid 290 through 296 removed outlier: 4.218A pdb=" N HIS Q 294 " --> pdb=" O ASN Q 290 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA Q 295 " --> pdb=" O ILE Q 291 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 30 removed outlier: 3.750A pdb=" N GLU R 29 " --> pdb=" O ILE R 25 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN R 30 " --> pdb=" O SER R 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 25 through 30' Processing helix chain 'R' and resid 34 through 45 Processing helix chain 'R' and resid 48 through 54 Processing helix chain 'R' and resid 57 through 63 removed outlier: 3.785A pdb=" N ILE R 63 " --> pdb=" O GLU R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 82 removed outlier: 3.767A pdb=" N LYS R 80 " --> pdb=" O ALA R 76 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU R 81 " --> pdb=" O GLU R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 113 Processing helix chain 'R' and resid 132 through 144 removed outlier: 3.814A pdb=" N VAL R 142 " --> pdb=" O HIS R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 146 No H-bonds generated for 'chain 'R' and resid 145 through 146' Processing helix chain 'R' and resid 147 through 151 Processing helix chain 'R' and resid 167 through 178 Processing helix chain 'R' and resid 181 through 188 Processing helix chain 'R' and resid 196 through 214 removed outlier: 4.100A pdb=" N LEU R 204 " --> pdb=" O GLN R 200 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR R 205 " --> pdb=" O THR R 201 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN R 206 " --> pdb=" O GLN R 202 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA R 209 " --> pdb=" O TYR R 205 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL R 212 " --> pdb=" O SER R 208 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU R 213 " --> pdb=" O ALA R 209 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER R 214 " --> pdb=" O MET R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 231 removed outlier: 3.589A pdb=" N ARG R 229 " --> pdb=" O THR R 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 260 Processing helix chain 'R' and resid 290 through 296 removed outlier: 4.218A pdb=" N HIS R 294 " --> pdb=" O ASN R 290 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA R 295 " --> pdb=" O ILE R 291 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 113 Processing helix chain 'S' and resid 132 through 144 removed outlier: 3.813A pdb=" N VAL S 142 " --> pdb=" O HIS S 138 " (cutoff:3.500A) Processing helix chain 'S' and resid 145 through 146 No H-bonds generated for 'chain 'S' and resid 145 through 146' Processing helix chain 'S' and resid 147 through 151 Processing helix chain 'S' and resid 167 through 178 Processing helix chain 'S' and resid 181 through 188 Processing helix chain 'S' and resid 196 through 214 removed outlier: 4.100A pdb=" N LEU S 204 " --> pdb=" O GLN S 200 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR S 205 " --> pdb=" O THR S 201 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN S 206 " --> pdb=" O GLN S 202 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA S 209 " --> pdb=" O TYR S 205 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL S 212 " --> pdb=" O SER S 208 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU S 213 " --> pdb=" O ALA S 209 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER S 214 " --> pdb=" O MET S 210 " (cutoff:3.500A) Processing helix chain 'S' and resid 225 through 231 removed outlier: 3.588A pdb=" N ARG S 229 " --> pdb=" O THR S 225 " (cutoff:3.500A) Processing helix chain 'S' and resid 237 through 260 Processing helix chain 'S' and resid 290 through 296 removed outlier: 4.218A pdb=" N HIS S 294 " --> pdb=" O ASN S 290 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA S 295 " --> pdb=" O ILE S 291 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 30 removed outlier: 3.750A pdb=" N GLU T 29 " --> pdb=" O ILE T 25 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN T 30 " --> pdb=" O SER T 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 25 through 30' Processing helix chain 'T' and resid 34 through 45 Processing helix chain 'T' and resid 48 through 54 Processing helix chain 'T' and resid 57 through 63 removed outlier: 3.785A pdb=" N ILE T 63 " --> pdb=" O GLU T 59 " (cutoff:3.500A) Processing helix chain 'T' and resid 67 through 82 removed outlier: 3.766A pdb=" N LYS T 80 " --> pdb=" O ALA T 76 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU T 81 " --> pdb=" O GLU T 77 " (cutoff:3.500A) Processing helix chain 'T' and resid 106 through 113 Processing helix chain 'T' and resid 132 through 144 removed outlier: 3.814A pdb=" N VAL T 142 " --> pdb=" O HIS T 138 " (cutoff:3.500A) Processing helix chain 'T' and resid 145 through 146 No H-bonds generated for 'chain 'T' and resid 145 through 146' Processing helix chain 'T' and resid 147 through 151 Processing helix chain 'T' and resid 167 through 178 Processing helix chain 'T' and resid 181 through 188 Processing helix chain 'T' and resid 196 through 214 removed outlier: 4.101A pdb=" N LEU T 204 " --> pdb=" O GLN T 200 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR T 205 " --> pdb=" O THR T 201 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN T 206 " --> pdb=" O GLN T 202 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA T 209 " --> pdb=" O TYR T 205 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL T 212 " --> pdb=" O SER T 208 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU T 213 " --> pdb=" O ALA T 209 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER T 214 " --> pdb=" O MET T 210 " (cutoff:3.500A) Processing helix chain 'T' and resid 225 through 231 removed outlier: 3.589A pdb=" N ARG T 229 " --> pdb=" O THR T 225 " (cutoff:3.500A) Processing helix chain 'T' and resid 237 through 260 Processing helix chain 'T' and resid 290 through 296 removed outlier: 4.218A pdb=" N HIS T 294 " --> pdb=" O ASN T 290 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA T 295 " --> pdb=" O ILE T 291 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.075A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.827A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.244A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.825A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 189 through 193 removed outlier: 3.591A pdb=" N ALA K 190 " --> pdb=" O ALA K 157 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR K 159 " --> pdb=" O ALA K 190 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA K 192 " --> pdb=" O TYR K 159 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS K 156 " --> pdb=" O LEU K 218 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ILE K 220 " --> pdb=" O LYS K 156 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N MET K 158 " --> pdb=" O ILE K 220 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ASP K 222 " --> pdb=" O MET K 158 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE K 160 " --> pdb=" O ASP K 222 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA K 217 " --> pdb=" O ALA K 262 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL K 264 " --> pdb=" O ALA K 217 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU K 219 " --> pdb=" O VAL K 264 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N THR K 266 " --> pdb=" O LEU K 219 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N VAL K 221 " --> pdb=" O THR K 266 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N GLN K 268 " --> pdb=" O VAL K 221 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE K 265 " --> pdb=" O THR K 123 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N MET K 125 " --> pdb=" O ILE K 265 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN K 267 " --> pdb=" O MET K 125 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY K 127 " --> pdb=" O ASN K 267 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ILE K 122 " --> pdb=" O THR K 298 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N LEU K 300 " --> pdb=" O ILE K 122 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU K 124 " --> pdb=" O LEU K 300 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU K 302 " --> pdb=" O GLU K 124 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE K 126 " --> pdb=" O LEU K 302 " (cutoff:3.500A) removed outlier: 9.370A pdb=" N LYS K 304 " --> pdb=" O PHE K 126 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG K 299 " --> pdb=" O TYR K 315 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 189 through 193 removed outlier: 3.591A pdb=" N ALA L 190 " --> pdb=" O ALA L 157 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR L 159 " --> pdb=" O ALA L 190 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA L 192 " --> pdb=" O TYR L 159 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS L 156 " --> pdb=" O LEU L 218 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ILE L 220 " --> pdb=" O LYS L 156 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N MET L 158 " --> pdb=" O ILE L 220 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASP L 222 " --> pdb=" O MET L 158 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE L 160 " --> pdb=" O ASP L 222 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA L 217 " --> pdb=" O ALA L 262 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL L 264 " --> pdb=" O ALA L 217 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU L 219 " --> pdb=" O VAL L 264 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR L 266 " --> pdb=" O LEU L 219 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL L 221 " --> pdb=" O THR L 266 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N GLN L 268 " --> pdb=" O VAL L 221 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE L 265 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N MET L 125 " --> pdb=" O ILE L 265 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN L 267 " --> pdb=" O MET L 125 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY L 127 " --> pdb=" O ASN L 267 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE L 122 " --> pdb=" O THR L 298 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N LEU L 300 " --> pdb=" O ILE L 122 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU L 124 " --> pdb=" O LEU L 300 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU L 302 " --> pdb=" O GLU L 124 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N PHE L 126 " --> pdb=" O LEU L 302 " (cutoff:3.500A) removed outlier: 9.370A pdb=" N LYS L 304 " --> pdb=" O PHE L 126 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG L 299 " --> pdb=" O TYR L 315 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 189 through 193 removed outlier: 3.591A pdb=" N ALA M 190 " --> pdb=" O ALA M 157 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR M 159 " --> pdb=" O ALA M 190 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA M 192 " --> pdb=" O TYR M 159 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS M 156 " --> pdb=" O LEU M 218 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N ILE M 220 " --> pdb=" O LYS M 156 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N MET M 158 " --> pdb=" O ILE M 220 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ASP M 222 " --> pdb=" O MET M 158 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ILE M 160 " --> pdb=" O ASP M 222 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA M 217 " --> pdb=" O ALA M 262 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL M 264 " --> pdb=" O ALA M 217 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU M 219 " --> pdb=" O VAL M 264 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N THR M 266 " --> pdb=" O LEU M 219 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N VAL M 221 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N GLN M 268 " --> pdb=" O VAL M 221 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE M 265 " --> pdb=" O THR M 123 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET M 125 " --> pdb=" O ILE M 265 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN M 267 " --> pdb=" O MET M 125 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY M 127 " --> pdb=" O ASN M 267 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ILE M 122 " --> pdb=" O THR M 298 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N LEU M 300 " --> pdb=" O ILE M 122 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLU M 124 " --> pdb=" O LEU M 300 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU M 302 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE M 126 " --> pdb=" O LEU M 302 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N LYS M 304 " --> pdb=" O PHE M 126 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG M 299 " --> pdb=" O TYR M 315 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 189 through 193 removed outlier: 3.591A pdb=" N ALA N 190 " --> pdb=" O ALA N 157 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR N 159 " --> pdb=" O ALA N 190 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA N 192 " --> pdb=" O TYR N 159 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LYS N 156 " --> pdb=" O LEU N 218 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ILE N 220 " --> pdb=" O LYS N 156 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N MET N 158 " --> pdb=" O ILE N 220 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ASP N 222 " --> pdb=" O MET N 158 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE N 160 " --> pdb=" O ASP N 222 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA N 217 " --> pdb=" O ALA N 262 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL N 264 " --> pdb=" O ALA N 217 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU N 219 " --> pdb=" O VAL N 264 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR N 266 " --> pdb=" O LEU N 219 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL N 221 " --> pdb=" O THR N 266 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N GLN N 268 " --> pdb=" O VAL N 221 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE N 265 " --> pdb=" O THR N 123 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N MET N 125 " --> pdb=" O ILE N 265 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN N 267 " --> pdb=" O MET N 125 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY N 127 " --> pdb=" O ASN N 267 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE N 122 " --> pdb=" O THR N 298 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N LEU N 300 " --> pdb=" O ILE N 122 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU N 124 " --> pdb=" O LEU N 300 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU N 302 " --> pdb=" O GLU N 124 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N PHE N 126 " --> pdb=" O LEU N 302 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N LYS N 304 " --> pdb=" O PHE N 126 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG N 299 " --> pdb=" O TYR N 315 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 189 through 193 removed outlier: 3.591A pdb=" N ALA O 190 " --> pdb=" O ALA O 157 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR O 159 " --> pdb=" O ALA O 190 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA O 192 " --> pdb=" O TYR O 159 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS O 156 " --> pdb=" O LEU O 218 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ILE O 220 " --> pdb=" O LYS O 156 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N MET O 158 " --> pdb=" O ILE O 220 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ASP O 222 " --> pdb=" O MET O 158 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE O 160 " --> pdb=" O ASP O 222 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA O 217 " --> pdb=" O ALA O 262 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL O 264 " --> pdb=" O ALA O 217 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU O 219 " --> pdb=" O VAL O 264 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR O 266 " --> pdb=" O LEU O 219 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL O 221 " --> pdb=" O THR O 266 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N GLN O 268 " --> pdb=" O VAL O 221 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE O 265 " --> pdb=" O THR O 123 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N MET O 125 " --> pdb=" O ILE O 265 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN O 267 " --> pdb=" O MET O 125 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY O 127 " --> pdb=" O ASN O 267 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE O 122 " --> pdb=" O THR O 298 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N LEU O 300 " --> pdb=" O ILE O 122 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLU O 124 " --> pdb=" O LEU O 300 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU O 302 " --> pdb=" O GLU O 124 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N PHE O 126 " --> pdb=" O LEU O 302 " (cutoff:3.500A) removed outlier: 9.370A pdb=" N LYS O 304 " --> pdb=" O PHE O 126 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG O 299 " --> pdb=" O TYR O 315 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 189 through 193 removed outlier: 3.590A pdb=" N ALA P 190 " --> pdb=" O ALA P 157 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR P 159 " --> pdb=" O ALA P 190 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA P 192 " --> pdb=" O TYR P 159 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS P 156 " --> pdb=" O LEU P 218 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N ILE P 220 " --> pdb=" O LYS P 156 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N MET P 158 " --> pdb=" O ILE P 220 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASP P 222 " --> pdb=" O MET P 158 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE P 160 " --> pdb=" O ASP P 222 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA P 217 " --> pdb=" O ALA P 262 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL P 264 " --> pdb=" O ALA P 217 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU P 219 " --> pdb=" O VAL P 264 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N THR P 266 " --> pdb=" O LEU P 219 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL P 221 " --> pdb=" O THR P 266 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N GLN P 268 " --> pdb=" O VAL P 221 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE P 265 " --> pdb=" O THR P 123 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET P 125 " --> pdb=" O ILE P 265 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN P 267 " --> pdb=" O MET P 125 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY P 127 " --> pdb=" O ASN P 267 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE P 122 " --> pdb=" O THR P 298 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N LEU P 300 " --> pdb=" O ILE P 122 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLU P 124 " --> pdb=" O LEU P 300 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU P 302 " --> pdb=" O GLU P 124 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE P 126 " --> pdb=" O LEU P 302 " (cutoff:3.500A) removed outlier: 9.370A pdb=" N LYS P 304 " --> pdb=" O PHE P 126 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG P 299 " --> pdb=" O TYR P 315 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Q' and resid 189 through 193 removed outlier: 3.592A pdb=" N ALA Q 190 " --> pdb=" O ALA Q 157 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR Q 159 " --> pdb=" O ALA Q 190 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA Q 192 " --> pdb=" O TYR Q 159 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS Q 156 " --> pdb=" O LEU Q 218 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ILE Q 220 " --> pdb=" O LYS Q 156 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N MET Q 158 " --> pdb=" O ILE Q 220 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ASP Q 222 " --> pdb=" O MET Q 158 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE Q 160 " --> pdb=" O ASP Q 222 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA Q 217 " --> pdb=" O ALA Q 262 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL Q 264 " --> pdb=" O ALA Q 217 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU Q 219 " --> pdb=" O VAL Q 264 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR Q 266 " --> pdb=" O LEU Q 219 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL Q 221 " --> pdb=" O THR Q 266 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N GLN Q 268 " --> pdb=" O VAL Q 221 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE Q 265 " --> pdb=" O THR Q 123 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N MET Q 125 " --> pdb=" O ILE Q 265 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN Q 267 " --> pdb=" O MET Q 125 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY Q 127 " --> pdb=" O ASN Q 267 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE Q 122 " --> pdb=" O THR Q 298 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N LEU Q 300 " --> pdb=" O ILE Q 122 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU Q 124 " --> pdb=" O LEU Q 300 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU Q 302 " --> pdb=" O GLU Q 124 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE Q 126 " --> pdb=" O LEU Q 302 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N LYS Q 304 " --> pdb=" O PHE Q 126 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ARG Q 299 " --> pdb=" O TYR Q 315 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'R' and resid 189 through 193 removed outlier: 3.591A pdb=" N ALA R 190 " --> pdb=" O ALA R 157 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR R 159 " --> pdb=" O ALA R 190 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA R 192 " --> pdb=" O TYR R 159 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS R 156 " --> pdb=" O LEU R 218 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ILE R 220 " --> pdb=" O LYS R 156 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N MET R 158 " --> pdb=" O ILE R 220 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ASP R 222 " --> pdb=" O MET R 158 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE R 160 " --> pdb=" O ASP R 222 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA R 217 " --> pdb=" O ALA R 262 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL R 264 " --> pdb=" O ALA R 217 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU R 219 " --> pdb=" O VAL R 264 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR R 266 " --> pdb=" O LEU R 219 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL R 221 " --> pdb=" O THR R 266 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N GLN R 268 " --> pdb=" O VAL R 221 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE R 265 " --> pdb=" O THR R 123 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET R 125 " --> pdb=" O ILE R 265 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN R 267 " --> pdb=" O MET R 125 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY R 127 " --> pdb=" O ASN R 267 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ILE R 122 " --> pdb=" O THR R 298 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N LEU R 300 " --> pdb=" O ILE R 122 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU R 124 " --> pdb=" O LEU R 300 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU R 302 " --> pdb=" O GLU R 124 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N PHE R 126 " --> pdb=" O LEU R 302 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N LYS R 304 " --> pdb=" O PHE R 126 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG R 299 " --> pdb=" O TYR R 315 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'S' and resid 189 through 193 removed outlier: 3.590A pdb=" N ALA S 190 " --> pdb=" O ALA S 157 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR S 159 " --> pdb=" O ALA S 190 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA S 192 " --> pdb=" O TYR S 159 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS S 156 " --> pdb=" O LEU S 218 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N ILE S 220 " --> pdb=" O LYS S 156 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N MET S 158 " --> pdb=" O ILE S 220 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASP S 222 " --> pdb=" O MET S 158 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE S 160 " --> pdb=" O ASP S 222 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA S 217 " --> pdb=" O ALA S 262 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL S 264 " --> pdb=" O ALA S 217 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU S 219 " --> pdb=" O VAL S 264 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N THR S 266 " --> pdb=" O LEU S 219 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL S 221 " --> pdb=" O THR S 266 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N GLN S 268 " --> pdb=" O VAL S 221 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE S 265 " --> pdb=" O THR S 123 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET S 125 " --> pdb=" O ILE S 265 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN S 267 " --> pdb=" O MET S 125 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY S 127 " --> pdb=" O ASN S 267 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ILE S 122 " --> pdb=" O THR S 298 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N LEU S 300 " --> pdb=" O ILE S 122 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLU S 124 " --> pdb=" O LEU S 300 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU S 302 " --> pdb=" O GLU S 124 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N PHE S 126 " --> pdb=" O LEU S 302 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N LYS S 304 " --> pdb=" O PHE S 126 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ARG S 299 " --> pdb=" O TYR S 315 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'T' and resid 189 through 193 removed outlier: 3.590A pdb=" N ALA T 190 " --> pdb=" O ALA T 157 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR T 159 " --> pdb=" O ALA T 190 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA T 192 " --> pdb=" O TYR T 159 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS T 156 " --> pdb=" O LEU T 218 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ILE T 220 " --> pdb=" O LYS T 156 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N MET T 158 " --> pdb=" O ILE T 220 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASP T 222 " --> pdb=" O MET T 158 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE T 160 " --> pdb=" O ASP T 222 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA T 217 " --> pdb=" O ALA T 262 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL T 264 " --> pdb=" O ALA T 217 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU T 219 " --> pdb=" O VAL T 264 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR T 266 " --> pdb=" O LEU T 219 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL T 221 " --> pdb=" O THR T 266 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N GLN T 268 " --> pdb=" O VAL T 221 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE T 265 " --> pdb=" O THR T 123 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N MET T 125 " --> pdb=" O ILE T 265 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN T 267 " --> pdb=" O MET T 125 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY T 127 " --> pdb=" O ASN T 267 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE T 122 " --> pdb=" O THR T 298 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N LEU T 300 " --> pdb=" O ILE T 122 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU T 124 " --> pdb=" O LEU T 300 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU T 302 " --> pdb=" O GLU T 124 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N PHE T 126 " --> pdb=" O LEU T 302 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N LYS T 304 " --> pdb=" O PHE T 126 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG T 299 " --> pdb=" O TYR T 315 " (cutoff:3.500A) 1279 hydrogen bonds defined for protein. 3750 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 383 hydrogen bonds 762 hydrogen bond angles 0 basepair planarities 151 basepair parallelities 269 stacking parallelities Total time for adding SS restraints: 7.14 Time building geometry restraints manager: 3.52 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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.420 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 32.240 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.880 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.13), residues: 3328 helix: -0.01 (0.12), residues: 1618 sheet: 0.79 (0.20), residues: 530 loop : -0.25 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG M 250 TYR 0.023 0.003 TYR H 37 PHE 0.026 0.002 PHE E 78 HIS 0.011 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00887 (33673) covalent geometry : angle 0.95155 (46738) hydrogen bonds : bond 0.17716 ( 1662) hydrogen bonds : angle 6.40682 ( 4512) 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 : 1.130 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: A 97 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8355 (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: 0.8869 (ttp80) REVERT: C 25 PHE cc_start: 0.8795 (m-80) cc_final: 0.8304 (m-10) REVERT: C 90 ASP cc_start: 0.9085 (t70) cc_final: 0.8787 (t0) REVERT: C 102 ILE cc_start: 0.9276 (mm) cc_final: 0.9061 (tp) REVERT: D 43 LYS cc_start: 0.9317 (mttt) cc_final: 0.9104 (mmmm) REVERT: E 68 GLN cc_start: 0.9321 (tt0) cc_final: 0.9075 (pp30) REVERT: E 93 GLN cc_start: 0.9425 (tt0) cc_final: 0.8683 (tp40) REVERT: E 97 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8495 (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: 0.9019 (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: 0.9418 (p) REVERT: G 55 LEU cc_start: 0.9651 (mt) cc_final: 0.9421 (mt) REVERT: G 56 GLU cc_start: 0.9031 (tt0) cc_final: 0.8465 (tt0) REVERT: K 198 ASP cc_start: 0.8690 (t70) cc_final: 0.8307 (m-30) REVERT: K 318 PRO cc_start: 0.5211 (Cg_exo) cc_final: 0.4670 (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: 0.6533 (mmm) REVERT: L 210 MET cc_start: 0.7650 (tmm) cc_final: 0.7389 (tmm) REVERT: L 244 HIS cc_start: 0.8948 (t70) cc_final: 0.8449 (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: 0.7747 (p90) REVERT: N 290 ASN cc_start: 0.7675 (m-40) cc_final: 0.7131 (p0) REVERT: N 326 MET cc_start: 0.8738 (tpt) cc_final: 0.8271 (tpp) REVERT: O 195 PHE cc_start: 0.4616 (m-10) cc_final: 0.4166 (t80) REVERT: P 326 MET cc_start: 0.1786 (tpt) cc_final: 0.0546 (mtp) REVERT: R 30 GLN cc_start: -0.2648 (mp10) cc_final: -0.2949 (mm110) REVERT: S 210 MET cc_start: 0.1480 (tmm) cc_final: 0.0537 (tpp) REVERT: S 211 MET cc_start: 0.1390 (ttm) cc_final: 0.0854 (mtt) REVERT: S 243 MET cc_start: 0.2258 (mmt) cc_final: 0.1750 (tmm) REVERT: T 63 ILE cc_start: -0.0783 (mt) cc_final: -0.1100 (mm) REVERT: T 210 MET cc_start: 0.2232 (tmm) cc_final: 0.1188 (ttt) REVERT: T 251 MET cc_start: -0.0819 (mtp) cc_final: -0.1351 (mmm) outliers start: 4 outliers final: 0 residues processed: 473 average time/residue: 0.2361 time to fit residues: 170.7014 Evaluate side-chains 221 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.9558 > 50: distance: 37 - 71: 3.267 distance: 45 - 155: 3.031 distance: 49 - 146: 26.150 distance: 52 - 143: 28.041 distance: 73 - 78: 25.647 distance: 78 - 79: 34.080 distance: 79 - 80: 30.776 distance: 79 - 82: 50.666 distance: 80 - 81: 52.889 distance: 80 - 86: 48.375 distance: 83 - 84: 24.943 distance: 83 - 85: 10.844 distance: 86 - 87: 4.949 distance: 87 - 88: 15.238 distance: 87 - 90: 60.976 distance: 88 - 89: 24.131 distance: 88 - 92: 38.615 distance: 90 - 91: 15.322 distance: 92 - 93: 36.814 distance: 92 - 98: 43.043 distance: 93 - 94: 39.594 distance: 93 - 96: 17.401 distance: 94 - 95: 44.097 distance: 94 - 99: 20.596 distance: 96 - 97: 51.421 distance: 96 - 179: 20.291 distance: 97 - 98: 14.647 distance: 99 - 100: 31.279 distance: 100 - 101: 11.318 distance: 100 - 103: 46.067 distance: 101 - 102: 18.652 distance: 101 - 105: 28.342 distance: 103 - 104: 37.851 distance: 105 - 106: 23.016 distance: 106 - 107: 66.031 distance: 106 - 109: 5.292 distance: 107 - 108: 18.246 distance: 107 - 113: 54.961 distance: 109 - 110: 39.226 distance: 110 - 111: 29.866 distance: 110 - 112: 28.136 distance: 113 - 114: 57.397 distance: 113 - 119: 36.112 distance: 114 - 115: 25.830 distance: 114 - 117: 48.597 distance: 115 - 116: 34.560 distance: 115 - 120: 23.822 distance: 117 - 118: 35.287 distance: 118 - 119: 17.335 distance: 120 - 121: 14.846 distance: 121 - 122: 42.909 distance: 121 - 124: 9.188 distance: 122 - 123: 24.229 distance: 122 - 129: 44.920 distance: 124 - 125: 29.467 distance: 125 - 126: 19.730 distance: 126 - 127: 14.464 distance: 126 - 128: 17.468 distance: 130 - 131: 10.385 distance: 130 - 133: 31.191 distance: 131 - 132: 43.027 distance: 131 - 134: 17.497 distance: 134 - 135: 31.745 distance: 135 - 136: 33.178 distance: 135 - 138: 15.178 distance: 136 - 137: 16.671 distance: 136 - 143: 38.120 distance: 138 - 139: 22.721 distance: 139 - 140: 15.770 distance: 140 - 141: 13.920 distance: 140 - 142: 12.179 distance: 143 - 144: 30.788 distance: 144 - 145: 11.812 distance: 144 - 147: 16.503 distance: 145 - 146: 16.374 distance: 145 - 148: 19.863