Starting phenix.real_space_refine on Sat Jun 28 00:22:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xbu_38229/06_2025/8xbu_38229.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xbu_38229/06_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_38229/06_2025/8xbu_38229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xbu_38229/06_2025/8xbu_38229.map" model { file = "/net/cci-nas-00/data/ceres_data/8xbu_38229/06_2025/8xbu_38229.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xbu_38229/06_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 18.67, per 1000 atoms: 0.57 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: 7.49 Conformation dependent library (CDL) restraints added in 3.3 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: 13.18 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: 12.99 Time building geometry restraints manager: 8.97 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.130 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 77.200 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.180 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.330 ------------------------------------------------------------------------------- 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 : 3.063 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: 0.5060 time to fit residues: 369.6135 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 : 3.078 ------------------------------------------------------------------------------- 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 = 0.063876 restraints weight = 298998.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.063951 restraints weight = 124490.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.064568 restraints weight = 68609.305| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 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 : 3.082 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: 0.9320 (mt) cc_final: 0.8382 (mt) REVERT: B 60 VAL cc_start: 0.9740 (t) cc_final: 0.9382 (p) REVERT: B 63 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8754 (mt-10) REVERT: B 85 ASP cc_start: 0.8246 (m-30) cc_final: 0.7983 (m-30) REVERT: C 38 ASN cc_start: 0.8115 (t0) cc_final: 0.7861 (t0) REVERT: C 72 ASP cc_start: 0.8254 (m-30) cc_final: 0.8027 (m-30) REVERT: C 90 ASP cc_start: 0.8997 (t70) cc_final: 0.8761 (t0) REVERT: C 102 ILE cc_start: 0.9460 (mm) cc_final: 0.9180 (tp) REVERT: D 93 GLU cc_start: 0.9041 (mp0) cc_final: 0.8695 (mp0) REVERT: E 68 GLN cc_start: 0.9430 (tt0) cc_final: 0.9181 (pp30) REVERT: E 93 GLN cc_start: 0.9182 (tt0) cc_final: 0.8815 (tp40) REVERT: E 105 GLU cc_start: 0.7922 (pp20) cc_final: 0.7493 (pp20) REVERT: E 106 ASP cc_start: 0.8420 (m-30) cc_final: 0.8174 (m-30) REVERT: E 119 ILE cc_start: 0.9239 (pt) cc_final: 0.8865 (pt) REVERT: F 35 ARG cc_start: 0.9312 (ttp-110) cc_final: 0.8987 (ttm110) REVERT: F 44 LYS cc_start: 0.8859 (tttt) cc_final: 0.8652 (tppt) REVERT: F 68 ASP cc_start: 0.9133 (m-30) cc_final: 0.8924 (m-30) REVERT: F 79 LYS cc_start: 0.9386 (mppt) cc_final: 0.9093 (mmtm) REVERT: G 51 LEU cc_start: 0.9690 (tt) cc_final: 0.9445 (mt) REVERT: G 56 GLU cc_start: 0.8907 (tt0) cc_final: 0.8284 (mt-10) REVERT: H 64 SER cc_start: 0.9218 (m) cc_final: 0.8972 (p) REVERT: K 46 PHE cc_start: 0.8543 (m-80) cc_final: 0.7889 (m-80) REVERT: K 68 GLU cc_start: 0.9689 (pm20) cc_final: 0.9457 (mp0) REVERT: K 158 MET cc_start: 0.5973 (tpp) cc_final: 0.5705 (tpp) REVERT: K 198 ASP cc_start: 0.8622 (t70) cc_final: 0.8108 (m-30) REVERT: K 211 MET cc_start: 0.6171 (tpt) cc_final: 0.5964 (tpt) REVERT: L 125 MET cc_start: 0.8152 (pmm) cc_final: 0.7793 (pmm) REVERT: L 244 HIS cc_start: 0.8849 (t70) cc_final: 0.8499 (t-90) REVERT: L 251 MET cc_start: 0.9239 (mtm) cc_final: 0.8339 (mmm) REVERT: M 248 PHE cc_start: 0.9598 (t80) cc_final: 0.9389 (t80) REVERT: M 251 MET cc_start: 0.9567 (tpt) cc_final: 0.9191 (tpp) REVERT: N 52 VAL cc_start: -0.0434 (m) cc_final: -0.1158 (t) REVERT: N 290 ASN cc_start: 0.7554 (m-40) cc_final: 0.7156 (p0) REVERT: O 176 GLU cc_start: 0.8573 (pp20) cc_final: 0.8311 (pt0) REVERT: O 211 MET cc_start: -0.0692 (ttm) cc_final: -0.1034 (ttm) REVERT: O 251 MET cc_start: -0.1658 (mtp) cc_final: -0.1924 (ttm) REVERT: P 210 MET cc_start: 0.0821 (ppp) cc_final: 0.0267 (ppp) REVERT: P 309 THR cc_start: 0.4126 (OUTLIER) cc_final: 0.3761 (t) REVERT: P 326 MET cc_start: 0.1415 (tpt) cc_final: 0.0783 (mtt) REVERT: R 72 ASP cc_start: 0.6957 (m-30) cc_final: 0.6648 (t70) REVERT: S 210 MET cc_start: 0.0574 (tmm) cc_final: 0.0180 (tmm) REVERT: S 211 MET cc_start: 0.0899 (ttm) cc_final: 0.0119 (mtt) REVERT: S 243 MET cc_start: 0.2280 (mmt) cc_final: 0.1706 (tmm) REVERT: T 158 MET cc_start: -0.2629 (mtm) cc_final: -0.2858 (mtm) REVERT: T 210 MET cc_start: -0.0323 (tmm) cc_final: -0.0713 (ttt) REVERT: T 251 MET cc_start: -0.2244 (mtp) cc_final: -0.2959 (tpp) outliers start: 5 outliers final: 1 residues processed: 292 average time/residue: 0.4378 time to fit residues: 206.5133 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 : 3.387 ------------------------------------------------------------------------------- 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: 0.9980 chunk 200 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 330 optimal weight: 7.9990 chunk 281 optimal weight: 7.9990 chunk 169 optimal weight: 20.0000 chunk 17 optimal weight: 2.9990 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: 4.7988 ------------------------------------------------------------------------------- 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** ** 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 N 202 GLN P 114 GLN ** P 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 HIS T 244 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.088258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.061446 restraints weight = 300988.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.061358 restraints weight = 126166.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.061941 restraints weight = 69511.721| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33682 Z= 0.209 Angle : 0.592 17.444 46738 Z= 0.333 Chirality : 0.040 0.167 5351 Planarity : 0.004 0.048 4942 Dihedral : 24.910 93.407 7123 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.04 % Allowed : 2.27 % Favored : 97.70 % 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: 0.85 (0.14), residues: 3328 helix: 1.26 (0.12), residues: 1745 sheet: 0.98 (0.23), residues: 453 loop : -0.65 (0.17), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.023 0.002 HIS L 294 PHE 0.021 0.002 PHE K 129 TYR 0.034 0.002 TYR F 88 ARG 0.006 0.001 ARG E 42 Details of bonding type rmsd hydrogen bonds : bond 0.05230 ( 1662) hydrogen bonds : angle 4.20488 ( 4512) covalent geometry : bond 0.00443 (33673) covalent geometry : angle 0.59187 (46738) Misc. bond : bond 0.00480 ( 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 250 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 249 time to evaluate : 3.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8849 (tp30) cc_final: 0.8295 (tp30) REVERT: A 106 ASP cc_start: 0.8813 (t70) cc_final: 0.8557 (t70) REVERT: B 49 LEU cc_start: 0.9052 (mt) cc_final: 0.8365 (mm) REVERT: B 60 VAL cc_start: 0.9728 (t) cc_final: 0.9220 (p) REVERT: B 63 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8726 (mt-10) REVERT: C 38 ASN cc_start: 0.8334 (t0) cc_final: 0.7984 (t0) REVERT: C 90 ASP cc_start: 0.9014 (t70) cc_final: 0.8785 (t0) REVERT: D 71 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8587 (tm-30) REVERT: D 93 GLU cc_start: 0.8971 (mp0) cc_final: 0.8749 (mp0) REVERT: E 57 SER cc_start: 0.9367 (m) cc_final: 0.9115 (m) REVERT: E 93 GLN cc_start: 0.9177 (tt0) cc_final: 0.8831 (tp40) REVERT: E 105 GLU cc_start: 0.8292 (pp20) cc_final: 0.7966 (pp20) REVERT: E 119 ILE cc_start: 0.9381 (pt) cc_final: 0.8954 (pt) REVERT: E 120 MET cc_start: 0.8965 (mmp) cc_final: 0.8171 (mmm) REVERT: F 79 LYS cc_start: 0.9358 (mppt) cc_final: 0.9043 (mmtm) REVERT: G 56 GLU cc_start: 0.8876 (tt0) cc_final: 0.8287 (mt-10) REVERT: H 64 SER cc_start: 0.9293 (m) cc_final: 0.9049 (p) REVERT: K 46 PHE cc_start: 0.8652 (m-80) cc_final: 0.7882 (m-80) REVERT: K 198 ASP cc_start: 0.8511 (t70) cc_final: 0.8049 (m-30) REVERT: K 211 MET cc_start: 0.6432 (tpt) cc_final: 0.5909 (mmm) REVERT: K 232 TYR cc_start: 0.8032 (m-10) cc_final: 0.7775 (m-10) REVERT: L 125 MET cc_start: 0.8293 (pmm) cc_final: 0.7938 (pmm) REVERT: L 158 MET cc_start: 0.7644 (mmp) cc_final: 0.7096 (mmm) REVERT: L 251 MET cc_start: 0.9351 (mtm) cc_final: 0.8480 (mmm) REVERT: L 267 ASN cc_start: 0.9363 (m-40) cc_final: 0.9157 (m110) REVERT: M 248 PHE cc_start: 0.9553 (t80) cc_final: 0.9323 (t80) REVERT: M 251 MET cc_start: 0.9498 (tpt) cc_final: 0.9156 (tpp) REVERT: N 52 VAL cc_start: -0.0350 (m) cc_final: -0.1286 (t) REVERT: N 290 ASN cc_start: 0.7270 (m-40) cc_final: 0.6821 (p0) REVERT: N 326 MET cc_start: 0.8407 (tpt) cc_final: 0.8070 (tpp) REVERT: O 176 GLU cc_start: 0.8627 (pp20) cc_final: 0.8363 (pt0) REVERT: O 211 MET cc_start: 0.1055 (ttm) cc_final: 0.0685 (ttm) REVERT: O 251 MET cc_start: -0.1614 (mtp) cc_final: -0.1941 (ttm) REVERT: P 158 MET cc_start: -0.1647 (ptp) cc_final: -0.2073 (ptp) REVERT: P 326 MET cc_start: 0.0078 (tpt) cc_final: -0.0301 (mtt) REVERT: Q 210 MET cc_start: 0.4220 (tmm) cc_final: 0.3922 (tmm) REVERT: Q 211 MET cc_start: 0.2640 (mmt) cc_final: 0.2266 (mmt) REVERT: R 72 ASP cc_start: 0.6930 (m-30) cc_final: 0.6578 (t70) REVERT: S 210 MET cc_start: 0.0411 (tmm) cc_final: 0.0058 (tmm) REVERT: S 211 MET cc_start: 0.1439 (ttm) cc_final: 0.0796 (mtt) REVERT: S 243 MET cc_start: 0.2191 (mmt) cc_final: 0.1578 (tmm) REVERT: T 210 MET cc_start: -0.0790 (tmm) cc_final: -0.1085 (ttt) REVERT: T 251 MET cc_start: -0.2229 (mtp) cc_final: -0.3242 (tpp) outliers start: 1 outliers final: 0 residues processed: 250 average time/residue: 0.4348 time to fit residues: 177.4047 Evaluate side-chains 176 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 3.087 ------------------------------------------------------------------------------- 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: 0.2980 chunk 106 optimal weight: 5.9990 chunk 209 optimal weight: 30.0000 chunk 182 optimal weight: 8.9990 chunk 224 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 274 optimal weight: 3.9990 chunk 264 optimal weight: 2.9990 chunk 190 optimal weight: 40.0000 chunk 94 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 HIS T 47 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.089329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.063084 restraints weight = 299617.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.062912 restraints weight = 122849.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.063622 restraints weight = 68108.540| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33682 Z= 0.140 Angle : 0.518 12.819 46738 Z= 0.297 Chirality : 0.038 0.149 5351 Planarity : 0.003 0.049 4942 Dihedral : 24.754 94.983 7123 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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: 1.20 (0.14), residues: 3328 helix: 1.59 (0.13), residues: 1726 sheet: 1.09 (0.23), residues: 462 loop : -0.51 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.022 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 Q 193 Details of bonding type rmsd hydrogen bonds : bond 0.03976 ( 1662) hydrogen bonds : angle 3.72599 ( 4512) covalent geometry : bond 0.00295 (33673) covalent geometry : angle 0.51796 (46738) Misc. bond : bond 0.00474 ( 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 240 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 3.305 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: A 106 ASP cc_start: 0.8784 (t70) cc_final: 0.8282 (t70) REVERT: B 49 LEU cc_start: 0.8930 (mt) cc_final: 0.8001 (tp) REVERT: B 60 VAL cc_start: 0.9695 (t) cc_final: 0.9222 (p) REVERT: B 63 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8653 (mt-10) REVERT: C 38 ASN cc_start: 0.8373 (t0) cc_final: 0.7964 (t0) REVERT: C 72 ASP cc_start: 0.8389 (m-30) cc_final: 0.8165 (m-30) REVERT: E 57 SER cc_start: 0.9373 (m) cc_final: 0.8734 (p) REVERT: E 68 GLN cc_start: 0.9353 (tt0) cc_final: 0.9043 (pp30) REVERT: E 93 GLN cc_start: 0.9130 (tt0) cc_final: 0.8863 (tp40) REVERT: E 105 GLU cc_start: 0.8305 (pp20) cc_final: 0.8081 (pp20) REVERT: E 106 ASP cc_start: 0.8561 (m-30) cc_final: 0.8342 (m-30) REVERT: E 119 ILE cc_start: 0.9293 (pt) cc_final: 0.8920 (pt) REVERT: E 120 MET cc_start: 0.9040 (mmp) cc_final: 0.8231 (mmm) REVERT: F 35 ARG cc_start: 0.9316 (ttp-110) cc_final: 0.8964 (ttm110) REVERT: G 56 GLU cc_start: 0.8875 (tt0) cc_final: 0.8264 (mt-10) REVERT: H 64 SER cc_start: 0.9281 (m) cc_final: 0.9062 (p) REVERT: K 46 PHE cc_start: 0.8541 (m-80) cc_final: 0.7964 (m-80) REVERT: K 68 GLU cc_start: 0.9632 (mp0) cc_final: 0.9394 (mp0) REVERT: K 198 ASP cc_start: 0.8381 (t70) cc_final: 0.7915 (m-30) REVERT: K 211 MET cc_start: 0.6404 (tpt) cc_final: 0.6055 (mmm) REVERT: K 232 TYR cc_start: 0.7897 (m-10) cc_final: 0.7665 (m-10) REVERT: L 125 MET cc_start: 0.8705 (pmm) cc_final: 0.8440 (pmm) REVERT: L 158 MET cc_start: 0.7094 (mmp) cc_final: 0.6727 (mmm) REVERT: L 243 MET cc_start: 0.9618 (mmp) cc_final: 0.9286 (tpt) REVERT: L 251 MET cc_start: 0.9339 (mtp) cc_final: 0.8539 (mmm) REVERT: L 267 ASN cc_start: 0.9331 (m-40) cc_final: 0.9120 (m110) REVERT: M 251 MET cc_start: 0.9506 (tpt) cc_final: 0.9178 (tpp) REVERT: N 290 ASN cc_start: 0.7415 (m-40) cc_final: 0.6967 (p0) REVERT: O 176 GLU cc_start: 0.8524 (pp20) cc_final: 0.8254 (pt0) REVERT: O 211 MET cc_start: 0.1309 (ttm) cc_final: 0.0878 (ttm) REVERT: O 251 MET cc_start: -0.1699 (mtp) cc_final: -0.1950 (ttm) REVERT: P 125 MET cc_start: 0.3810 (pmm) cc_final: 0.3578 (pmm) REVERT: P 158 MET cc_start: -0.1642 (ptp) cc_final: -0.2280 (ptp) REVERT: R 72 ASP cc_start: 0.7078 (m-30) cc_final: 0.6802 (t70) REVERT: R 178 TYR cc_start: 0.6873 (m-10) cc_final: 0.6593 (m-80) REVERT: R 243 MET cc_start: 0.6376 (ppp) cc_final: 0.5754 (mmt) REVERT: S 210 MET cc_start: -0.0050 (tmm) cc_final: -0.0358 (tmm) REVERT: S 211 MET cc_start: 0.1760 (ttm) cc_final: 0.1101 (mtt) REVERT: S 243 MET cc_start: 0.2147 (mmt) cc_final: 0.1575 (tmm) REVERT: T 158 MET cc_start: -0.2516 (mtm) cc_final: -0.2740 (mtm) REVERT: T 210 MET cc_start: -0.0788 (tmm) cc_final: -0.1099 (ttt) REVERT: T 251 MET cc_start: -0.2091 (mtp) cc_final: -0.2586 (tpp) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.4274 time to fit residues: 168.9906 Evaluate side-chains 183 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 3.414 ------------------------------------------------------------------------------- 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: 50.0000 chunk 311 optimal weight: 6.9990 chunk 331 optimal weight: 20.0000 chunk 295 optimal weight: 30.0000 chunk 258 optimal weight: 9.9990 chunk 186 optimal weight: 20.0000 chunk 337 optimal weight: 20.0000 chunk 53 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 158 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 114 GLN ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 114 GLN M 206 GLN ** N 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 47 HIS ** N 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 206 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.074953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.046578 restraints weight = 277306.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.048010 restraints weight = 124351.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.048834 restraints weight = 74842.440| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 33682 Z= 0.247 Angle : 0.624 17.635 46738 Z= 0.348 Chirality : 0.041 0.153 5351 Planarity : 0.004 0.051 4942 Dihedral : 24.940 98.740 7123 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.04 % Allowed : 1.32 % Favored : 98.65 % 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: 0.90 (0.14), residues: 3328 helix: 1.21 (0.12), residues: 1748 sheet: 1.05 (0.23), residues: 472 loop : -0.50 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.021 0.002 HIS L 294 PHE 0.018 0.002 PHE A 104 TYR 0.026 0.002 TYR Q 54 ARG 0.011 0.001 ARG H 92 Details of bonding type rmsd hydrogen bonds : bond 0.05960 ( 1662) hydrogen bonds : angle 4.19004 ( 4512) covalent geometry : bond 0.00529 (33673) covalent geometry : angle 0.62386 (46738) Misc. bond : bond 0.00317 ( 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 208 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 207 time to evaluate : 3.312 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: 0.9168 (mm-30) cc_final: 0.8773 (tp30) REVERT: A 106 ASP cc_start: 0.8855 (t70) cc_final: 0.8557 (t70) REVERT: A 123 ASP cc_start: 0.8919 (m-30) cc_final: 0.8696 (m-30) REVERT: B 49 LEU cc_start: 0.8687 (mt) cc_final: 0.8158 (mm) REVERT: B 60 VAL cc_start: 0.9682 (t) cc_final: 0.9185 (p) REVERT: B 85 ASP cc_start: 0.8698 (m-30) cc_final: 0.8462 (m-30) REVERT: C 38 ASN cc_start: 0.8557 (t0) cc_final: 0.8226 (t0) REVERT: C 72 ASP cc_start: 0.8454 (m-30) cc_final: 0.8244 (m-30) REVERT: E 120 MET cc_start: 0.9044 (mmp) cc_final: 0.8453 (mmm) REVERT: F 63 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8395 (tm-30) REVERT: F 68 ASP cc_start: 0.9144 (m-30) cc_final: 0.8847 (m-30) REVERT: H 64 SER cc_start: 0.9369 (m) cc_final: 0.9135 (p) REVERT: K 46 PHE cc_start: 0.8455 (m-80) cc_final: 0.7861 (m-80) REVERT: K 198 ASP cc_start: 0.8584 (t70) cc_final: 0.8077 (m-30) REVERT: K 211 MET cc_start: 0.6611 (tpt) cc_final: 0.5859 (mmm) REVERT: K 232 TYR cc_start: 0.7792 (m-10) cc_final: 0.7496 (m-10) REVERT: K 326 MET cc_start: 0.9133 (pmm) cc_final: 0.8873 (pmm) REVERT: L 158 MET cc_start: 0.7426 (mmp) cc_final: 0.6825 (mmm) REVERT: L 243 MET cc_start: 0.9628 (mmp) cc_final: 0.9323 (tpt) REVERT: L 251 MET cc_start: 0.9352 (mtp) cc_final: 0.8971 (mtp) REVERT: M 248 PHE cc_start: 0.9433 (t80) cc_final: 0.9232 (t80) REVERT: M 251 MET cc_start: 0.9482 (tpt) cc_final: 0.9194 (tpp) REVERT: N 290 ASN cc_start: 0.7494 (m-40) cc_final: 0.7058 (p0) REVERT: N 326 MET cc_start: 0.8132 (tpt) cc_final: 0.7924 (tpp) REVERT: O 211 MET cc_start: -0.2228 (ttm) cc_final: -0.2479 (ttm) REVERT: O 251 MET cc_start: -0.1211 (mtp) cc_final: -0.1519 (ttm) REVERT: P 125 MET cc_start: 0.4224 (pmm) cc_final: 0.3974 (pmm) REVERT: P 158 MET cc_start: -0.1776 (ptp) cc_final: -0.2216 (ptp) REVERT: P 294 HIS cc_start: 0.0102 (p-80) cc_final: -0.0366 (m-70) REVERT: Q 338 LYS cc_start: 0.4467 (mmtt) cc_final: 0.3466 (mptt) REVERT: R 72 ASP cc_start: 0.7052 (m-30) cc_final: 0.6705 (t70) REVERT: R 178 TYR cc_start: 0.6626 (m-10) cc_final: 0.6359 (m-80) REVERT: S 125 MET cc_start: -0.2982 (ttp) cc_final: -0.3376 (mtt) REVERT: S 210 MET cc_start: -0.0390 (tmm) cc_final: -0.0644 (tmm) REVERT: S 211 MET cc_start: 0.1006 (ttm) cc_final: 0.0135 (mtt) REVERT: S 243 MET cc_start: 0.1923 (mmt) cc_final: 0.1183 (tmm) REVERT: T 251 MET cc_start: -0.2566 (mtp) cc_final: -0.2940 (tpp) outliers start: 1 outliers final: 0 residues processed: 208 average time/residue: 0.4472 time to fit residues: 153.0861 Evaluate side-chains 162 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 3.026 ------------------------------------------------------------------------------- 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: 1.9990 chunk 333 optimal weight: 20.0000 chunk 330 optimal weight: 6.9990 chunk 176 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 248 optimal weight: 20.0000 chunk 314 optimal weight: 6.9990 chunk 341 optimal weight: 50.0000 chunk 307 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 244 HIS ** N 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 206 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 = 0.4014 r_free = 0.4014 target = 0.076026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.047594 restraints weight = 275654.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.049095 restraints weight = 122328.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.049943 restraints weight = 73374.918| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.5482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 33682 Z= 0.164 Angle : 0.542 14.831 46738 Z= 0.308 Chirality : 0.038 0.147 5351 Planarity : 0.004 0.078 4942 Dihedral : 24.868 100.165 7123 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % 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: 1.12 (0.14), residues: 3328 helix: 1.44 (0.13), residues: 1746 sheet: 1.16 (0.24), residues: 458 loop : -0.47 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.001 HIS L 294 PHE 0.023 0.001 PHE N 248 TYR 0.025 0.001 TYR Q 54 ARG 0.020 0.000 ARG M 235 Details of bonding type rmsd hydrogen bonds : bond 0.04315 ( 1662) hydrogen bonds : angle 3.82646 ( 4512) covalent geometry : bond 0.00348 (33673) covalent geometry : angle 0.54181 (46738) Misc. bond : bond 0.00388 ( 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 215 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 3.630 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: 0.9160 (mm-30) cc_final: 0.8735 (tp30) REVERT: A 106 ASP cc_start: 0.8782 (t70) cc_final: 0.8493 (t70) REVERT: A 123 ASP cc_start: 0.8933 (m-30) cc_final: 0.8727 (m-30) REVERT: B 49 LEU cc_start: 0.8796 (mt) cc_final: 0.8277 (tp) REVERT: B 60 VAL cc_start: 0.9698 (t) cc_final: 0.9213 (p) REVERT: B 63 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8630 (mt-10) REVERT: B 85 ASP cc_start: 0.8718 (m-30) cc_final: 0.8488 (m-30) REVERT: C 38 ASN cc_start: 0.8502 (t0) cc_final: 0.8158 (t0) REVERT: C 72 ASP cc_start: 0.8432 (m-30) cc_final: 0.8213 (m-30) REVERT: E 57 SER cc_start: 0.9410 (m) cc_final: 0.9029 (p) REVERT: E 105 GLU cc_start: 0.8724 (pp20) cc_final: 0.8495 (pp20) REVERT: E 106 ASP cc_start: 0.8691 (m-30) cc_final: 0.8466 (m-30) REVERT: E 120 MET cc_start: 0.9047 (mmp) cc_final: 0.8498 (mmm) REVERT: F 63 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8366 (tm-30) REVERT: F 68 ASP cc_start: 0.9156 (m-30) cc_final: 0.8953 (m-30) REVERT: H 64 SER cc_start: 0.9345 (m) cc_final: 0.9128 (p) REVERT: K 46 PHE cc_start: 0.8300 (m-80) cc_final: 0.7669 (m-80) REVERT: K 198 ASP cc_start: 0.8443 (t70) cc_final: 0.7928 (m-30) REVERT: K 211 MET cc_start: 0.6559 (tpt) cc_final: 0.5981 (mmm) REVERT: K 232 TYR cc_start: 0.7772 (m-10) cc_final: 0.7497 (m-80) REVERT: K 326 MET cc_start: 0.9099 (pmm) cc_final: 0.8814 (pmm) REVERT: L 137 CYS cc_start: 0.8779 (m) cc_final: 0.8208 (p) REVERT: L 158 MET cc_start: 0.7364 (mmp) cc_final: 0.6809 (mmm) REVERT: L 243 MET cc_start: 0.9600 (mmp) cc_final: 0.9332 (tpt) REVERT: L 251 MET cc_start: 0.9349 (mtp) cc_final: 0.8525 (mmm) REVERT: M 251 MET cc_start: 0.9496 (tpt) cc_final: 0.9176 (tpp) REVERT: N 290 ASN cc_start: 0.7358 (m-40) cc_final: 0.6951 (p0) REVERT: N 326 MET cc_start: 0.8003 (tpt) cc_final: 0.7797 (tpp) REVERT: O 176 GLU cc_start: 0.8587 (pp20) cc_final: 0.8325 (pt0) REVERT: O 210 MET cc_start: 0.0070 (ptp) cc_final: -0.0164 (ptt) REVERT: O 211 MET cc_start: -0.2130 (ttm) cc_final: -0.2444 (ttm) REVERT: P 125 MET cc_start: 0.4758 (pmm) cc_final: 0.4538 (pmm) REVERT: P 158 MET cc_start: -0.1710 (ptp) cc_final: -0.1987 (ptp) REVERT: P 294 HIS cc_start: 0.0365 (p-80) cc_final: 0.0056 (m170) REVERT: R 72 ASP cc_start: 0.6925 (m-30) cc_final: 0.6581 (t70) REVERT: R 178 TYR cc_start: 0.6689 (m-10) cc_final: 0.6444 (m-10) REVERT: R 251 MET cc_start: 0.8696 (mpp) cc_final: 0.8435 (mtm) REVERT: S 125 MET cc_start: -0.3019 (ttp) cc_final: -0.3438 (mtt) REVERT: S 211 MET cc_start: 0.0787 (ttm) cc_final: -0.0079 (mtt) REVERT: S 243 MET cc_start: 0.1984 (mmt) cc_final: 0.1311 (tmm) REVERT: T 251 MET cc_start: -0.2629 (mtp) cc_final: -0.2983 (tpp) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.4546 time to fit residues: 165.7669 Evaluate side-chains 168 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 2.999 ------------------------------------------------------------------------------- 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: 50.0000 chunk 212 optimal weight: 20.0000 chunk 82 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 221 optimal weight: 9.9990 chunk 351 optimal weight: 10.0000 chunk 26 optimal weight: 0.0030 chunk 331 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 chunk 190 optimal weight: 50.0000 overall best weight: 4.5998 ------------------------------------------------------------------------------- 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** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.074856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.046623 restraints weight = 276581.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.048087 restraints weight = 123559.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.048903 restraints weight = 74410.626| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.5976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33682 Z= 0.197 Angle : 0.575 17.094 46738 Z= 0.322 Chirality : 0.039 0.145 5351 Planarity : 0.004 0.053 4942 Dihedral : 24.875 101.844 7123 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % 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: 1.08 (0.14), residues: 3328 helix: 1.35 (0.13), residues: 1748 sheet: 1.21 (0.24), residues: 465 loop : -0.43 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.001 HIS L 294 PHE 0.024 0.002 PHE Q 195 TYR 0.025 0.001 TYR Q 54 ARG 0.008 0.000 ARG M 235 Details of bonding type rmsd hydrogen bonds : bond 0.05081 ( 1662) hydrogen bonds : angle 3.99437 ( 4512) covalent geometry : bond 0.00422 (33673) covalent geometry : angle 0.57453 (46738) Misc. bond : bond 0.00333 ( 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 : 3.240 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: 0.9175 (mm-30) cc_final: 0.8721 (tp30) REVERT: A 106 ASP cc_start: 0.8779 (t70) cc_final: 0.8447 (t70) REVERT: A 123 ASP cc_start: 0.8953 (m-30) cc_final: 0.8571 (m-30) REVERT: B 43 VAL cc_start: 0.9707 (t) cc_final: 0.9487 (p) REVERT: B 49 LEU cc_start: 0.8731 (mt) cc_final: 0.8209 (tp) REVERT: B 60 VAL cc_start: 0.9689 (t) cc_final: 0.9233 (p) REVERT: B 63 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8668 (mt-10) REVERT: B 85 ASP cc_start: 0.8721 (m-30) cc_final: 0.8516 (m-30) REVERT: C 38 ASN cc_start: 0.8565 (t0) cc_final: 0.8243 (t0) REVERT: E 57 SER cc_start: 0.9428 (m) cc_final: 0.8898 (p) REVERT: E 106 ASP cc_start: 0.8707 (m-30) cc_final: 0.8474 (m-30) REVERT: E 120 MET cc_start: 0.8989 (mmp) cc_final: 0.8488 (mmm) REVERT: F 63 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8380 (tm-30) REVERT: K 46 PHE cc_start: 0.8508 (m-80) cc_final: 0.7843 (m-80) REVERT: K 198 ASP cc_start: 0.8473 (t70) cc_final: 0.7958 (m-30) REVERT: K 211 MET cc_start: 0.6373 (tpt) cc_final: 0.5736 (mmm) REVERT: K 232 TYR cc_start: 0.7787 (m-10) cc_final: 0.7497 (m-80) REVERT: K 326 MET cc_start: 0.9166 (pmm) cc_final: 0.8918 (pmm) REVERT: L 137 CYS cc_start: 0.8908 (m) cc_final: 0.8353 (p) REVERT: L 158 MET cc_start: 0.7328 (mmp) cc_final: 0.6844 (mmm) REVERT: L 243 MET cc_start: 0.9572 (mmp) cc_final: 0.9352 (tpt) REVERT: M 251 MET cc_start: 0.9494 (tpt) cc_final: 0.9182 (tpp) REVERT: N 290 ASN cc_start: 0.7461 (m-40) cc_final: 0.7105 (p0) REVERT: N 326 MET cc_start: 0.8149 (tpt) cc_final: 0.7856 (tpp) REVERT: O 176 GLU cc_start: 0.8683 (pp20) cc_final: 0.8404 (pt0) REVERT: O 211 MET cc_start: -0.1677 (ttm) cc_final: -0.2035 (ttm) REVERT: O 251 MET cc_start: -0.1024 (mtp) cc_final: -0.1293 (ttm) REVERT: P 125 MET cc_start: 0.5324 (pmm) cc_final: 0.5116 (pmm) REVERT: P 158 MET cc_start: -0.1676 (ptp) cc_final: -0.1899 (ptp) REVERT: P 294 HIS cc_start: 0.0074 (p-80) cc_final: -0.0597 (m170) REVERT: R 72 ASP cc_start: 0.6811 (m-30) cc_final: 0.6457 (t70) REVERT: S 125 MET cc_start: -0.3031 (ttp) cc_final: -0.3423 (mtt) REVERT: S 211 MET cc_start: 0.0739 (ttm) cc_final: -0.0111 (mtt) REVERT: S 243 MET cc_start: 0.2115 (mmt) cc_final: 0.1408 (tmm) REVERT: T 251 MET cc_start: -0.2442 (mtp) cc_final: -0.3441 (mmm) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.6342 time to fit residues: 233.3163 Evaluate side-chains 163 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 3.035 ------------------------------------------------------------------------------- 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: 40.0000 chunk 121 optimal weight: 30.0000 chunk 89 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 359 optimal weight: 30.0000 chunk 35 optimal weight: 0.0770 chunk 303 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 165 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 overall best weight: 1.9942 ------------------------------------------------------------------------------- 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** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 206 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 = 0.4070 r_free = 0.4070 target = 0.082359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.052315 restraints weight = 268231.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.053648 restraints weight = 124901.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.054517 restraints weight = 77427.276| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.6107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33682 Z= 0.130 Angle : 0.518 12.475 46738 Z= 0.293 Chirality : 0.038 0.153 5351 Planarity : 0.003 0.053 4942 Dihedral : 24.728 101.762 7123 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % 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: 1.36 (0.15), residues: 3328 helix: 1.60 (0.13), residues: 1744 sheet: 1.39 (0.24), residues: 452 loop : -0.33 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.001 HIS L 294 PHE 0.019 0.001 PHE T 248 TYR 0.023 0.001 TYR Q 54 ARG 0.005 0.000 ARG E 129 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 1662) hydrogen bonds : angle 3.66066 ( 4512) covalent geometry : bond 0.00277 (33673) covalent geometry : angle 0.51804 (46738) Misc. bond : bond 0.00293 ( 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 224 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 3.049 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: 0.9045 (mm-30) cc_final: 0.8488 (mm-30) REVERT: A 106 ASP cc_start: 0.8693 (t70) cc_final: 0.8403 (t70) REVERT: A 123 ASP cc_start: 0.8915 (m-30) cc_final: 0.8707 (m-30) REVERT: B 49 LEU cc_start: 0.8838 (mt) cc_final: 0.8248 (tp) REVERT: B 60 VAL cc_start: 0.9666 (t) cc_final: 0.9213 (p) REVERT: B 63 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8608 (mt-10) REVERT: B 98 TYR cc_start: 0.8888 (m-10) cc_final: 0.8575 (m-80) REVERT: C 38 ASN cc_start: 0.8494 (t0) cc_final: 0.8222 (t0) REVERT: E 57 SER cc_start: 0.9393 (m) cc_final: 0.8947 (p) REVERT: E 119 ILE cc_start: 0.9326 (pt) cc_final: 0.8934 (pt) REVERT: E 120 MET cc_start: 0.9034 (mmp) cc_final: 0.8544 (mmm) REVERT: F 63 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8371 (tm-30) REVERT: F 84 MET cc_start: 0.9060 (mmm) cc_final: 0.8860 (tpt) REVERT: K 46 PHE cc_start: 0.8654 (m-80) cc_final: 0.8003 (m-80) REVERT: K 198 ASP cc_start: 0.8476 (t70) cc_final: 0.7942 (m-30) REVERT: K 211 MET cc_start: 0.6371 (tpt) cc_final: 0.5825 (mmm) REVERT: K 232 TYR cc_start: 0.7916 (m-10) cc_final: 0.7553 (m-80) REVERT: K 326 MET cc_start: 0.9180 (pmm) cc_final: 0.8932 (pmm) REVERT: L 137 CYS cc_start: 0.8870 (m) cc_final: 0.8277 (p) REVERT: L 158 MET cc_start: 0.7082 (mmp) cc_final: 0.6649 (mmm) REVERT: M 251 MET cc_start: 0.9482 (tpt) cc_final: 0.9174 (tpp) REVERT: N 290 ASN cc_start: 0.7344 (m-40) cc_final: 0.7038 (p0) REVERT: N 326 MET cc_start: 0.8068 (tpt) cc_final: 0.7804 (tpp) REVERT: O 176 GLU cc_start: 0.8645 (pp20) cc_final: 0.8370 (pt0) REVERT: O 211 MET cc_start: -0.1123 (ttm) cc_final: -0.1474 (ttm) REVERT: O 251 MET cc_start: -0.0970 (mtp) cc_final: -0.1281 (ttm) REVERT: P 125 MET cc_start: 0.5436 (pmm) cc_final: 0.5216 (pmm) REVERT: P 158 MET cc_start: -0.1465 (ptp) cc_final: -0.1699 (ptp) REVERT: P 294 HIS cc_start: 0.0252 (p-80) cc_final: -0.0223 (m170) REVERT: Q 210 MET cc_start: 0.4375 (ppp) cc_final: 0.3915 (ppp) REVERT: R 72 ASP cc_start: 0.6724 (m-30) cc_final: 0.6349 (t70) REVERT: R 251 MET cc_start: 0.8642 (mpp) cc_final: 0.8404 (mtm) REVERT: S 125 MET cc_start: -0.3100 (ttp) cc_final: -0.3435 (mtt) REVERT: S 211 MET cc_start: 0.1226 (ttm) cc_final: 0.0674 (tpt) REVERT: S 243 MET cc_start: 0.2195 (mmt) cc_final: 0.1602 (tmm) REVERT: T 251 MET cc_start: -0.2454 (mtp) cc_final: -0.3435 (mmm) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.4523 time to fit residues: 170.8476 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 : 3.588 ------------------------------------------------------------------------------- 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: 0.0370 chunk 167 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 213 optimal weight: 10.0000 chunk 131 optimal weight: 30.0000 chunk 38 optimal weight: 0.8980 chunk 249 optimal weight: 50.0000 chunk 244 optimal weight: 6.9990 chunk 173 optimal weight: 7.9990 chunk 217 optimal weight: 7.9990 overall best weight: 4.5864 ------------------------------------------------------------------------------- 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** ** 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** ** N 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 200 GLN ** T 23 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 = 0.3991 r_free = 0.3991 target = 0.074659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.046609 restraints weight = 274672.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.048043 restraints weight = 124346.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.048857 restraints weight = 75397.914| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.6410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 33682 Z= 0.192 Angle : 0.560 17.123 46738 Z= 0.314 Chirality : 0.039 0.166 5351 Planarity : 0.003 0.053 4942 Dihedral : 24.792 102.291 7123 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.50 (0.13), residues: 1733 sheet: 1.22 (0.24), residues: 469 loop : -0.23 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.019 0.001 HIS L 294 PHE 0.018 0.001 PHE T 248 TYR 0.024 0.001 TYR F 88 ARG 0.004 0.000 ARG M 235 Details of bonding type rmsd hydrogen bonds : bond 0.04748 ( 1662) hydrogen bonds : angle 3.89786 ( 4512) covalent geometry : bond 0.00412 (33673) covalent geometry : angle 0.55970 (46738) Misc. bond : bond 0.00250 ( 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 210 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 3.084 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: 0.9175 (mm-30) cc_final: 0.8737 (tp30) REVERT: A 106 ASP cc_start: 0.8804 (t70) cc_final: 0.8508 (t70) REVERT: A 123 ASP cc_start: 0.8967 (m-30) cc_final: 0.8566 (m-30) REVERT: B 49 LEU cc_start: 0.8727 (mt) cc_final: 0.8209 (tp) REVERT: B 60 VAL cc_start: 0.9673 (t) cc_final: 0.9170 (p) REVERT: B 85 ASP cc_start: 0.8661 (m-30) cc_final: 0.8423 (m-30) REVERT: C 38 ASN cc_start: 0.8603 (t0) cc_final: 0.8283 (t0) REVERT: E 57 SER cc_start: 0.9440 (m) cc_final: 0.8932 (p) REVERT: E 120 MET cc_start: 0.9056 (mmp) cc_final: 0.8581 (mmm) REVERT: F 63 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8363 (tm-30) REVERT: H 59 MET cc_start: 0.8689 (tpt) cc_final: 0.8453 (tpt) REVERT: K 46 PHE cc_start: 0.8559 (m-80) cc_final: 0.7886 (m-80) REVERT: K 198 ASP cc_start: 0.8421 (t70) cc_final: 0.7799 (m-30) REVERT: K 211 MET cc_start: 0.6467 (tpt) cc_final: 0.5873 (mmm) REVERT: K 232 TYR cc_start: 0.7679 (m-10) cc_final: 0.7350 (m-80) REVERT: K 326 MET cc_start: 0.9207 (pmm) cc_final: 0.8956 (pmm) REVERT: L 137 CYS cc_start: 0.8905 (m) cc_final: 0.8358 (p) REVERT: L 158 MET cc_start: 0.6954 (mmp) cc_final: 0.6551 (mmm) REVERT: M 251 MET cc_start: 0.9412 (tpt) cc_final: 0.9123 (tpp) REVERT: N 290 ASN cc_start: 0.7263 (m-40) cc_final: 0.6899 (p0) REVERT: N 326 MET cc_start: 0.7912 (tpt) cc_final: 0.7624 (tpp) REVERT: O 176 GLU cc_start: 0.8775 (pp20) cc_final: 0.8506 (pt0) REVERT: O 211 MET cc_start: -0.1780 (ttm) cc_final: -0.2080 (ttm) REVERT: O 251 MET cc_start: -0.0754 (mtp) cc_final: -0.1071 (ttm) REVERT: P 125 MET cc_start: 0.5466 (pmm) cc_final: 0.5234 (pmm) REVERT: P 158 MET cc_start: -0.1688 (ptp) cc_final: -0.2057 (ptp) REVERT: P 294 HIS cc_start: 0.0087 (p-80) cc_final: -0.0643 (m170) REVERT: Q 210 MET cc_start: 0.4285 (ppp) cc_final: 0.3766 (ppp) REVERT: R 72 ASP cc_start: 0.6694 (m-30) cc_final: 0.6319 (t70) REVERT: R 251 MET cc_start: 0.8664 (mpp) cc_final: 0.8405 (mtm) REVERT: S 125 MET cc_start: -0.2963 (ttp) cc_final: -0.3337 (mtt) REVERT: S 211 MET cc_start: 0.0687 (ttm) cc_final: -0.0103 (mtt) REVERT: S 243 MET cc_start: 0.2103 (mmt) cc_final: 0.1448 (tmm) REVERT: T 251 MET cc_start: -0.2452 (mtp) cc_final: -0.3479 (mmm) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.4147 time to fit residues: 147.3560 Evaluate side-chains 159 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 3.417 ------------------------------------------------------------------------------- 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: 20.0000 chunk 144 optimal weight: 20.0000 chunk 151 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 219 optimal weight: 20.0000 chunk 112 optimal weight: 20.0000 chunk 272 optimal weight: 8.9990 chunk 340 optimal weight: 20.0000 chunk 339 optimal weight: 30.0000 chunk 157 optimal weight: 0.0030 overall best weight: 7.9800 ------------------------------------------------------------------------------- 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** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 199 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.074498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.046177 restraints weight = 270848.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.045789 restraints weight = 165498.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.046168 restraints weight = 120550.022| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.7213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.130 33682 Z= 0.303 Angle : 0.700 20.872 46738 Z= 0.387 Chirality : 0.043 0.245 5351 Planarity : 0.004 0.053 4942 Dihedral : 25.288 104.346 7123 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 0.57 (0.14), residues: 3328 helix: 0.84 (0.12), residues: 1735 sheet: 1.07 (0.24), residues: 457 loop : -0.51 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.023 0.002 HIS L 294 PHE 0.036 0.002 PHE N 259 TYR 0.031 0.002 TYR F 88 ARG 0.006 0.001 ARG M 235 Details of bonding type rmsd hydrogen bonds : bond 0.06784 ( 1662) hydrogen bonds : angle 4.63792 ( 4512) covalent geometry : bond 0.00652 (33673) covalent geometry : angle 0.70021 (46738) Misc. bond : bond 0.00279 ( 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 190 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 3.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8827 (tp30) REVERT: A 123 ASP cc_start: 0.8983 (m-30) cc_final: 0.8460 (m-30) REVERT: B 60 VAL cc_start: 0.9697 (t) cc_final: 0.9190 (p) REVERT: C 38 ASN cc_start: 0.8655 (t0) cc_final: 0.8455 (t0) REVERT: E 57 SER cc_start: 0.9506 (m) cc_final: 0.9175 (p) REVERT: E 120 MET cc_start: 0.8950 (mmp) cc_final: 0.8485 (mmm) REVERT: F 63 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8384 (tm-30) REVERT: H 59 MET cc_start: 0.8868 (tpt) cc_final: 0.8610 (tpt) REVERT: H 63 ASN cc_start: 0.9056 (m-40) cc_final: 0.8831 (t0) REVERT: K 198 ASP cc_start: 0.8453 (t70) cc_final: 0.7785 (m-30) REVERT: K 211 MET cc_start: 0.6631 (tpt) cc_final: 0.6107 (mmm) REVERT: K 232 TYR cc_start: 0.8055 (m-10) cc_final: 0.7662 (m-80) REVERT: L 158 MET cc_start: 0.6769 (mmp) cc_final: 0.6348 (mmm) REVERT: M 251 MET cc_start: 0.9431 (tpt) cc_final: 0.9078 (tpp) REVERT: N 290 ASN cc_start: 0.7116 (m-40) cc_final: 0.6837 (p0) REVERT: N 326 MET cc_start: 0.8079 (tpt) cc_final: 0.7564 (mmp) REVERT: O 251 MET cc_start: -0.0232 (mtp) cc_final: -0.0445 (ttm) REVERT: P 158 MET cc_start: -0.1827 (ptp) cc_final: -0.2146 (ptp) REVERT: P 211 MET cc_start: -0.5773 (ttt) cc_final: -0.5982 (ttt) REVERT: P 294 HIS cc_start: 0.0382 (p-80) cc_final: -0.0009 (m170) REVERT: Q 210 MET cc_start: 0.4260 (ppp) cc_final: 0.3709 (ptt) REVERT: R 72 ASP cc_start: 0.6496 (m-30) cc_final: 0.5960 (t70) REVERT: S 125 MET cc_start: -0.2373 (ttp) cc_final: -0.2873 (mtt) REVERT: S 211 MET cc_start: -0.1758 (ttm) cc_final: -0.2224 (mtt) REVERT: S 243 MET cc_start: 0.1738 (mmt) cc_final: 0.1013 (tmm) REVERT: T 251 MET cc_start: -0.2685 (mtp) cc_final: -0.3031 (mtp) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.3988 time to fit residues: 128.2153 Evaluate side-chains 145 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 2.970 ------------------------------------------------------------------------------- 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: 40.0000 chunk 327 optimal weight: 30.0000 chunk 6 optimal weight: 0.7980 chunk 235 optimal weight: 8.9990 chunk 229 optimal weight: 30.0000 chunk 286 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 312 optimal weight: 7.9990 chunk 154 optimal weight: 10.0000 chunk 290 optimal weight: 30.0000 chunk 239 optimal weight: 9.9990 overall best weight: 6.3588 ------------------------------------------------------------------------------- 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** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.074719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.047325 restraints weight = 271751.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 76)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.047986 restraints weight = 146532.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.047258 restraints weight = 91490.875| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.7464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 33682 Z= 0.241 Angle : 0.622 17.660 46738 Z= 0.347 Chirality : 0.041 0.187 5351 Planarity : 0.004 0.051 4942 Dihedral : 25.253 103.015 7123 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % 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: 0.67 (0.14), residues: 3328 helix: 0.96 (0.12), residues: 1739 sheet: 1.07 (0.24), residues: 448 loop : -0.51 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.002 HIS L 294 PHE 0.026 0.002 PHE N 259 TYR 0.042 0.002 TYR B 98 ARG 0.005 0.001 ARG M 235 Details of bonding type rmsd hydrogen bonds : bond 0.05479 ( 1662) hydrogen bonds : angle 4.34651 ( 4512) covalent geometry : bond 0.00515 (33673) covalent geometry : angle 0.62215 (46738) Misc. bond : bond 0.00405 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16013.39 seconds wall clock time: 285 minutes 9.80 seconds (17109.80 seconds total)