Starting phenix.real_space_refine on Mon Jul 6 04:19:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jne_36443/07_2026/8jne_36443.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jne_36443/07_2026/8jne_36443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jne_36443/07_2026/8jne_36443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jne_36443/07_2026/8jne_36443.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jne_36443/07_2026/8jne_36443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jne_36443/07_2026/8jne_36443.map" } resolution = 4.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 309 5.49 5 S 132 5.16 5 C 19680 2.51 5 N 5946 2.21 5 O 6889 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 259 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32956 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: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} 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: 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: "O" 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: "P" 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: "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: 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: "T" 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 Time building chain proxies: 6.57, per 1000 atoms: 0.20 Number of scatterers: 32956 At special positions: 0 Unit cell: (204.58, 163.24, 136.74, 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 132 16.00 P 309 15.00 O 6889 8.00 N 5946 7.00 C 19680 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=0, symmetry=0 Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 1.2 seconds 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6318 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 20 sheets defined 57.8% alpha, 13.8% beta 142 base pairs and 288 stacking pairs defined. Time for finding SS restraints: 4.67 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.808A 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 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 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 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 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 46 through 73 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 removed outlier: 3.755A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 25 through 31 removed outlier: 3.703A pdb=" N GLU K 29 " --> pdb=" O ILE K 25 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN K 30 " --> pdb=" O SER K 26 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS K 31 " --> pdb=" O ARG K 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 25 through 31' Processing helix chain 'K' and resid 34 through 45 Processing helix chain 'K' and resid 48 through 54 Processing helix chain 'K' and resid 56 through 62 removed outlier: 4.358A pdb=" N LEU K 60 " --> pdb=" O PRO K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 82 Processing helix chain 'K' and resid 106 through 113 Processing helix chain 'K' and resid 132 through 144 removed outlier: 3.701A 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: 3.835A pdb=" N LEU K 204 " --> pdb=" O GLN K 200 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR K 205 " --> pdb=" O THR K 201 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL K 212 " --> pdb=" O SER K 208 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU K 213 " --> pdb=" O ALA K 209 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER K 214 " --> pdb=" O MET K 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 231 Processing helix chain 'K' and resid 237 through 260 Processing helix chain 'K' and resid 290 through 296 removed outlier: 4.063A pdb=" N HIS K 294 " --> pdb=" O ASN K 290 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA K 295 " --> pdb=" O ILE K 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 31 removed outlier: 3.703A pdb=" N GLU L 29 " --> pdb=" O ILE L 25 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN L 30 " --> pdb=" O SER L 26 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS L 31 " --> pdb=" O ARG L 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 25 through 31' Processing helix chain 'L' and resid 34 through 45 Processing helix chain 'L' and resid 48 through 54 Processing helix chain 'L' and resid 56 through 62 removed outlier: 4.357A pdb=" N LEU L 60 " --> pdb=" O PRO L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 82 Processing helix chain 'L' and resid 106 through 113 Processing helix chain 'L' and resid 132 through 144 removed outlier: 3.701A 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: 3.835A pdb=" N LEU L 204 " --> pdb=" O GLN L 200 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR L 205 " --> pdb=" O THR L 201 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL L 212 " --> pdb=" O SER L 208 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU L 213 " --> pdb=" O ALA L 209 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER L 214 " --> pdb=" O MET L 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 231 Processing helix chain 'L' and resid 237 through 260 Processing helix chain 'L' and resid 290 through 296 removed outlier: 4.062A pdb=" N HIS L 294 " --> pdb=" O ASN L 290 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA L 295 " --> pdb=" O ILE L 291 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 31 removed outlier: 3.703A pdb=" N GLU M 29 " --> pdb=" O ILE M 25 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN M 30 " --> pdb=" O SER M 26 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS M 31 " --> pdb=" O ARG M 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 25 through 31' Processing helix chain 'M' and resid 34 through 45 Processing helix chain 'M' and resid 48 through 54 Processing helix chain 'M' and resid 56 through 62 removed outlier: 4.358A pdb=" N LEU M 60 " --> pdb=" O PRO M 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 82 Processing helix chain 'M' and resid 106 through 113 Processing helix chain 'M' and resid 132 through 144 removed outlier: 3.700A 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: 3.835A pdb=" N LEU M 204 " --> pdb=" O GLN M 200 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR M 205 " --> pdb=" O THR M 201 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL M 212 " --> pdb=" O SER M 208 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU M 213 " --> pdb=" O ALA M 209 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER M 214 " --> pdb=" O MET M 210 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 231 Processing helix chain 'M' and resid 237 through 260 Processing helix chain 'M' and resid 290 through 296 removed outlier: 4.062A pdb=" N HIS M 294 " --> pdb=" O ASN M 290 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA M 295 " --> pdb=" O ILE M 291 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 113 Processing helix chain 'N' and resid 132 through 144 removed outlier: 3.632A 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: 3.780A pdb=" N LEU N 204 " --> pdb=" O GLN N 200 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR N 205 " --> pdb=" O THR N 201 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN N 206 " --> pdb=" O GLN N 202 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL N 212 " --> pdb=" O SER N 208 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU N 213 " --> pdb=" O ALA N 209 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER N 214 " --> pdb=" O MET N 210 " (cutoff:3.500A) Processing helix chain 'N' and resid 225 through 231 removed outlier: 3.519A 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 291 through 296 removed outlier: 3.612A pdb=" N ALA N 295 " --> pdb=" O ILE N 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 25 through 31 removed outlier: 3.703A pdb=" N GLU O 29 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN O 30 " --> pdb=" O SER O 26 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS O 31 " --> pdb=" O ARG O 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 25 through 31' Processing helix chain 'O' and resid 34 through 45 Processing helix chain 'O' and resid 48 through 54 Processing helix chain 'O' and resid 56 through 62 removed outlier: 4.357A pdb=" N LEU O 60 " --> pdb=" O PRO O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 82 Processing helix chain 'O' and resid 106 through 113 Processing helix chain 'O' and resid 132 through 144 removed outlier: 3.701A 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: 3.836A pdb=" N LEU O 204 " --> pdb=" O GLN O 200 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR O 205 " --> pdb=" O THR O 201 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL O 212 " --> pdb=" O SER O 208 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU O 213 " --> pdb=" O ALA O 209 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER O 214 " --> pdb=" O MET O 210 " (cutoff:3.500A) Processing helix chain 'O' and resid 225 through 231 Processing helix chain 'O' and resid 237 through 260 Processing helix chain 'O' and resid 290 through 296 removed outlier: 4.063A pdb=" N HIS O 294 " --> pdb=" O ASN O 290 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA O 295 " --> pdb=" O ILE O 291 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 31 removed outlier: 3.703A pdb=" N GLU P 29 " --> pdb=" O ILE P 25 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN P 30 " --> pdb=" O SER P 26 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N CYS P 31 " --> pdb=" O ARG P 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 25 through 31' Processing helix chain 'P' and resid 34 through 45 Processing helix chain 'P' and resid 48 through 54 Processing helix chain 'P' and resid 56 through 62 removed outlier: 4.358A pdb=" N LEU P 60 " --> pdb=" O PRO P 56 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 82 Processing helix chain 'P' and resid 106 through 113 Processing helix chain 'P' and resid 132 through 144 removed outlier: 3.701A 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: 3.835A pdb=" N LEU P 204 " --> pdb=" O GLN P 200 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR P 205 " --> pdb=" O THR P 201 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL P 212 " --> pdb=" O SER P 208 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU P 213 " --> pdb=" O ALA P 209 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER P 214 " --> pdb=" O MET P 210 " (cutoff:3.500A) Processing helix chain 'P' and resid 225 through 231 Processing helix chain 'P' and resid 237 through 260 Processing helix chain 'P' and resid 290 through 296 removed outlier: 4.062A pdb=" N HIS P 294 " --> pdb=" O ASN P 290 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA P 295 " --> pdb=" O ILE P 291 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 31 removed outlier: 3.703A pdb=" N GLU Q 29 " --> pdb=" O ILE Q 25 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN Q 30 " --> pdb=" O SER Q 26 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS Q 31 " --> pdb=" O ARG Q 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 25 through 31' Processing helix chain 'Q' and resid 34 through 45 Processing helix chain 'Q' and resid 48 through 54 Processing helix chain 'Q' and resid 56 through 62 removed outlier: 4.357A pdb=" N LEU Q 60 " --> pdb=" O PRO Q 56 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 82 Processing helix chain 'Q' and resid 106 through 113 Processing helix chain 'Q' and resid 132 through 144 removed outlier: 3.700A 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: 3.835A pdb=" N LEU Q 204 " --> pdb=" O GLN Q 200 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR Q 205 " --> pdb=" O THR Q 201 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL Q 212 " --> pdb=" O SER Q 208 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU Q 213 " --> pdb=" O ALA Q 209 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER Q 214 " --> pdb=" O MET Q 210 " (cutoff:3.500A) Processing helix chain 'Q' and resid 225 through 231 Processing helix chain 'Q' and resid 237 through 260 Processing helix chain 'Q' and resid 290 through 296 removed outlier: 4.062A pdb=" N HIS Q 294 " --> pdb=" O ASN Q 290 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA Q 295 " --> pdb=" O ILE Q 291 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 31 removed outlier: 3.703A pdb=" N GLU R 29 " --> pdb=" O ILE R 25 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN R 30 " --> pdb=" O SER R 26 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYS R 31 " --> pdb=" O ARG R 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 25 through 31' Processing helix chain 'R' and resid 34 through 45 Processing helix chain 'R' and resid 48 through 54 Processing helix chain 'R' and resid 56 through 62 removed outlier: 4.358A pdb=" N LEU R 60 " --> pdb=" O PRO R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 82 Processing helix chain 'R' and resid 106 through 113 Processing helix chain 'R' and resid 132 through 144 removed outlier: 3.702A 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: 3.836A pdb=" N LEU R 204 " --> pdb=" O GLN R 200 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR R 205 " --> pdb=" O THR R 201 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL R 212 " --> pdb=" O SER R 208 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU R 213 " --> pdb=" O ALA R 209 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER R 214 " --> pdb=" O MET R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 231 Processing helix chain 'R' and resid 237 through 260 Processing helix chain 'R' and resid 290 through 296 removed outlier: 4.063A pdb=" N HIS R 294 " --> pdb=" O ASN R 290 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA R 295 " --> pdb=" O ILE R 291 " (cutoff:3.500A) Processing helix chain 'S' and resid 25 through 31 removed outlier: 3.703A pdb=" N GLU S 29 " --> pdb=" O ILE S 25 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN S 30 " --> pdb=" O SER S 26 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS S 31 " --> pdb=" O ARG S 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 25 through 31' Processing helix chain 'S' and resid 34 through 45 Processing helix chain 'S' and resid 48 through 54 Processing helix chain 'S' and resid 56 through 62 removed outlier: 4.358A pdb=" N LEU S 60 " --> pdb=" O PRO S 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 67 through 82 Processing helix chain 'S' and resid 106 through 113 Processing helix chain 'S' and resid 132 through 144 removed outlier: 3.701A 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: 3.835A pdb=" N LEU S 204 " --> pdb=" O GLN S 200 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR S 205 " --> pdb=" O THR S 201 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL S 212 " --> pdb=" O SER S 208 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU S 213 " --> pdb=" O ALA S 209 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER S 214 " --> pdb=" O MET S 210 " (cutoff:3.500A) Processing helix chain 'S' and resid 225 through 231 Processing helix chain 'S' and resid 237 through 260 Processing helix chain 'S' and resid 290 through 296 removed outlier: 4.062A pdb=" N HIS S 294 " --> pdb=" O ASN S 290 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA S 295 " --> pdb=" O ILE S 291 " (cutoff:3.500A) Processing helix chain 'T' and resid 106 through 113 Processing helix chain 'T' and resid 132 through 144 removed outlier: 3.633A 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: 3.780A pdb=" N LEU T 204 " --> pdb=" O GLN T 200 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR T 205 " --> pdb=" O THR T 201 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN T 206 " --> pdb=" O GLN T 202 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL T 212 " --> pdb=" O SER T 208 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU T 213 " --> pdb=" O ALA T 209 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER T 214 " --> pdb=" O MET T 210 " (cutoff:3.500A) Processing helix chain 'T' and resid 225 through 231 removed outlier: 3.520A 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 291 through 296 removed outlier: 3.613A 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: 6.865A 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 96 through 98 removed outlier: 6.902A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.975A 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: 6.761A 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: 6.978A 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: 3.709A pdb=" N TYR K 159 " --> pdb=" O ALA K 190 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA K 192 " --> pdb=" O TYR K 159 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LYS K 156 " --> pdb=" O LEU K 218 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE K 220 " --> pdb=" O LYS K 156 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N MET K 158 " --> pdb=" O ILE K 220 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASP K 222 " --> pdb=" O MET K 158 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ILE K 160 " --> pdb=" O ASP K 222 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA K 217 " --> pdb=" O ALA K 262 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL K 264 " --> pdb=" O ALA K 217 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU K 219 " --> pdb=" O VAL K 264 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N THR K 266 " --> pdb=" O LEU K 219 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL K 221 " --> pdb=" O THR K 266 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE K 265 " --> pdb=" O THR K 123 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET K 125 " --> pdb=" O ILE K 265 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN K 267 " --> pdb=" O MET K 125 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLY K 127 " --> pdb=" O ASN K 267 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ILE K 122 " --> pdb=" O THR K 298 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N LEU K 300 " --> pdb=" O ILE K 122 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU K 124 " --> pdb=" O LEU K 300 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N LEU K 302 " --> pdb=" O GLU K 124 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N PHE K 126 " --> pdb=" O LEU K 302 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N LYS K 304 " --> pdb=" O PHE K 126 " (cutoff:3.500A) removed outlier: 7.107A 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: 3.590A pdb=" N ALA L 190 " --> pdb=" O ALA L 157 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR L 159 " --> pdb=" O ALA L 190 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA L 192 " --> pdb=" O TYR L 159 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS L 156 " --> pdb=" O LEU L 218 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE L 220 " --> pdb=" O LYS L 156 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N MET L 158 " --> pdb=" O ILE L 220 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASP L 222 " --> pdb=" O MET L 158 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE L 160 " --> pdb=" O ASP L 222 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA L 217 " --> pdb=" O ALA L 262 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL L 264 " --> pdb=" O ALA L 217 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU L 219 " --> pdb=" O VAL L 264 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N THR L 266 " --> pdb=" O LEU L 219 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N VAL L 221 " --> pdb=" O THR L 266 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE L 265 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET L 125 " --> pdb=" O ILE L 265 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN L 267 " --> pdb=" O MET L 125 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLY L 127 " --> pdb=" O ASN L 267 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ILE L 122 " --> pdb=" O THR L 298 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N LEU L 300 " --> pdb=" O ILE L 122 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLU L 124 " --> pdb=" O LEU L 300 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N LEU L 302 " --> pdb=" O GLU L 124 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N PHE L 126 " --> pdb=" O LEU L 302 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N LYS L 304 " --> pdb=" O PHE L 126 " (cutoff:3.500A) removed outlier: 7.107A 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: 3.709A pdb=" N TYR M 159 " --> pdb=" O ALA M 190 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA M 192 " --> pdb=" O TYR M 159 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS M 156 " --> pdb=" O LEU M 218 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE M 220 " --> pdb=" O LYS M 156 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N MET M 158 " --> pdb=" O ILE M 220 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASP M 222 " --> pdb=" O MET M 158 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ILE M 160 " --> pdb=" O ASP M 222 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA M 217 " --> pdb=" O ALA M 262 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL M 264 " --> pdb=" O ALA M 217 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU M 219 " --> pdb=" O VAL M 264 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N THR M 266 " --> pdb=" O LEU M 219 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL M 221 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE M 265 " --> pdb=" O THR M 123 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET M 125 " --> pdb=" O ILE M 265 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN M 267 " --> pdb=" O MET M 125 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY M 127 " --> pdb=" O ASN M 267 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE M 122 " --> pdb=" O THR M 298 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N LEU M 300 " --> pdb=" O ILE M 122 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU M 124 " --> pdb=" O LEU M 300 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N LEU M 302 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N PHE M 126 " --> pdb=" O LEU M 302 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N LYS M 304 " --> pdb=" O PHE M 126 " (cutoff:3.500A) removed outlier: 7.107A 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: 6.848A pdb=" N ALA N 157 " --> pdb=" O ALA N 190 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N ALA N 192 " --> pdb=" O ALA N 157 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N TYR N 159 " --> pdb=" O ALA N 192 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS N 156 " --> pdb=" O LEU N 218 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ILE N 220 " --> pdb=" O LYS N 156 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N MET N 158 " --> pdb=" O ILE N 220 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ASP N 222 " --> pdb=" O MET N 158 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE N 160 " --> pdb=" O ASP N 222 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA N 217 " --> pdb=" O ALA N 262 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL N 264 " --> pdb=" O ALA N 217 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU N 219 " --> pdb=" O VAL N 264 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N THR N 266 " --> pdb=" O LEU N 219 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL N 221 " --> pdb=" O THR N 266 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N GLN N 268 " --> pdb=" O VAL N 221 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE N 122 " --> pdb=" O THR N 298 " (cutoff:3.500A) removed outlier: 9.144A pdb=" N LEU N 300 " --> pdb=" O ILE N 122 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N GLU N 124 " --> pdb=" O LEU N 300 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N LEU N 302 " --> pdb=" O GLU N 124 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N PHE N 126 " --> pdb=" O LEU N 302 " (cutoff:3.500A) removed outlier: 9.478A pdb=" N LYS N 304 " --> pdb=" O PHE N 126 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ARG N 299 " --> pdb=" O TYR N 315 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR N 315 " --> pdb=" O ARG N 299 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 189 through 193 removed outlier: 3.590A pdb=" N ALA O 190 " --> pdb=" O ALA O 157 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR O 159 " --> pdb=" O ALA O 190 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA O 192 " --> pdb=" O TYR O 159 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS O 156 " --> pdb=" O LEU O 218 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ILE O 220 " --> pdb=" O LYS O 156 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N MET O 158 " --> pdb=" O ILE O 220 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASP O 222 " --> pdb=" O MET O 158 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE O 160 " --> pdb=" O ASP O 222 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA O 217 " --> pdb=" O ALA O 262 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL O 264 " --> pdb=" O ALA O 217 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU O 219 " --> pdb=" O VAL O 264 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N THR O 266 " --> pdb=" O LEU O 219 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL O 221 " --> pdb=" O THR O 266 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE O 265 " --> pdb=" O THR O 123 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET O 125 " --> pdb=" O ILE O 265 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN O 267 " --> pdb=" O MET O 125 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY O 127 " --> pdb=" O ASN O 267 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE O 122 " --> pdb=" O THR O 298 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N LEU O 300 " --> pdb=" O ILE O 122 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLU O 124 " --> pdb=" O LEU O 300 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N LEU O 302 " --> pdb=" O GLU O 124 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N PHE O 126 " --> pdb=" O LEU O 302 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N LYS O 304 " --> pdb=" O PHE O 126 " (cutoff:3.500A) removed outlier: 7.107A 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: 3.591A pdb=" N ALA P 190 " --> pdb=" O ALA P 157 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR P 159 " --> pdb=" O ALA P 190 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA P 192 " --> pdb=" O TYR P 159 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LYS P 156 " --> pdb=" O LEU P 218 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ILE P 220 " --> pdb=" O LYS P 156 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N MET P 158 " --> pdb=" O ILE P 220 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ASP P 222 " --> pdb=" O MET P 158 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ILE P 160 " --> pdb=" O ASP P 222 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA P 217 " --> pdb=" O ALA P 262 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL P 264 " --> pdb=" O ALA P 217 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU P 219 " --> pdb=" O VAL P 264 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N THR P 266 " --> pdb=" O LEU P 219 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL P 221 " --> pdb=" O THR P 266 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE P 265 " --> pdb=" O THR P 123 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET P 125 " --> pdb=" O ILE P 265 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN P 267 " --> pdb=" O MET P 125 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY P 127 " --> pdb=" O ASN P 267 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE P 122 " --> pdb=" O THR P 298 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N LEU P 300 " --> pdb=" O ILE P 122 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLU P 124 " --> pdb=" O LEU P 300 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N LEU P 302 " --> pdb=" O GLU P 124 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N PHE P 126 " --> pdb=" O LEU P 302 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N LYS P 304 " --> pdb=" O PHE P 126 " (cutoff:3.500A) removed outlier: 7.107A 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: 3.590A pdb=" N ALA Q 190 " --> pdb=" O ALA Q 157 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR Q 159 " --> pdb=" O ALA Q 190 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA Q 192 " --> pdb=" O TYR Q 159 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS Q 156 " --> pdb=" O LEU Q 218 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ILE Q 220 " --> pdb=" O LYS Q 156 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N MET Q 158 " --> pdb=" O ILE Q 220 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASP Q 222 " --> pdb=" O MET Q 158 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE Q 160 " --> pdb=" O ASP Q 222 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA Q 217 " --> pdb=" O ALA Q 262 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL Q 264 " --> pdb=" O ALA Q 217 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU Q 219 " --> pdb=" O VAL Q 264 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N THR Q 266 " --> pdb=" O LEU Q 219 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N VAL Q 221 " --> pdb=" O THR Q 266 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE Q 265 " --> pdb=" O THR Q 123 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET Q 125 " --> pdb=" O ILE Q 265 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN Q 267 " --> pdb=" O MET Q 125 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY Q 127 " --> pdb=" O ASN Q 267 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ILE Q 122 " --> pdb=" O THR Q 298 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N LEU Q 300 " --> pdb=" O ILE Q 122 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU Q 124 " --> pdb=" O LEU Q 300 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N LEU Q 302 " --> pdb=" O GLU Q 124 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N PHE Q 126 " --> pdb=" O LEU Q 302 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N LYS Q 304 " --> pdb=" O PHE Q 126 " (cutoff:3.500A) removed outlier: 7.107A 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: 3.590A pdb=" N ALA R 190 " --> pdb=" O ALA R 157 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR R 159 " --> pdb=" O ALA R 190 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA R 192 " --> pdb=" O TYR R 159 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS R 156 " --> pdb=" O LEU R 218 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ILE R 220 " --> pdb=" O LYS R 156 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N MET R 158 " --> pdb=" O ILE R 220 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASP R 222 " --> pdb=" O MET R 158 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ILE R 160 " --> pdb=" O ASP R 222 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA R 217 " --> pdb=" O ALA R 262 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL R 264 " --> pdb=" O ALA R 217 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU R 219 " --> pdb=" O VAL R 264 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N THR R 266 " --> pdb=" O LEU R 219 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N VAL R 221 " --> pdb=" O THR R 266 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE R 265 " --> pdb=" O THR R 123 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET R 125 " --> pdb=" O ILE R 265 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN R 267 " --> pdb=" O MET R 125 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLY R 127 " --> pdb=" O ASN R 267 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE R 122 " --> pdb=" O THR R 298 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N LEU R 300 " --> pdb=" O ILE R 122 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLU R 124 " --> pdb=" O LEU R 300 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N LEU R 302 " --> pdb=" O GLU R 124 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N PHE R 126 " --> pdb=" O LEU R 302 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N LYS R 304 " --> pdb=" O PHE R 126 " (cutoff:3.500A) removed outlier: 7.107A 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: 3.591A pdb=" N ALA S 190 " --> pdb=" O ALA S 157 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR S 159 " --> pdb=" O ALA S 190 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA S 192 " --> pdb=" O TYR S 159 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LYS S 156 " --> pdb=" O LEU S 218 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ILE S 220 " --> pdb=" O LYS S 156 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N MET S 158 " --> pdb=" O ILE S 220 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASP S 222 " --> pdb=" O MET S 158 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE S 160 " --> pdb=" O ASP S 222 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA S 217 " --> pdb=" O ALA S 262 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL S 264 " --> pdb=" O ALA S 217 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU S 219 " --> pdb=" O VAL S 264 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N THR S 266 " --> pdb=" O LEU S 219 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL S 221 " --> pdb=" O THR S 266 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE S 265 " --> pdb=" O THR S 123 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET S 125 " --> pdb=" O ILE S 265 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN S 267 " --> pdb=" O MET S 125 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLY S 127 " --> pdb=" O ASN S 267 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ILE S 122 " --> pdb=" O THR S 298 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N LEU S 300 " --> pdb=" O ILE S 122 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU S 124 " --> pdb=" O LEU S 300 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N LEU S 302 " --> pdb=" O GLU S 124 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N PHE S 126 " --> pdb=" O LEU S 302 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N LYS S 304 " --> pdb=" O PHE S 126 " (cutoff:3.500A) removed outlier: 7.107A 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: 6.849A pdb=" N ALA T 157 " --> pdb=" O ALA T 190 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N ALA T 192 " --> pdb=" O ALA T 157 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N TYR T 159 " --> pdb=" O ALA T 192 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS T 156 " --> pdb=" O LEU T 218 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ILE T 220 " --> pdb=" O LYS T 156 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N MET T 158 " --> pdb=" O ILE T 220 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ASP T 222 " --> pdb=" O MET T 158 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE T 160 " --> pdb=" O ASP T 222 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA T 217 " --> pdb=" O ALA T 262 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N VAL T 264 " --> pdb=" O ALA T 217 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU T 219 " --> pdb=" O VAL T 264 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N THR T 266 " --> pdb=" O LEU T 219 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL T 221 " --> pdb=" O THR T 266 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N GLN T 268 " --> pdb=" O VAL T 221 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE T 122 " --> pdb=" O THR T 298 " (cutoff:3.500A) removed outlier: 9.144A pdb=" N LEU T 300 " --> pdb=" O ILE T 122 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N GLU T 124 " --> pdb=" O LEU T 300 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N LEU T 302 " --> pdb=" O GLU T 124 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N PHE T 126 " --> pdb=" O LEU T 302 " (cutoff:3.500A) removed outlier: 9.478A pdb=" N LYS T 304 " --> pdb=" O PHE T 126 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ARG T 299 " --> pdb=" O TYR T 315 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR T 315 " --> pdb=" O ARG T 299 " (cutoff:3.500A) 1348 hydrogen bonds defined for protein. 3957 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 363 hydrogen bonds 722 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 288 stacking parallelities Total time for adding SS restraints: 8.71 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10204 1.34 - 1.47: 9005 1.47 - 1.59: 14037 1.59 - 1.72: 608 1.72 - 1.84: 212 Bond restraints: 34066 Sorted by residual: bond pdb=" C5' DG I 143 " pdb=" C4' DG I 143 " ideal model delta sigma weight residual 1.512 1.540 -0.028 7.00e-03 2.04e+04 1.63e+01 bond pdb=" C5' DC J 11 " pdb=" C4' DC J 11 " ideal model delta sigma weight residual 1.512 1.539 -0.027 7.00e-03 2.04e+04 1.47e+01 bond pdb=" C3' DC I 11 " pdb=" C2' DC I 11 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.29e+01 bond pdb=" C5' DG I 149 " pdb=" C4' DG I 149 " ideal model delta sigma weight residual 1.512 1.536 -0.024 7.00e-03 2.04e+04 1.19e+01 bond pdb=" C3' DG I 20 " pdb=" C2' DG I 20 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.18e+01 ... (remaining 34061 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 45226 2.46 - 4.92: 1861 4.92 - 7.38: 146 7.38 - 9.83: 27 9.83 - 12.29: 10 Bond angle restraints: 47270 Sorted by residual: angle pdb=" O5' DC I 142 " pdb=" C5' DC I 142 " pdb=" C4' DC I 142 " ideal model delta sigma weight residual 109.40 116.99 -7.59 8.00e-01 1.56e+00 8.99e+01 angle pdb=" O5' DC I 122 " pdb=" C5' DC I 122 " pdb=" C4' DC I 122 " ideal model delta sigma weight residual 109.40 116.74 -7.34 8.00e-01 1.56e+00 8.41e+01 angle pdb=" C4' DC I 122 " pdb=" O4' DC I 122 " pdb=" C1' DC I 122 " ideal model delta sigma weight residual 110.10 103.56 6.54 1.00e+00 1.00e+00 4.28e+01 angle pdb=" O4' DC I 122 " pdb=" C1' DC I 122 " pdb=" N1 DC I 122 " ideal model delta sigma weight residual 108.00 112.41 -4.41 7.00e-01 2.04e+00 3.96e+01 angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 113.10 107.09 6.01 9.70e-01 1.06e+00 3.84e+01 ... (remaining 47265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.87: 16575 18.87 - 37.74: 1652 37.74 - 56.60: 1354 56.60 - 75.47: 218 75.47 - 94.34: 31 Dihedral angle restraints: 19830 sinusoidal: 9968 harmonic: 9862 Sorted by residual: dihedral pdb=" CA VAL R 334 " pdb=" C VAL R 334 " pdb=" N GLY R 335 " pdb=" CA GLY R 335 " ideal model delta harmonic sigma weight residual -180.00 -154.42 -25.58 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA VAL S 334 " pdb=" C VAL S 334 " pdb=" N GLY S 335 " pdb=" CA GLY S 335 " ideal model delta harmonic sigma weight residual -180.00 -154.43 -25.57 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA VAL L 334 " pdb=" C VAL L 334 " pdb=" N GLY L 335 " pdb=" CA GLY L 335 " ideal model delta harmonic sigma weight residual -180.00 -154.44 -25.56 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 19827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 5331 0.130 - 0.260: 55 0.260 - 0.390: 0 0.390 - 0.521: 7 0.521 - 0.651: 22 Chirality restraints: 5415 Sorted by residual: chirality pdb=" P DT J 1 " pdb=" OP1 DT J 1 " pdb=" OP2 DT J 1 " pdb=" O5' DT J 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.99 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" P DT J 14 " pdb=" OP1 DT J 14 " pdb=" OP2 DT J 14 " pdb=" O5' DT J 14 " both_signs ideal model delta sigma weight residual True 2.34 -2.95 -0.61 2.00e-01 2.50e+01 9.38e+00 chirality pdb=" P DA I 153 " pdb=" OP1 DA I 153 " pdb=" OP2 DA I 153 " pdb=" O5' DA I 153 " both_signs ideal model delta sigma weight residual True 2.34 -2.94 -0.61 2.00e-01 2.50e+01 9.28e+00 ... (remaining 5412 not shown) Planarity restraints: 5012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE T 195 " -0.062 2.00e-02 2.50e+03 4.48e-02 3.52e+01 pdb=" CG PHE T 195 " 0.096 2.00e-02 2.50e+03 pdb=" CD1 PHE T 195 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE T 195 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE T 195 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE T 195 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE T 195 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE N 195 " 0.062 2.00e-02 2.50e+03 4.48e-02 3.52e+01 pdb=" CG PHE N 195 " -0.096 2.00e-02 2.50e+03 pdb=" CD1 PHE N 195 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE N 195 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE N 195 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE N 195 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE N 195 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 39 " -0.043 2.00e-02 2.50e+03 3.57e-02 1.91e+01 pdb=" CG HIS A 39 " 0.058 2.00e-02 2.50e+03 pdb=" ND1 HIS A 39 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS A 39 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 HIS A 39 " 0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS A 39 " -0.044 2.00e-02 2.50e+03 ... (remaining 5009 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 172 2.41 - 3.03: 20447 3.03 - 3.66: 56082 3.66 - 4.28: 87165 4.28 - 4.90: 132621 Nonbonded interactions: 296487 Sorted by model distance: nonbonded pdb=" NH1 ARG E 72 " pdb=" OP1 DC I 50 " model vdw 1.788 3.120 nonbonded pdb=" OH TYR H 42 " pdb=" O5' DG I 20 " model vdw 1.818 3.040 nonbonded pdb=" NH2 ARG C 20 " pdb=" OP1 DG J 39 " model vdw 1.851 3.120 nonbonded pdb=" NH2 ARG E 72 " pdb=" OP2 DC I 50 " model vdw 1.876 3.120 nonbonded pdb=" OG1 THR G 76 " pdb=" C3' DG J 138 " model vdw 1.905 3.470 ... (remaining 296482 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 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'N' selection = chain 'T' } 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: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 34.710 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 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 : 0.006 0.074 34066 Z= 0.518 Angle : 1.102 12.292 47270 Z= 0.848 Chirality : 0.064 0.651 5415 Planarity : 0.006 0.089 5012 Dihedral : 20.643 94.338 13512 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 24.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Rotamer: Outliers : 0.14 % Allowed : 0.79 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.13), residues: 3380 helix: 0.03 (0.11), residues: 1697 sheet: 0.30 (0.20), residues: 542 loop : -0.25 (0.17), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG N 299 TYR 0.016 0.003 TYR F 51 PHE 0.096 0.003 PHE N 195 HIS 0.030 0.002 HIS T 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.52 (34066) covalent geometry : angle 1.10154 / 0.85 (47270) hydrogen bonds : bond 0.20823 / 14.54 ( 1711) hydrogen bonds : angle 6.82401 / 5.00 ( 4679) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 352 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8059 (mt) cc_final: 0.7688 (mp) REVERT: A 61 LEU cc_start: 0.7677 (mt) cc_final: 0.7470 (mt) REVERT: A 74 ILE cc_start: 0.9526 (mt) cc_final: 0.9321 (mm) REVERT: A 106 ASP cc_start: 0.9045 (m-30) cc_final: 0.8491 (m-30) REVERT: B 46 ILE cc_start: 0.9438 (mt) cc_final: 0.9129 (tp) REVERT: B 68 ASP cc_start: 0.8931 (m-30) cc_final: 0.8668 (m-30) REVERT: B 81 VAL cc_start: 0.9020 (t) cc_final: 0.8771 (t) REVERT: B 96 THR cc_start: 0.9038 (m) cc_final: 0.8750 (p) REVERT: D 37 TYR cc_start: 0.8137 (m-80) cc_final: 0.7619 (m-80) REVERT: D 54 ILE cc_start: 0.8586 (tt) cc_final: 0.8329 (tt) REVERT: D 62 MET cc_start: 0.8330 (mmm) cc_final: 0.8121 (mmm) REVERT: D 106 LEU cc_start: 0.8866 (tp) cc_final: 0.8527 (mt) REVERT: E 54 TYR cc_start: 0.8426 (m-80) cc_final: 0.7956 (m-10) REVERT: E 94 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8182 (mm-30) REVERT: E 99 TYR cc_start: 0.8394 (t80) cc_final: 0.8141 (t80) REVERT: E 119 ILE cc_start: 0.9374 (pt) cc_final: 0.8872 (pt) REVERT: E 124 ILE cc_start: 0.9515 (mt) cc_final: 0.9176 (mm) REVERT: F 44 LYS cc_start: 0.9022 (tttt) cc_final: 0.8519 (mtpp) REVERT: F 46 ILE cc_start: 0.9154 (mt) cc_final: 0.8880 (tt) REVERT: F 81 VAL cc_start: 0.8462 (t) cc_final: 0.8074 (t) REVERT: F 85 ASP cc_start: 0.8538 (m-30) cc_final: 0.8300 (m-30) REVERT: G 114 VAL cc_start: 0.8434 (t) cc_final: 0.8099 (p) REVERT: G 115 LEU cc_start: 0.8884 (mt) cc_final: 0.8138 (mp) REVERT: H 37 TYR cc_start: 0.7981 (m-80) cc_final: 0.7715 (m-10) REVERT: H 61 ILE cc_start: 0.9678 (mt) cc_final: 0.9301 (mm) REVERT: H 65 PHE cc_start: 0.8983 (t80) cc_final: 0.8738 (t80) REVERT: H 73 ILE cc_start: 0.9790 (mt) cc_final: 0.9582 (tp) REVERT: H 100 LEU cc_start: 0.9236 (mt) cc_final: 0.9024 (mt) REVERT: K 326 MET cc_start: 0.3037 (tpt) cc_final: 0.2619 (tpt) REVERT: L 50 GLU cc_start: 0.7985 (tt0) cc_final: 0.7410 (tt0) REVERT: L 210 MET cc_start: 0.2391 (tmm) cc_final: 0.0946 (ppp) REVERT: L 211 MET cc_start: 0.2829 (ttm) cc_final: 0.2417 (ttm) REVERT: L 254 ARG cc_start: 0.1415 (ttm170) cc_final: 0.0891 (ptt-90) REVERT: L 326 MET cc_start: 0.2701 (tpt) cc_final: 0.1685 (ptm) REVERT: M 30 GLN cc_start: 0.4970 (mp10) cc_final: 0.4350 (tm-30) REVERT: M 235 ARG cc_start: -0.0296 (mmt180) cc_final: -0.0589 (mpt180) REVERT: N 210 MET cc_start: 0.2131 (tmm) cc_final: 0.1826 (tmm) REVERT: S 210 MET cc_start: 0.4584 (tmm) cc_final: 0.3226 (ppp) REVERT: S 243 MET cc_start: 0.6316 (mmt) cc_final: 0.5909 (ppp) REVERT: T 306 ARG cc_start: 0.2747 (mmm160) cc_final: 0.1926 (tpt170) outliers start: 4 outliers final: 1 residues processed: 353 average time/residue: 0.2161 time to fit residues: 120.5380 Evaluate side-chains 184 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 197 optimal weight: 40.0000 chunk 215 optimal weight: 50.0000 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS E 108 ASN K 202 GLN ** L 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 294 HIS P 294 HIS Q 62 ASN T 114 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.066635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.047648 restraints weight = 399816.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.049191 restraints weight = 206756.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.050124 restraints weight = 130474.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.050717 restraints weight = 94158.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.051111 restraints weight = 75208.089| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.134 34066 Z= 0.228 Angle : 0.781 10.048 47270 Z= 0.423 Chirality : 0.050 0.286 5415 Planarity : 0.006 0.070 5012 Dihedral : 25.296 102.830 7175 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.11 % Allowed : 3.38 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.13), residues: 3380 helix: 0.35 (0.12), residues: 1779 sheet: 0.33 (0.22), residues: 406 loop : -0.85 (0.16), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG S 235 TYR 0.047 0.003 TYR B 98 PHE 0.044 0.003 PHE K 248 HIS 0.010 0.001 HIS Q 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.23 (34066) covalent geometry : angle 0.78110 / 0.42 (47270) hydrogen bonds : bond 0.06010 / 4.11 ( 1711) hydrogen bonds : angle 5.43688 / 4.03 ( 4679) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 206 time to evaluate : 0.928 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 60 LEU cc_start: 0.8340 (mt) cc_final: 0.7941 (mm) REVERT: A 110 CYS cc_start: 0.9181 (m) cc_final: 0.8884 (m) REVERT: A 120 MET cc_start: 0.7351 (mmm) cc_final: 0.6519 (mmm) REVERT: B 46 ILE cc_start: 0.9555 (mt) cc_final: 0.9081 (tp) REVERT: B 68 ASP cc_start: 0.8943 (m-30) cc_final: 0.8485 (m-30) REVERT: B 81 VAL cc_start: 0.9200 (t) cc_final: 0.8983 (t) REVERT: C 112 GLN cc_start: 0.8905 (mp10) cc_final: 0.8452 (mp10) REVERT: D 37 TYR cc_start: 0.8664 (m-80) cc_final: 0.8464 (m-80) REVERT: D 62 MET cc_start: 0.9299 (mmm) cc_final: 0.8696 (mmm) REVERT: D 68 ASP cc_start: 0.9351 (t70) cc_final: 0.9129 (t0) REVERT: D 69 ILE cc_start: 0.9634 (mm) cc_final: 0.9345 (tt) REVERT: E 54 TYR cc_start: 0.8652 (m-80) cc_final: 0.8441 (m-10) REVERT: E 82 LEU cc_start: 0.8584 (mt) cc_final: 0.8346 (mt) REVERT: E 105 GLU cc_start: 0.8979 (tm-30) cc_final: 0.8609 (tm-30) REVERT: E 110 CYS cc_start: 0.9531 (m) cc_final: 0.9266 (m) REVERT: E 119 ILE cc_start: 0.9552 (pt) cc_final: 0.9062 (pt) REVERT: E 120 MET cc_start: 0.7264 (mpp) cc_final: 0.6745 (mpp) REVERT: E 130 ILE cc_start: 0.9643 (mt) cc_final: 0.9239 (mt) REVERT: F 44 LYS cc_start: 0.9283 (tttt) cc_final: 0.8932 (ttpp) REVERT: F 81 VAL cc_start: 0.8735 (t) cc_final: 0.8395 (t) REVERT: F 98 TYR cc_start: 0.8731 (m-80) cc_final: 0.8320 (m-80) REVERT: G 55 LEU cc_start: 0.9825 (mt) cc_final: 0.9616 (mm) REVERT: K 211 MET cc_start: 0.0037 (ttm) cc_final: -0.0259 (ttm) REVERT: K 326 MET cc_start: 0.4009 (tpt) cc_final: 0.3708 (tpt) REVERT: L 125 MET cc_start: 0.3996 (pmm) cc_final: 0.3396 (ptm) REVERT: L 210 MET cc_start: 0.2346 (tmm) cc_final: 0.0900 (ppp) REVERT: L 211 MET cc_start: 0.3892 (ttm) cc_final: 0.3565 (ttm) REVERT: L 326 MET cc_start: 0.2246 (tpt) cc_final: 0.1328 (ptm) REVERT: M 30 GLN cc_start: 0.4871 (mp10) cc_final: 0.4379 (tm-30) REVERT: M 158 MET cc_start: 0.5709 (mmp) cc_final: 0.5311 (mmm) REVERT: M 210 MET cc_start: 0.2620 (ppp) cc_final: 0.2172 (ptm) REVERT: R 210 MET cc_start: -0.0272 (tmm) cc_final: -0.0642 (tmm) REVERT: S 243 MET cc_start: 0.6293 (mmt) cc_final: 0.5906 (ppp) REVERT: T 306 ARG cc_start: 0.2562 (mmm160) cc_final: 0.2073 (tpt170) outliers start: 3 outliers final: 2 residues processed: 209 average time/residue: 0.1847 time to fit residues: 64.4371 Evaluate side-chains 158 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 156 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 342 optimal weight: 50.0000 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 212 optimal weight: 50.0000 chunk 9 optimal weight: 5.9990 chunk 311 optimal weight: 40.0000 chunk 295 optimal weight: 40.0000 chunk 116 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 310 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS E 108 ASN H 49 HIS T 206 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.065528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.046570 restraints weight = 393347.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.048084 restraints weight = 205381.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.049023 restraints weight = 130940.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.049626 restraints weight = 95295.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.050003 restraints weight = 76456.103| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34066 Z= 0.162 Angle : 0.635 7.794 47270 Z= 0.353 Chirality : 0.045 0.262 5415 Planarity : 0.004 0.057 5012 Dihedral : 25.166 99.045 7175 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 0.04 % Allowed : 1.91 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.14), residues: 3380 helix: 0.53 (0.12), residues: 1827 sheet: 0.12 (0.23), residues: 438 loop : -0.83 (0.17), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 170 TYR 0.046 0.002 TYR A 54 PHE 0.027 0.002 PHE R 259 HIS 0.006 0.001 HIS K 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.16 (34066) covalent geometry : angle 0.63462 / 0.35 (47270) hydrogen bonds : bond 0.05426 / 3.74 ( 1711) hydrogen bonds : angle 4.95428 / 3.67 ( 4679) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 198 time to evaluate : 1.097 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 94 GLU cc_start: 0.9281 (mm-30) cc_final: 0.9059 (mm-30) REVERT: B 46 ILE cc_start: 0.9579 (mt) cc_final: 0.9059 (tp) REVERT: B 68 ASP cc_start: 0.8961 (m-30) cc_final: 0.8633 (m-30) REVERT: C 72 ASP cc_start: 0.7938 (m-30) cc_final: 0.7727 (m-30) REVERT: C 112 GLN cc_start: 0.8836 (mp10) cc_final: 0.8515 (mp10) REVERT: D 62 MET cc_start: 0.9274 (mmm) cc_final: 0.8861 (mmm) REVERT: D 68 ASP cc_start: 0.9353 (t70) cc_final: 0.9129 (t0) REVERT: D 69 ILE cc_start: 0.9706 (mm) cc_final: 0.9460 (tt) REVERT: E 54 TYR cc_start: 0.8590 (m-80) cc_final: 0.8227 (m-10) REVERT: E 105 GLU cc_start: 0.9072 (tm-30) cc_final: 0.8675 (tm-30) REVERT: E 110 CYS cc_start: 0.9590 (m) cc_final: 0.9366 (m) REVERT: E 119 ILE cc_start: 0.9455 (pt) cc_final: 0.8943 (pt) REVERT: E 120 MET cc_start: 0.7612 (mpp) cc_final: 0.6824 (mpp) REVERT: F 44 LYS cc_start: 0.9245 (tttt) cc_final: 0.8803 (mtpp) REVERT: F 84 MET cc_start: 0.9365 (mmt) cc_final: 0.9011 (tpp) REVERT: F 85 ASP cc_start: 0.8735 (m-30) cc_final: 0.8531 (m-30) REVERT: F 98 TYR cc_start: 0.8862 (m-80) cc_final: 0.8387 (m-80) REVERT: G 64 GLU cc_start: 0.9086 (tm-30) cc_final: 0.8740 (tm-30) REVERT: K 158 MET cc_start: -0.2197 (mmm) cc_final: -0.2720 (mmm) REVERT: K 210 MET cc_start: 0.6605 (ppp) cc_final: 0.6246 (ppp) REVERT: L 125 MET cc_start: 0.4008 (pmm) cc_final: 0.3588 (ptm) REVERT: L 326 MET cc_start: 0.1748 (tpt) cc_final: 0.0848 (ptm) REVERT: M 30 GLN cc_start: 0.4962 (mp10) cc_final: 0.4494 (tm-30) REVERT: M 210 MET cc_start: 0.2535 (ppp) cc_final: 0.1497 (ptm) REVERT: M 211 MET cc_start: -0.0172 (ttt) cc_final: -0.1263 (ttt) REVERT: R 158 MET cc_start: 0.1705 (mmm) cc_final: 0.1210 (mmm) REVERT: R 210 MET cc_start: -0.0473 (tmm) cc_final: -0.1015 (tmm) REVERT: R 211 MET cc_start: 0.0687 (ttp) cc_final: 0.0289 (ptm) REVERT: S 243 MET cc_start: 0.6331 (mmt) cc_final: 0.5941 (ppp) REVERT: T 306 ARG cc_start: 0.2567 (mmm160) cc_final: 0.2050 (tpt170) outliers start: 1 outliers final: 0 residues processed: 199 average time/residue: 0.1894 time to fit residues: 62.5131 Evaluate side-chains 154 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 106 optimal weight: 40.0000 chunk 162 optimal weight: 50.0000 chunk 276 optimal weight: 8.9990 chunk 119 optimal weight: 40.0000 chunk 92 optimal weight: 30.0000 chunk 137 optimal weight: 8.9990 chunk 166 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 217 optimal weight: 4.9990 chunk 143 optimal weight: 40.0000 chunk 34 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS D 82 HIS G 38 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 206 GLN N 244 HIS ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.061851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.043007 restraints weight = 400669.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.044361 restraints weight = 212342.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.045195 restraints weight = 137031.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.045735 restraints weight = 100715.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.046075 restraints weight = 81671.259| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 34066 Z= 0.233 Angle : 0.729 12.500 47270 Z= 0.397 Chirality : 0.046 0.272 5415 Planarity : 0.006 0.087 5012 Dihedral : 25.431 100.671 7175 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.14), residues: 3380 helix: 0.46 (0.12), residues: 1730 sheet: -0.18 (0.25), residues: 432 loop : -0.29 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.001 ARG C 32 TYR 0.100 0.003 TYR Q 216 PHE 0.036 0.003 PHE E 104 HIS 0.013 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.23 (34066) covalent geometry : angle 0.72874 / 0.40 (47270) hydrogen bonds : bond 0.07790 / 5.34 ( 1711) hydrogen bonds : angle 4.95329 / 3.64 ( 4679) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 CYS cc_start: 0.9153 (m) cc_final: 0.8898 (t) REVERT: A 120 MET cc_start: 0.8157 (mmm) cc_final: 0.7477 (mmm) REVERT: B 68 ASP cc_start: 0.9286 (m-30) cc_final: 0.8967 (m-30) REVERT: C 55 LEU cc_start: 0.9682 (mt) cc_final: 0.9467 (mm) REVERT: D 62 MET cc_start: 0.9363 (mmm) cc_final: 0.8922 (mmm) REVERT: D 93 GLU cc_start: 0.9271 (mp0) cc_final: 0.9008 (mp0) REVERT: E 54 TYR cc_start: 0.8787 (m-80) cc_final: 0.8498 (m-10) REVERT: E 110 CYS cc_start: 0.9533 (m) cc_final: 0.8952 (t) REVERT: E 119 ILE cc_start: 0.9457 (pt) cc_final: 0.9231 (pt) REVERT: F 44 LYS cc_start: 0.9309 (tttt) cc_final: 0.8988 (mtpp) REVERT: F 84 MET cc_start: 0.9358 (mmt) cc_final: 0.9009 (tpp) REVERT: F 98 TYR cc_start: 0.8783 (m-80) cc_final: 0.8097 (m-80) REVERT: G 51 LEU cc_start: 0.9798 (tp) cc_final: 0.9471 (tp) REVERT: G 64 GLU cc_start: 0.9133 (tm-30) cc_final: 0.8809 (tm-30) REVERT: H 61 ILE cc_start: 0.9654 (mm) cc_final: 0.9441 (mm) REVERT: K 158 MET cc_start: -0.1760 (mmm) cc_final: -0.2032 (mmm) REVERT: K 210 MET cc_start: 0.6665 (ppp) cc_final: 0.6338 (ppp) REVERT: K 211 MET cc_start: -0.0329 (ttp) cc_final: -0.0563 (ttm) REVERT: K 326 MET cc_start: 0.4997 (tpt) cc_final: 0.4460 (tpt) REVERT: M 30 GLN cc_start: 0.5146 (mp10) cc_final: 0.4608 (tm-30) REVERT: M 210 MET cc_start: 0.3344 (ppp) cc_final: 0.2852 (ptm) REVERT: M 211 MET cc_start: 0.1233 (ttm) cc_final: 0.0520 (ttm) REVERT: P 326 MET cc_start: 0.6117 (mmp) cc_final: 0.5307 (tpp) REVERT: R 158 MET cc_start: 0.1558 (mmm) cc_final: 0.1164 (mmm) REVERT: R 210 MET cc_start: -0.0636 (tmm) cc_final: -0.0949 (tmm) REVERT: R 211 MET cc_start: 0.0336 (ttp) cc_final: 0.0008 (ptm) REVERT: S 243 MET cc_start: 0.6308 (mmt) cc_final: 0.5921 (ppp) REVERT: T 306 ARG cc_start: 0.2740 (mmm160) cc_final: 0.2285 (tpt170) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1797 time to fit residues: 53.6137 Evaluate side-chains 134 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 204 optimal weight: 0.1980 chunk 178 optimal weight: 5.9990 chunk 184 optimal weight: 6.9990 chunk 237 optimal weight: 9.9990 chunk 230 optimal weight: 10.0000 chunk 331 optimal weight: 8.9990 chunk 80 optimal weight: 40.0000 chunk 355 optimal weight: 40.0000 chunk 31 optimal weight: 9.9990 chunk 353 optimal weight: 20.0000 chunk 81 optimal weight: 30.0000 overall best weight: 6.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN E 108 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 244 HIS ** L 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.061432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.042561 restraints weight = 400607.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.043928 restraints weight = 209693.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.044747 restraints weight = 134624.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 73)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.045266 restraints weight = 99512.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.045577 restraints weight = 81195.149| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 34066 Z= 0.186 Angle : 0.640 9.743 47270 Z= 0.356 Chirality : 0.045 0.267 5415 Planarity : 0.004 0.051 5012 Dihedral : 25.467 100.361 7175 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.14), residues: 3380 helix: 0.60 (0.12), residues: 1742 sheet: -0.28 (0.24), residues: 452 loop : -0.31 (0.18), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 129 TYR 0.033 0.002 TYR S 216 PHE 0.021 0.002 PHE H 70 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.19 (34066) covalent geometry : angle 0.64018 / 0.36 (47270) hydrogen bonds : bond 0.05698 / 3.89 ( 1711) hydrogen bonds : angle 4.70360 / 3.44 ( 4679) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 ILE cc_start: 0.9723 (mt) cc_final: 0.9470 (tp) REVERT: B 68 ASP cc_start: 0.8847 (m-30) cc_final: 0.8296 (m-30) REVERT: D 62 MET cc_start: 0.9406 (mmm) cc_final: 0.9108 (mmm) REVERT: E 54 TYR cc_start: 0.8718 (m-80) cc_final: 0.8376 (m-10) REVERT: E 86 SER cc_start: 0.9278 (t) cc_final: 0.8950 (p) REVERT: E 110 CYS cc_start: 0.9620 (m) cc_final: 0.9331 (p) REVERT: E 119 ILE cc_start: 0.9368 (pt) cc_final: 0.9041 (pt) REVERT: E 120 MET cc_start: 0.7939 (mpp) cc_final: 0.7496 (mpp) REVERT: F 44 LYS cc_start: 0.9350 (tttt) cc_final: 0.9025 (mtpp) REVERT: F 84 MET cc_start: 0.9292 (mmt) cc_final: 0.8789 (mmt) REVERT: F 98 TYR cc_start: 0.8964 (m-80) cc_final: 0.8393 (m-80) REVERT: G 64 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8830 (tm-30) REVERT: H 35 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7191 (pm20) REVERT: H 80 LEU cc_start: 0.9729 (mt) cc_final: 0.8881 (mt) REVERT: K 210 MET cc_start: 0.6814 (ppp) cc_final: 0.6514 (ppp) REVERT: M 30 GLN cc_start: 0.5080 (mp10) cc_final: 0.4451 (tm-30) REVERT: M 158 MET cc_start: 0.6187 (tpp) cc_final: 0.5710 (mmm) REVERT: O 211 MET cc_start: 0.1529 (mmm) cc_final: 0.1105 (mmp) REVERT: P 326 MET cc_start: 0.6072 (mmp) cc_final: 0.5796 (mmp) REVERT: R 210 MET cc_start: -0.1217 (tmm) cc_final: -0.1580 (tmm) REVERT: S 243 MET cc_start: 0.6309 (mmt) cc_final: 0.5911 (ppp) REVERT: T 306 ARG cc_start: 0.2986 (mmm160) cc_final: 0.2469 (tpt170) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1904 time to fit residues: 53.8217 Evaluate side-chains 128 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 150 optimal weight: 6.9990 chunk 109 optimal weight: 30.0000 chunk 296 optimal weight: 40.0000 chunk 337 optimal weight: 30.0000 chunk 350 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 216 optimal weight: 40.0000 chunk 252 optimal weight: 50.0000 chunk 65 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 318 optimal weight: 0.9980 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** L 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.061126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.042121 restraints weight = 399142.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.043485 restraints weight = 207659.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.044313 restraints weight = 132857.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.044802 restraints weight = 97996.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.045151 restraints weight = 80575.790| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 34066 Z= 0.160 Angle : 0.618 7.668 47270 Z= 0.343 Chirality : 0.044 0.246 5415 Planarity : 0.004 0.087 5012 Dihedral : 25.365 100.136 7175 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.04 % Allowed : 1.19 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.14), residues: 3380 helix: 0.84 (0.12), residues: 1700 sheet: -0.07 (0.28), residues: 354 loop : -0.46 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 170 TYR 0.025 0.002 TYR L 216 PHE 0.016 0.002 PHE E 104 HIS 0.012 0.001 HIS K 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 (34066) covalent geometry : angle 0.61790 / 0.34 (47270) hydrogen bonds : bond 0.05386 / 3.71 ( 1711) hydrogen bonds : angle 4.47621 / 3.27 ( 4679) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 ASP cc_start: 0.9020 (m-30) cc_final: 0.8568 (t70) REVERT: D 62 MET cc_start: 0.9432 (mmm) cc_final: 0.9130 (mmm) REVERT: E 54 TYR cc_start: 0.8666 (m-80) cc_final: 0.8305 (m-10) REVERT: E 56 LYS cc_start: 0.9467 (tmtt) cc_final: 0.9246 (ttmm) REVERT: E 86 SER cc_start: 0.9255 (t) cc_final: 0.8949 (p) REVERT: E 110 CYS cc_start: 0.9570 (m) cc_final: 0.9294 (p) REVERT: E 119 ILE cc_start: 0.9350 (pt) cc_final: 0.8959 (pt) REVERT: E 120 MET cc_start: 0.8051 (mpp) cc_final: 0.7522 (mpp) REVERT: F 44 LYS cc_start: 0.9362 (tttt) cc_final: 0.9056 (mtpp) REVERT: F 84 MET cc_start: 0.9198 (mmt) cc_final: 0.8728 (mmt) REVERT: F 98 TYR cc_start: 0.8972 (m-80) cc_final: 0.8322 (m-80) REVERT: H 35 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7454 (pm20) REVERT: K 210 MET cc_start: 0.7124 (ppp) cc_final: 0.6874 (ppp) REVERT: K 326 MET cc_start: 0.4804 (tpt) cc_final: 0.4363 (tpt) REVERT: L 158 MET cc_start: 0.5842 (mmm) cc_final: 0.5416 (mmt) REVERT: M 30 GLN cc_start: 0.4891 (mp10) cc_final: 0.4258 (tm-30) REVERT: M 158 MET cc_start: 0.6262 (tpp) cc_final: 0.5431 (mmt) REVERT: M 210 MET cc_start: 0.0953 (ptm) cc_final: 0.0751 (ptt) REVERT: N 211 MET cc_start: -0.3858 (tpt) cc_final: -0.4059 (tpt) REVERT: P 326 MET cc_start: 0.6155 (mmp) cc_final: 0.5880 (mmp) REVERT: R 210 MET cc_start: -0.1906 (tmm) cc_final: -0.2199 (tmm) REVERT: R 211 MET cc_start: 0.0011 (ptp) cc_final: -0.0649 (ttm) REVERT: S 243 MET cc_start: 0.6301 (mmt) cc_final: 0.5909 (ppp) REVERT: T 306 ARG cc_start: 0.2835 (mmm160) cc_final: 0.2216 (tpt170) outliers start: 1 outliers final: 1 residues processed: 162 average time/residue: 0.1906 time to fit residues: 52.6688 Evaluate side-chains 126 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 136 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 294 optimal weight: 20.0000 chunk 307 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 83 optimal weight: 50.0000 chunk 192 optimal weight: 10.0000 chunk 237 optimal weight: 8.9990 chunk 141 optimal weight: 30.0000 chunk 56 optimal weight: 1.9990 chunk 102 optimal weight: 30.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** K 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.061089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.041818 restraints weight = 405062.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.043178 restraints weight = 205102.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.044036 restraints weight = 129335.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.044570 restraints weight = 94147.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.044898 restraints weight = 75970.404| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 34066 Z= 0.148 Angle : 0.599 10.439 47270 Z= 0.332 Chirality : 0.043 0.233 5415 Planarity : 0.004 0.080 5012 Dihedral : 25.271 99.889 7175 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.14), residues: 3380 helix: 0.90 (0.12), residues: 1756 sheet: -0.19 (0.28), residues: 356 loop : -0.56 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 45 TYR 0.024 0.001 TYR L 216 PHE 0.016 0.002 PHE H 70 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 (34066) covalent geometry : angle 0.59855 / 0.33 (47270) hydrogen bonds : bond 0.04867 / 3.34 ( 1711) hydrogen bonds : angle 4.31939 / 3.15 ( 4679) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.9063 (mp10) cc_final: 0.8758 (mm-40) REVERT: B 63 GLU cc_start: 0.9343 (mt-10) cc_final: 0.8933 (mp0) REVERT: B 68 ASP cc_start: 0.9169 (m-30) cc_final: 0.8803 (m-30) REVERT: C 91 GLU cc_start: 0.8708 (pp20) cc_final: 0.8394 (pp20) REVERT: D 62 MET cc_start: 0.9435 (mmm) cc_final: 0.9179 (mmm) REVERT: E 54 TYR cc_start: 0.8651 (m-80) cc_final: 0.8250 (m-10) REVERT: E 56 LYS cc_start: 0.9444 (tmtt) cc_final: 0.9235 (ttmm) REVERT: E 94 GLU cc_start: 0.9305 (tp30) cc_final: 0.9099 (tp30) REVERT: E 110 CYS cc_start: 0.9560 (m) cc_final: 0.9244 (p) REVERT: E 119 ILE cc_start: 0.9305 (pt) cc_final: 0.8929 (pt) REVERT: E 120 MET cc_start: 0.8193 (mpp) cc_final: 0.7711 (mpp) REVERT: F 44 LYS cc_start: 0.9358 (tttt) cc_final: 0.9069 (mtpp) REVERT: F 84 MET cc_start: 0.9149 (mmt) cc_final: 0.8723 (mmt) REVERT: H 35 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7383 (pm20) REVERT: K 210 MET cc_start: 0.7066 (ppp) cc_final: 0.6783 (ppp) REVERT: K 326 MET cc_start: 0.4879 (tpt) cc_final: 0.4413 (tpp) REVERT: M 30 GLN cc_start: 0.5043 (mp10) cc_final: 0.4418 (tm-30) REVERT: M 158 MET cc_start: 0.6419 (tpp) cc_final: 0.5464 (mmt) REVERT: N 211 MET cc_start: -0.3715 (tpt) cc_final: -0.4071 (tpt) REVERT: O 211 MET cc_start: 0.1808 (mmm) cc_final: 0.1407 (mmm) REVERT: P 326 MET cc_start: 0.6006 (mmp) cc_final: 0.5796 (mmp) REVERT: S 243 MET cc_start: 0.6302 (mmt) cc_final: 0.5920 (ppp) REVERT: T 306 ARG cc_start: 0.3030 (mmm160) cc_final: 0.2310 (tpt170) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1902 time to fit residues: 50.4475 Evaluate side-chains 126 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 262 optimal weight: 40.0000 chunk 87 optimal weight: 40.0000 chunk 8 optimal weight: 0.8980 chunk 231 optimal weight: 40.0000 chunk 116 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 321 optimal weight: 7.9990 chunk 135 optimal weight: 40.0000 chunk 16 optimal weight: 8.9990 chunk 286 optimal weight: 30.0000 chunk 20 optimal weight: 6.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** L 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.060470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.041270 restraints weight = 405433.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.042635 restraints weight = 206155.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.043458 restraints weight = 129815.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.043973 restraints weight = 94736.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 68)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.044292 restraints weight = 76942.541| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.5410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 34066 Z= 0.159 Angle : 0.609 12.112 47270 Z= 0.336 Chirality : 0.043 0.227 5415 Planarity : 0.004 0.067 5012 Dihedral : 25.238 100.536 7175 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.14), residues: 3380 helix: 0.93 (0.12), residues: 1760 sheet: -0.25 (0.28), residues: 356 loop : -0.57 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 170 TYR 0.018 0.002 TYR T 232 PHE 0.022 0.002 PHE H 65 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.16 (34066) covalent geometry : angle 0.60943 / 0.34 (47270) hydrogen bonds : bond 0.05374 / 3.69 ( 1711) hydrogen bonds : angle 4.28080 / 3.11 ( 4679) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.9126 (mp10) cc_final: 0.8846 (mm-40) REVERT: B 63 GLU cc_start: 0.9343 (mt-10) cc_final: 0.8952 (mp0) REVERT: B 68 ASP cc_start: 0.9286 (m-30) cc_final: 0.8889 (m-30) REVERT: B 97 LEU cc_start: 0.9611 (tp) cc_final: 0.9335 (tp) REVERT: D 62 MET cc_start: 0.9444 (mmm) cc_final: 0.9176 (mmm) REVERT: E 54 TYR cc_start: 0.8669 (m-80) cc_final: 0.8269 (m-10) REVERT: E 56 LYS cc_start: 0.9459 (tmtt) cc_final: 0.9257 (ttmm) REVERT: E 110 CYS cc_start: 0.9538 (m) cc_final: 0.9274 (p) REVERT: E 119 ILE cc_start: 0.9267 (pt) cc_final: 0.8904 (pt) REVERT: E 120 MET cc_start: 0.8311 (mpp) cc_final: 0.7891 (mpp) REVERT: F 44 LYS cc_start: 0.9377 (tttt) cc_final: 0.9099 (mtpp) REVERT: F 63 GLU cc_start: 0.9281 (pp20) cc_final: 0.9000 (pp20) REVERT: F 84 MET cc_start: 0.9147 (mmt) cc_final: 0.8745 (mmt) REVERT: H 80 LEU cc_start: 0.9627 (mt) cc_final: 0.9244 (mt) REVERT: K 326 MET cc_start: 0.4814 (tpt) cc_final: 0.4386 (tpp) REVERT: M 30 GLN cc_start: 0.4943 (mp10) cc_final: 0.4316 (tm-30) REVERT: M 158 MET cc_start: 0.5920 (tpp) cc_final: 0.5510 (mmt) REVERT: N 211 MET cc_start: -0.3742 (tpt) cc_final: -0.4015 (tpt) REVERT: P 326 MET cc_start: 0.6008 (mmp) cc_final: 0.5791 (mmp) REVERT: S 243 MET cc_start: 0.6343 (mmt) cc_final: 0.5957 (ppp) REVERT: T 306 ARG cc_start: 0.2652 (mmm160) cc_final: 0.1943 (tpt170) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1935 time to fit residues: 48.5111 Evaluate side-chains 120 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 236 optimal weight: 20.0000 chunk 316 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 309 optimal weight: 0.9980 chunk 211 optimal weight: 20.0000 chunk 229 optimal weight: 50.0000 chunk 53 optimal weight: 5.9990 chunk 79 optimal weight: 40.0000 chunk 297 optimal weight: 40.0000 chunk 142 optimal weight: 6.9990 chunk 92 optimal weight: 30.0000 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN E 108 ASN ** K 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.060749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.041433 restraints weight = 400404.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.042806 restraints weight = 202504.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.043640 restraints weight = 127227.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.044177 restraints weight = 92993.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.044483 restraints weight = 75201.796| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.5547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34066 Z= 0.132 Angle : 0.578 8.227 47270 Z= 0.320 Chirality : 0.042 0.219 5415 Planarity : 0.004 0.060 5012 Dihedral : 25.173 99.924 7175 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.14), residues: 3380 helix: 1.07 (0.12), residues: 1755 sheet: -0.28 (0.28), residues: 356 loop : -0.59 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 35 TYR 0.015 0.001 TYR T 232 PHE 0.015 0.001 PHE H 65 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.13 (34066) covalent geometry : angle 0.57779 / 0.32 (47270) hydrogen bonds : bond 0.04563 / 3.14 ( 1711) hydrogen bonds : angle 4.15638 / 3.02 ( 4679) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.9306 (mt-10) cc_final: 0.8945 (mp0) REVERT: B 68 ASP cc_start: 0.9292 (m-30) cc_final: 0.8826 (m-30) REVERT: C 91 GLU cc_start: 0.8758 (pp20) cc_final: 0.8470 (pp20) REVERT: D 62 MET cc_start: 0.9449 (mmm) cc_final: 0.9175 (mmm) REVERT: E 56 LYS cc_start: 0.9445 (tmtt) cc_final: 0.9242 (ttmm) REVERT: E 110 CYS cc_start: 0.9533 (m) cc_final: 0.9270 (p) REVERT: E 119 ILE cc_start: 0.9195 (pt) cc_final: 0.8942 (mm) REVERT: E 120 MET cc_start: 0.8266 (mpp) cc_final: 0.7828 (mpp) REVERT: F 44 LYS cc_start: 0.9377 (tttt) cc_final: 0.9075 (tptm) REVERT: F 84 MET cc_start: 0.9122 (mmt) cc_final: 0.8725 (mmt) REVERT: K 210 MET cc_start: 0.7121 (ppp) cc_final: 0.6851 (ppp) REVERT: K 211 MET cc_start: -0.0422 (ttp) cc_final: -0.0646 (ttm) REVERT: K 326 MET cc_start: 0.5027 (tpt) cc_final: 0.4634 (tpp) REVERT: M 30 GLN cc_start: 0.4949 (mp10) cc_final: 0.4329 (tm-30) REVERT: M 158 MET cc_start: 0.6361 (tpp) cc_final: 0.5900 (mmm) REVERT: O 211 MET cc_start: 0.1877 (mmm) cc_final: 0.1518 (mmm) REVERT: O 326 MET cc_start: 0.5871 (tpt) cc_final: 0.5453 (tpp) REVERT: P 326 MET cc_start: 0.6027 (mmp) cc_final: 0.5804 (mmp) REVERT: R 210 MET cc_start: -0.2774 (tmm) cc_final: -0.3072 (tmm) REVERT: R 211 MET cc_start: -0.0899 (ptp) cc_final: -0.1327 (pmm) REVERT: S 243 MET cc_start: 0.6273 (mmt) cc_final: 0.5879 (ppp) REVERT: T 306 ARG cc_start: 0.2556 (mmm160) cc_final: 0.1917 (tpt170) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.1844 time to fit residues: 47.4859 Evaluate side-chains 123 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 18 optimal weight: 0.9980 chunk 353 optimal weight: 5.9990 chunk 303 optimal weight: 20.0000 chunk 173 optimal weight: 10.0000 chunk 326 optimal weight: 7.9990 chunk 206 optimal weight: 20.0000 chunk 351 optimal weight: 1.9990 chunk 254 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 133 optimal weight: 30.0000 chunk 68 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** K 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.060786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.041346 restraints weight = 404861.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.042719 restraints weight = 202770.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.043565 restraints weight = 126770.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.044048 restraints weight = 91909.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.044399 restraints weight = 75415.935| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.5735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 34066 Z= 0.125 Angle : 0.576 8.829 47270 Z= 0.318 Chirality : 0.042 0.217 5415 Planarity : 0.004 0.058 5012 Dihedral : 25.035 99.362 7175 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.14), residues: 3380 helix: 1.09 (0.12), residues: 1763 sheet: -0.31 (0.28), residues: 356 loop : -0.52 (0.17), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 99 TYR 0.014 0.001 TYR T 232 PHE 0.013 0.001 PHE S 126 HIS 0.006 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 (34066) covalent geometry : angle 0.57579 / 0.32 (47270) hydrogen bonds : bond 0.04363 / 2.99 ( 1711) hydrogen bonds : angle 4.06772 / 2.95 ( 4679) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.9303 (mt-10) cc_final: 0.8876 (mp0) REVERT: B 68 ASP cc_start: 0.9314 (m-30) cc_final: 0.8818 (m-30) REVERT: C 91 GLU cc_start: 0.8756 (pp20) cc_final: 0.8455 (pp20) REVERT: D 62 MET cc_start: 0.9457 (mmm) cc_final: 0.9182 (mmm) REVERT: E 94 GLU cc_start: 0.9303 (mm-30) cc_final: 0.9001 (tp30) REVERT: E 110 CYS cc_start: 0.9515 (m) cc_final: 0.9306 (p) REVERT: E 120 MET cc_start: 0.8292 (mpp) cc_final: 0.7876 (mpp) REVERT: F 44 LYS cc_start: 0.9389 (tttt) cc_final: 0.9085 (tptm) REVERT: F 81 VAL cc_start: 0.8878 (t) cc_final: 0.8652 (t) REVERT: F 84 MET cc_start: 0.9046 (mmt) cc_final: 0.8452 (mmt) REVERT: F 85 ASP cc_start: 0.8826 (m-30) cc_final: 0.8547 (m-30) REVERT: K 210 MET cc_start: 0.7160 (ppp) cc_final: 0.6893 (ppp) REVERT: K 211 MET cc_start: -0.0380 (ttp) cc_final: -0.0584 (ttm) REVERT: K 326 MET cc_start: 0.5487 (tpt) cc_final: 0.4951 (tpp) REVERT: M 30 GLN cc_start: 0.5135 (mp10) cc_final: 0.4547 (tm-30) REVERT: O 211 MET cc_start: 0.1924 (mmm) cc_final: 0.1561 (mmm) REVERT: O 326 MET cc_start: 0.5833 (tpt) cc_final: 0.5419 (tpp) REVERT: P 326 MET cc_start: 0.5999 (mmp) cc_final: 0.5783 (mmp) REVERT: S 243 MET cc_start: 0.6197 (mmt) cc_final: 0.5819 (ppp) REVERT: T 306 ARG cc_start: 0.2577 (mmm160) cc_final: 0.1944 (tpt170) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1835 time to fit residues: 48.0678 Evaluate side-chains 121 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 151 optimal weight: 40.0000 chunk 37 optimal weight: 4.9990 chunk 244 optimal weight: 10.0000 chunk 192 optimal weight: 0.7980 chunk 82 optimal weight: 40.0000 chunk 23 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 123 optimal weight: 30.0000 chunk 296 optimal weight: 50.0000 chunk 118 optimal weight: 20.0000 chunk 138 optimal weight: 40.0000 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 244 HIS ** L 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 114 GLN ** O 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.059488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.043265 restraints weight = 373461.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.042326 restraints weight = 340402.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.042748 restraints weight = 224423.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.042573 restraints weight = 182492.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.042609 restraints weight = 198492.085| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.6091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 34066 Z= 0.167 Angle : 0.618 13.226 47270 Z= 0.339 Chirality : 0.043 0.221 5415 Planarity : 0.004 0.059 5012 Dihedral : 25.135 103.123 7175 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.14), residues: 3380 helix: 0.99 (0.12), residues: 1797 sheet: -0.34 (0.29), residues: 356 loop : -0.51 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 170 TYR 0.020 0.002 TYR H 40 PHE 0.020 0.002 PHE E 104 HIS 0.011 0.001 HIS K 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.17 (34066) covalent geometry : angle 0.61835 / 0.34 (47270) hydrogen bonds : bond 0.05978 / 4.09 ( 1711) hydrogen bonds : angle 4.21331 / 3.05 ( 4679) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7617.85 seconds wall clock time: 131 minutes 46.63 seconds (7906.63 seconds total)