Starting phenix.real_space_refine on Sun Aug 9 04:38:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jne_36443/08_2026/8jne_36443.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jne_36443/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jne_36443/08_2026/8jne_36443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jne_36443/08_2026/8jne_36443.map" model { file = "/net/cci-nas-00/data/ceres_data/8jne_36443/08_2026/8jne_36443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jne_36443/08_2026/8jne_36443.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.24, per 1000 atoms: 0.19 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: 2.38 Conformation dependent library (CDL) restraints added in 1.3 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: 4.05 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: 6.77 Time building geometry restraints manager: 3.28 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: 45206 2.46 - 4.92: 1881 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: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 31.030 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.670 ------------------------------------------------------------------------------- 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= 0.519 Angle : 1.105 12.292 47270 Z= 0.852 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 1.10550 / 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 : 0.921 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: 0.7676 (mp) REVERT: A 61 LEU cc_start: 0.7677 (mt) cc_final: 0.7437 (mt) REVERT: A 74 ILE cc_start: 0.9526 (mt) cc_final: 0.9319 (mm) REVERT: A 106 ASP cc_start: 0.9045 (m-30) cc_final: 0.8498 (m-30) REVERT: B 68 ASP cc_start: 0.8931 (m-30) cc_final: 0.8672 (m-30) REVERT: B 81 VAL cc_start: 0.9020 (t) cc_final: 0.8792 (t) REVERT: B 96 THR cc_start: 0.9038 (m) cc_final: 0.8752 (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: 0.8332 (tt) REVERT: D 62 MET cc_start: 0.8330 (mmm) cc_final: 0.8122 (mmm) REVERT: D 106 LEU cc_start: 0.8866 (tp) cc_final: 0.8525 (mt) REVERT: E 54 TYR cc_start: 0.8426 (m-80) cc_final: 0.7971 (m-10) REVERT: E 94 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8177 (mm-30) REVERT: E 99 TYR cc_start: 0.8394 (t80) cc_final: 0.8138 (t80) REVERT: E 119 ILE cc_start: 0.9374 (pt) cc_final: 0.8876 (pt) REVERT: E 124 ILE cc_start: 0.9515 (mt) cc_final: 0.9175 (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: 0.8878 (tt) REVERT: F 81 VAL cc_start: 0.8462 (t) cc_final: 0.8087 (t) REVERT: F 85 ASP cc_start: 0.8538 (m-30) cc_final: 0.8305 (m-30) REVERT: G 114 VAL cc_start: 0.8434 (t) cc_final: 0.8111 (p) REVERT: G 115 LEU cc_start: 0.8884 (mt) cc_final: 0.8151 (mp) REVERT: H 37 TYR cc_start: 0.7981 (m-80) cc_final: 0.7716 (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: 0.8739 (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: 0.2418 (ttm) REVERT: L 254 ARG cc_start: 0.1415 (ttm170) cc_final: 0.0890 (ptt-90) REVERT: L 326 MET cc_start: 0.2701 (tpt) cc_final: 0.1686 (ptm) REVERT: M 30 GLN cc_start: 0.4970 (mp10) cc_final: 0.4352 (tm-30) REVERT: M 235 ARG cc_start: -0.0296 (mmt180) cc_final: -0.0588 (mpt180) REVERT: N 210 MET cc_start: 0.2131 (tmm) cc_final: 0.1823 (tmm) REVERT: S 210 MET cc_start: 0.4584 (tmm) cc_final: 0.3228 (ppp) REVERT: S 243 MET cc_start: 0.6316 (mmt) cc_final: 0.5910 (ppp) REVERT: T 306 ARG cc_start: 0.2747 (mmm160) cc_final: 0.1930 (tpt170) outliers start: 4 outliers final: 1 residues processed: 353 average time/residue: 0.2226 time to fit residues: 124.2795 Evaluate side-chains 183 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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: 0.4980 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 8.9990 overall best weight: 5.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS E 108 ASN K 202 GLN 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 = 0.3978 r_free = 0.3978 target = 0.066863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.048078 restraints weight = 392110.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.049590 restraints weight = 205900.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.050552 restraints weight = 131158.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.051156 restraints weight = 95012.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.051554 restraints weight = 75922.471| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 34066 Z= 0.228 Angle : 0.777 10.378 47270 Z= 0.423 Chirality : 0.049 0.268 5415 Planarity : 0.006 0.057 5012 Dihedral : 25.139 100.241 7175 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.11 % Allowed : 2.95 % Favored : 96.94 % 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 (0.13), residues: 3380 helix: 0.46 (0.12), residues: 1778 sheet: 0.44 (0.23), residues: 406 loop : -0.81 (0.16), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG S 235 TYR 0.042 0.003 TYR B 98 PHE 0.040 0.003 PHE K 248 HIS 0.011 0.001 HIS Q 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.23 (34066) covalent geometry : angle 0.77725 / 0.42 (47270) hydrogen bonds : bond 0.06297 / 4.33 ( 1711) hydrogen bonds : angle 5.34895 / 3.97 ( 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 210 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 207 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8229 (mt) cc_final: 0.7860 (mm) REVERT: A 110 CYS cc_start: 0.9188 (m) cc_final: 0.8884 (m) REVERT: A 120 MET cc_start: 0.7302 (mmm) cc_final: 0.6499 (mmm) REVERT: B 68 ASP cc_start: 0.9014 (m-30) cc_final: 0.8524 (m-30) REVERT: C 112 GLN cc_start: 0.8886 (mp10) cc_final: 0.8502 (mp10) REVERT: D 37 TYR cc_start: 0.8571 (m-80) cc_final: 0.8368 (m-80) REVERT: D 48 VAL cc_start: 0.9375 (t) cc_final: 0.9170 (p) REVERT: D 62 MET cc_start: 0.9286 (mmm) cc_final: 0.8721 (mmm) REVERT: D 68 ASP cc_start: 0.9364 (t70) cc_final: 0.9087 (t0) REVERT: D 69 ILE cc_start: 0.9623 (mm) cc_final: 0.9364 (mm) REVERT: E 54 TYR cc_start: 0.8587 (m-80) cc_final: 0.8365 (m-10) REVERT: E 82 LEU cc_start: 0.8559 (mt) cc_final: 0.8320 (mt) REVERT: E 105 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8533 (tm-30) REVERT: E 110 CYS cc_start: 0.9497 (m) cc_final: 0.9224 (m) REVERT: E 119 ILE cc_start: 0.9557 (pt) cc_final: 0.9074 (pt) REVERT: E 120 MET cc_start: 0.7250 (mpp) cc_final: 0.6771 (mpp) REVERT: E 130 ILE cc_start: 0.9634 (mt) cc_final: 0.9224 (mt) REVERT: F 44 LYS cc_start: 0.9293 (tttt) cc_final: 0.8730 (mtpp) REVERT: F 81 VAL cc_start: 0.8713 (t) cc_final: 0.8373 (t) REVERT: F 98 TYR cc_start: 0.8788 (m-80) cc_final: 0.8383 (m-80) REVERT: G 55 LEU cc_start: 0.9812 (mt) cc_final: 0.9584 (mt) REVERT: K 210 MET cc_start: 0.7105 (tmm) cc_final: 0.6707 (ppp) REVERT: K 211 MET cc_start: 0.0075 (ttm) cc_final: -0.0362 (ttm) REVERT: K 326 MET cc_start: 0.3920 (tpt) cc_final: 0.3660 (tpt) REVERT: L 326 MET cc_start: 0.2384 (tpt) cc_final: 0.1376 (ptm) REVERT: M 30 GLN cc_start: 0.4866 (mp10) cc_final: 0.4358 (tm-30) REVERT: M 210 MET cc_start: 0.2568 (ppp) cc_final: 0.2097 (ptm) REVERT: R 158 MET cc_start: 0.1996 (mmm) cc_final: 0.1172 (mmm) REVERT: R 210 MET cc_start: -0.0281 (tmm) cc_final: -0.1379 (ptt) REVERT: S 243 MET cc_start: 0.6297 (mmt) cc_final: 0.5902 (ppp) REVERT: T 306 ARG cc_start: 0.2545 (mmm160) cc_final: 0.2064 (tpt170) outliers start: 3 outliers final: 1 residues processed: 210 average time/residue: 0.2173 time to fit residues: 76.1815 Evaluate side-chains 160 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 1.252 ------------------------------------------------------------------------------- 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: 20.0000 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 311 optimal weight: 20.0000 chunk 295 optimal weight: 50.0000 chunk 116 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 310 optimal weight: 6.9990 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 = 0.3956 r_free = 0.3956 target = 0.065708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.046756 restraints weight = 393427.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.048272 restraints weight = 205666.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.049224 restraints weight = 131086.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.049837 restraints weight = 95124.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.050202 restraints weight = 76143.637| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 34066 Z= 0.158 Angle : 0.644 8.329 47270 Z= 0.356 Chirality : 0.045 0.257 5415 Planarity : 0.004 0.053 5012 Dihedral : 25.060 98.239 7175 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 0.04 % Allowed : 2.45 % Favored : 97.52 % 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: 0.64 (0.12), residues: 1796 sheet: 0.37 (0.23), residues: 422 loop : -0.93 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 170 TYR 0.032 0.002 TYR H 40 PHE 0.022 0.002 PHE N 195 HIS 0.008 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.16 (34066) covalent geometry : angle 0.64405 / 0.36 (47270) hydrogen bonds : bond 0.05458 / 3.78 ( 1711) hydrogen bonds : angle 4.91321 / 3.64 ( 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 198 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9342 (mm-30) cc_final: 0.8796 (mm-30) REVERT: A 94 GLU cc_start: 0.9241 (mm-30) cc_final: 0.9021 (mm-30) REVERT: B 68 ASP cc_start: 0.8922 (m-30) cc_final: 0.8529 (m-30) REVERT: C 72 ASP cc_start: 0.7967 (m-30) cc_final: 0.7749 (m-30) REVERT: C 112 GLN cc_start: 0.8828 (mp10) cc_final: 0.8526 (mp10) REVERT: D 62 MET cc_start: 0.9239 (mmm) cc_final: 0.8854 (mmm) REVERT: D 68 ASP cc_start: 0.9330 (t70) cc_final: 0.9114 (t0) REVERT: D 69 ILE cc_start: 0.9693 (mm) cc_final: 0.9458 (tt) REVERT: E 54 TYR cc_start: 0.8587 (m-80) cc_final: 0.8237 (m-10) REVERT: E 105 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8653 (tm-30) REVERT: E 110 CYS cc_start: 0.9594 (m) cc_final: 0.9386 (m) REVERT: F 44 LYS cc_start: 0.9254 (tttt) cc_final: 0.8823 (mtpp) REVERT: F 84 MET cc_start: 0.9392 (mmt) cc_final: 0.8964 (tpp) REVERT: F 85 ASP cc_start: 0.8799 (m-30) cc_final: 0.8555 (m-30) REVERT: F 98 TYR cc_start: 0.8751 (m-80) cc_final: 0.8314 (m-80) REVERT: G 64 GLU cc_start: 0.9083 (tm-30) cc_final: 0.8713 (tm-30) REVERT: G 110 ASN cc_start: 0.9034 (m110) cc_final: 0.8773 (m110) REVERT: L 125 MET cc_start: 0.4005 (pmm) cc_final: 0.3588 (ptm) REVERT: L 326 MET cc_start: 0.1731 (tpt) cc_final: 0.0866 (ptm) REVERT: M 30 GLN cc_start: 0.4961 (mp10) cc_final: 0.4501 (tm-30) REVERT: M 158 MET cc_start: 0.5802 (mmp) cc_final: 0.5587 (mmm) REVERT: M 210 MET cc_start: 0.2566 (ppp) cc_final: 0.1964 (ptm) REVERT: M 211 MET cc_start: -0.0326 (ttt) cc_final: -0.0577 (ttt) REVERT: P 326 MET cc_start: 0.6021 (mmp) cc_final: 0.5744 (mmp) REVERT: R 210 MET cc_start: -0.0189 (tmm) cc_final: -0.0567 (tmm) REVERT: S 243 MET cc_start: 0.6331 (mmt) cc_final: 0.5937 (ppp) REVERT: T 306 ARG cc_start: 0.2533 (mmm160) cc_final: 0.2020 (tpt170) outliers start: 1 outliers final: 0 residues processed: 198 average time/residue: 0.2036 time to fit residues: 67.4924 Evaluate side-chains 152 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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: 50.0000 chunk 162 optimal weight: 30.0000 chunk 276 optimal weight: 7.9990 chunk 119 optimal weight: 40.0000 chunk 92 optimal weight: 30.0000 chunk 137 optimal weight: 10.0000 chunk 166 optimal weight: 7.9990 chunk 110 optimal weight: 40.0000 chunk 217 optimal weight: 0.2980 chunk 143 optimal weight: 30.0000 chunk 34 optimal weight: 5.9990 overall best weight: 6.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN D 49 HIS G 38 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 202 GLN ** L 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 206 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.062652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.043727 restraints weight = 399429.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.045121 restraints weight = 211765.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.045981 restraints weight = 136317.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.046534 restraints weight = 100332.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.046884 restraints weight = 80994.087| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 34066 Z= 0.212 Angle : 0.694 10.607 47270 Z= 0.379 Chirality : 0.045 0.277 5415 Planarity : 0.005 0.069 5012 Dihedral : 25.236 97.067 7175 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.04 % Allowed : 2.34 % Favored : 97.62 % 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: 0.10 (0.14), residues: 3380 helix: 0.57 (0.12), residues: 1778 sheet: -0.17 (0.25), residues: 432 loop : -0.41 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG A 42 TYR 0.035 0.002 TYR R 216 PHE 0.025 0.002 PHE E 104 HIS 0.012 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.21 (34066) covalent geometry : angle 0.69385 / 0.38 (47270) hydrogen bonds : bond 0.06933 / 4.76 ( 1711) hydrogen bonds : angle 4.79814 / 3.52 ( 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 182 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 ASP cc_start: 0.9183 (m-30) cc_final: 0.8856 (m-30) REVERT: C 55 LEU cc_start: 0.9652 (mt) cc_final: 0.9407 (mm) REVERT: D 62 MET cc_start: 0.9404 (mmm) cc_final: 0.8992 (mmm) REVERT: D 93 GLU cc_start: 0.9275 (mp0) cc_final: 0.8992 (mp0) REVERT: E 54 TYR cc_start: 0.8653 (m-80) cc_final: 0.8340 (m-10) REVERT: E 110 CYS cc_start: 0.9559 (m) cc_final: 0.8932 (t) REVERT: E 119 ILE cc_start: 0.9410 (pt) cc_final: 0.8982 (pt) REVERT: E 120 MET cc_start: 0.7798 (mpp) cc_final: 0.7215 (mpp) REVERT: F 44 LYS cc_start: 0.9312 (tttt) cc_final: 0.8947 (mtpp) REVERT: F 84 MET cc_start: 0.9334 (mmt) cc_final: 0.8903 (mmt) REVERT: F 98 TYR cc_start: 0.8763 (m-80) cc_final: 0.8085 (m-80) REVERT: G 51 LEU cc_start: 0.9786 (tp) cc_final: 0.9441 (tp) REVERT: G 55 LEU cc_start: 0.9772 (mt) cc_final: 0.9569 (mt) REVERT: G 64 GLU cc_start: 0.9119 (tm-30) cc_final: 0.8814 (tm-30) REVERT: G 112 GLN cc_start: 0.7475 (mm-40) cc_final: 0.7076 (tm-30) REVERT: G 114 VAL cc_start: 0.8408 (t) cc_final: 0.8105 (t) REVERT: H 64 SER cc_start: 0.9444 (m) cc_final: 0.9213 (p) REVERT: K 326 MET cc_start: 0.5004 (tpt) cc_final: 0.4540 (tpt) REVERT: L 326 MET cc_start: 0.1344 (tpt) cc_final: 0.1067 (ptp) REVERT: M 30 GLN cc_start: 0.5044 (mp10) cc_final: 0.4592 (tm-30) REVERT: M 158 MET cc_start: 0.6054 (mmp) cc_final: 0.5535 (mmm) REVERT: M 210 MET cc_start: 0.3099 (ppp) cc_final: 0.2633 (ptm) REVERT: M 326 MET cc_start: 0.8413 (mtm) cc_final: 0.8011 (mmm) REVERT: O 158 MET cc_start: -0.1972 (mmm) cc_final: -0.2259 (mmm) REVERT: O 211 MET cc_start: 0.1996 (mmm) cc_final: 0.1691 (mmm) REVERT: P 326 MET cc_start: 0.5800 (mmp) cc_final: 0.5489 (mmp) REVERT: R 210 MET cc_start: -0.1019 (tmm) cc_final: -0.1373 (tmm) REVERT: R 211 MET cc_start: 0.0491 (ttp) cc_final: 0.0122 (ptm) REVERT: S 243 MET cc_start: 0.6310 (mmt) cc_final: 0.5923 (ppp) REVERT: T 306 ARG cc_start: 0.2841 (mmm160) cc_final: 0.2359 (tpt170) outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 0.2036 time to fit residues: 62.6554 Evaluate side-chains 139 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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: 9.9990 chunk 178 optimal weight: 5.9990 chunk 184 optimal weight: 8.9990 chunk 237 optimal weight: 7.9990 chunk 230 optimal weight: 6.9990 chunk 331 optimal weight: 5.9990 chunk 80 optimal weight: 40.0000 chunk 355 optimal weight: 50.0000 chunk 31 optimal weight: 10.0000 chunk 353 optimal weight: 10.0000 chunk 81 optimal weight: 40.0000 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** B 93 GLN E 108 ASN ** G 73 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** ** 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** ** T 138 HIS ** 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 = 0.3856 r_free = 0.3856 target = 0.061138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.042167 restraints weight = 398453.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.043512 restraints weight = 208275.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.044348 restraints weight = 134014.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.044881 restraints weight = 98593.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.045209 restraints weight = 80016.102| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 34066 Z= 0.204 Angle : 0.670 9.767 47270 Z= 0.369 Chirality : 0.046 0.280 5415 Planarity : 0.005 0.059 5012 Dihedral : 25.373 99.318 7175 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % 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: 0.04 (0.14), residues: 3380 helix: 0.55 (0.12), residues: 1749 sheet: -0.09 (0.28), residues: 356 loop : -0.52 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 128 TYR 0.019 0.002 TYR L 159 PHE 0.024 0.002 PHE H 65 HIS 0.011 0.001 HIS K 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.20 (34066) covalent geometry : angle 0.66960 / 0.37 (47270) hydrogen bonds : bond 0.06027 / 4.13 ( 1711) hydrogen bonds : angle 4.72034 / 3.46 ( 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 162 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 ASP cc_start: 0.9310 (m-30) cc_final: 0.8895 (m-30) REVERT: B 84 MET cc_start: 0.9223 (mmm) cc_final: 0.8893 (tpp) REVERT: C 55 LEU cc_start: 0.9705 (mt) cc_final: 0.9503 (mm) REVERT: D 62 MET cc_start: 0.9393 (mmm) cc_final: 0.9089 (mmm) REVERT: E 54 TYR cc_start: 0.8737 (m-80) cc_final: 0.8395 (m-10) REVERT: E 110 CYS cc_start: 0.9589 (m) cc_final: 0.9291 (p) REVERT: E 120 MET cc_start: 0.7802 (mpp) cc_final: 0.7525 (mpp) REVERT: F 44 LYS cc_start: 0.9387 (tttt) cc_final: 0.9059 (mtpp) REVERT: F 84 MET cc_start: 0.9217 (mmt) cc_final: 0.8757 (mmt) REVERT: F 98 TYR cc_start: 0.8994 (m-80) cc_final: 0.8335 (m-80) REVERT: G 56 GLU cc_start: 0.8829 (tt0) cc_final: 0.8176 (mt-10) REVERT: G 64 GLU cc_start: 0.9123 (tm-30) cc_final: 0.8848 (tm-30) REVERT: G 112 GLN cc_start: 0.7372 (mm-40) cc_final: 0.6971 (tm-30) REVERT: G 114 VAL cc_start: 0.8540 (t) cc_final: 0.8284 (t) REVERT: H 35 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7141 (pm20) REVERT: H 80 LEU cc_start: 0.9722 (mt) cc_final: 0.9106 (mm) REVERT: K 158 MET cc_start: -0.2048 (mmm) cc_final: -0.2295 (mmm) REVERT: K 210 MET cc_start: 0.7152 (ppp) cc_final: 0.6872 (ppp) REVERT: K 211 MET cc_start: -0.0551 (ttp) cc_final: -0.0985 (ttm) REVERT: L 158 MET cc_start: 0.4149 (mmt) cc_final: 0.3651 (mmt) REVERT: L 326 MET cc_start: 0.1313 (tpt) cc_final: 0.1039 (ptp) REVERT: M 30 GLN cc_start: 0.4991 (mp10) cc_final: 0.4421 (tm-30) REVERT: M 210 MET cc_start: 0.3410 (ppp) cc_final: 0.2941 (ptm) REVERT: P 326 MET cc_start: 0.5907 (mmp) cc_final: 0.5575 (mmp) REVERT: R 158 MET cc_start: -0.0067 (mmp) cc_final: -0.0424 (mmp) REVERT: R 210 MET cc_start: -0.1861 (tmm) cc_final: -0.2173 (tmm) REVERT: S 243 MET cc_start: 0.6306 (mmt) cc_final: 0.5917 (ppp) REVERT: T 306 ARG cc_start: 0.2904 (mmm160) cc_final: 0.2309 (tpt170) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1928 time to fit residues: 52.6087 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 : 0.934 ------------------------------------------------------------------------------- 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: 20.0000 chunk 109 optimal weight: 5.9990 chunk 296 optimal weight: 40.0000 chunk 337 optimal weight: 30.0000 chunk 350 optimal weight: 0.0980 chunk 126 optimal weight: 7.9990 chunk 216 optimal weight: 30.0000 chunk 252 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 318 optimal weight: 0.6980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 ** L 202 GLN ** 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 = 0.3880 r_free = 0.3880 target = 0.062249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.042977 restraints weight = 401456.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.044373 restraints weight = 204354.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.045234 restraints weight = 129074.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.045770 restraints weight = 94440.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.046088 restraints weight = 76699.918| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 34066 Z= 0.124 Angle : 0.587 8.601 47270 Z= 0.325 Chirality : 0.043 0.256 5415 Planarity : 0.004 0.054 5012 Dihedral : 25.152 97.271 7175 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % 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: 0.94 (0.12), residues: 1708 sheet: -0.09 (0.28), residues: 356 loop : -0.39 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 129 TYR 0.030 0.001 TYR M 216 PHE 0.016 0.002 PHE H 65 HIS 0.008 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.12 (34066) covalent geometry : angle 0.58707 / 0.33 (47270) hydrogen bonds : bond 0.04502 / 3.10 ( 1711) hydrogen bonds : angle 4.32103 / 3.18 ( 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 170 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8952 (mp10) cc_final: 0.8567 (mm110) REVERT: B 68 ASP cc_start: 0.8651 (m-30) cc_final: 0.8033 (t70) REVERT: D 62 MET cc_start: 0.9390 (mmm) cc_final: 0.9080 (mmm) REVERT: E 54 TYR cc_start: 0.8594 (m-80) cc_final: 0.8177 (m-10) REVERT: E 56 LYS cc_start: 0.9406 (tmtt) cc_final: 0.9199 (ttmm) REVERT: E 105 GLU cc_start: 0.9143 (tm-30) cc_final: 0.8806 (tm-30) REVERT: E 110 CYS cc_start: 0.9564 (m) cc_final: 0.9247 (p) REVERT: E 119 ILE cc_start: 0.9314 (pt) cc_final: 0.8954 (mm) REVERT: E 120 MET cc_start: 0.7870 (mpp) cc_final: 0.7244 (mpp) REVERT: F 44 LYS cc_start: 0.9356 (tttt) cc_final: 0.8999 (mtpp) REVERT: F 81 VAL cc_start: 0.8740 (t) cc_final: 0.8485 (t) REVERT: F 84 MET cc_start: 0.9160 (mmt) cc_final: 0.8709 (tpp) REVERT: F 85 ASP cc_start: 0.8848 (m-30) cc_final: 0.8612 (m-30) REVERT: F 98 TYR cc_start: 0.8894 (m-80) cc_final: 0.8262 (m-80) REVERT: G 51 LEU cc_start: 0.9839 (tt) cc_final: 0.9608 (tp) REVERT: G 56 GLU cc_start: 0.8798 (tt0) cc_final: 0.8116 (mm-30) REVERT: G 112 GLN cc_start: 0.7318 (mm-40) cc_final: 0.6882 (tm-30) REVERT: G 114 VAL cc_start: 0.8489 (t) cc_final: 0.8196 (t) REVERT: H 35 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7175 (pm20) REVERT: K 210 MET cc_start: 0.7350 (ppp) cc_final: 0.7104 (ppp) REVERT: K 211 MET cc_start: -0.0259 (ttp) cc_final: -0.0564 (ttm) REVERT: K 326 MET cc_start: 0.4887 (tpt) cc_final: 0.4493 (tpp) REVERT: M 30 GLN cc_start: 0.4924 (mp10) cc_final: 0.4371 (tm-30) REVERT: M 158 MET cc_start: 0.5817 (mmp) cc_final: 0.5511 (mmm) REVERT: M 210 MET cc_start: 0.3151 (ppp) cc_final: 0.2439 (ptm) REVERT: M 211 MET cc_start: 0.1818 (mtm) cc_final: 0.1283 (ttp) REVERT: N 211 MET cc_start: -0.3963 (tpt) cc_final: -0.4195 (tpt) REVERT: P 326 MET cc_start: 0.6236 (mmp) cc_final: 0.5908 (mmp) REVERT: S 243 MET cc_start: 0.6296 (mmt) cc_final: 0.5907 (ppp) REVERT: T 306 ARG cc_start: 0.2859 (mmm160) cc_final: 0.2262 (tpt170) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1965 time to fit residues: 56.6427 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 : 0.872 ------------------------------------------------------------------------------- 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: 30.0000 chunk 12 optimal weight: 9.9990 chunk 294 optimal weight: 4.9990 chunk 307 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 83 optimal weight: 50.0000 chunk 192 optimal weight: 20.0000 chunk 237 optimal weight: 9.9990 chunk 141 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 108 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 202 GLN K 244 HIS ** 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** ** M 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 114 GLN N 244 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.059744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.045117 restraints weight = 371790.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.044325 restraints weight = 262027.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.044409 restraints weight = 214636.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.044298 restraints weight = 201493.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.044323 restraints weight = 176994.989| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.5197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 34066 Z= 0.211 Angle : 0.670 8.873 47270 Z= 0.366 Chirality : 0.044 0.247 5415 Planarity : 0.005 0.087 5012 Dihedral : 25.238 101.289 7175 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.16 (0.14), residues: 3380 helix: 0.73 (0.12), residues: 1758 sheet: -0.19 (0.28), residues: 356 loop : -0.55 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 92 TYR 0.055 0.002 TYR A 54 PHE 0.019 0.002 PHE E 104 HIS 0.014 0.001 HIS K 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.21 (34066) covalent geometry : angle 0.66978 / 0.37 (47270) hydrogen bonds : bond 0.07357 / 5.05 ( 1711) hydrogen bonds : angle 4.53848 / 3.32 ( 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 149 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9287 (tp30) cc_final: 0.8807 (tp30) REVERT: B 97 LEU cc_start: 0.9414 (tp) cc_final: 0.9076 (tp) REVERT: C 55 LEU cc_start: 0.9740 (mt) cc_final: 0.9502 (mm) REVERT: D 62 MET cc_start: 0.9213 (mmm) cc_final: 0.8999 (mmm) REVERT: E 54 TYR cc_start: 0.8614 (m-80) cc_final: 0.8254 (m-10) REVERT: E 119 ILE cc_start: 0.9183 (pt) cc_final: 0.8791 (pt) REVERT: E 120 MET cc_start: 0.8229 (mpp) cc_final: 0.7940 (mpp) REVERT: F 84 MET cc_start: 0.9160 (mmt) cc_final: 0.8777 (mmt) REVERT: G 55 LEU cc_start: 0.9834 (mt) cc_final: 0.9623 (mm) REVERT: G 56 GLU cc_start: 0.8562 (tt0) cc_final: 0.8136 (mt-10) REVERT: G 112 GLN cc_start: 0.7508 (mm-40) cc_final: 0.7105 (tm-30) REVERT: G 114 VAL cc_start: 0.8525 (t) cc_final: 0.8315 (t) REVERT: H 64 SER cc_start: 0.9540 (m) cc_final: 0.9226 (p) REVERT: K 210 MET cc_start: 0.7243 (ppp) cc_final: 0.6864 (ppp) REVERT: K 211 MET cc_start: -0.0314 (ttp) cc_final: -0.0715 (ttm) REVERT: K 326 MET cc_start: 0.4734 (tpt) cc_final: 0.4354 (tpp) REVERT: L 158 MET cc_start: 0.3163 (mmt) cc_final: 0.2912 (mmt) REVERT: M 30 GLN cc_start: 0.4896 (mp10) cc_final: 0.3992 (tm-30) REVERT: M 158 MET cc_start: 0.7081 (mmp) cc_final: 0.6594 (mmm) REVERT: M 210 MET cc_start: 0.2611 (ppp) cc_final: 0.1230 (ptm) REVERT: M 211 MET cc_start: 0.0411 (mtm) cc_final: -0.0680 (ttm) REVERT: N 125 MET cc_start: 0.8308 (pmm) cc_final: 0.8102 (pmm) REVERT: P 326 MET cc_start: 0.7259 (mmp) cc_final: 0.6781 (mmp) REVERT: S 243 MET cc_start: 0.6316 (mmt) cc_final: 0.5744 (ppp) REVERT: T 306 ARG cc_start: 0.2530 (mmm160) cc_final: 0.1924 (tpt170) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1902 time to fit residues: 48.2902 Evaluate side-chains 122 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 1.169 ------------------------------------------------------------------------------- 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: 20.0000 chunk 87 optimal weight: 40.0000 chunk 8 optimal weight: 1.9990 chunk 231 optimal weight: 30.0000 chunk 116 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 321 optimal weight: 30.0000 chunk 135 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 286 optimal weight: 50.0000 chunk 20 optimal weight: 3.9990 overall best weight: 4.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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** K 244 HIS ** 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 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 = 0.3834 r_free = 0.3834 target = 0.060315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.041346 restraints weight = 399335.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 74)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.042681 restraints weight = 205220.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.043501 restraints weight = 130304.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.044023 restraints weight = 95800.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 68)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.044339 restraints weight = 77772.042| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.5455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 34066 Z= 0.151 Angle : 0.604 9.173 47270 Z= 0.333 Chirality : 0.044 0.234 5415 Planarity : 0.004 0.058 5012 Dihedral : 25.255 99.991 7175 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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: 0.34 (0.14), residues: 3380 helix: 0.93 (0.12), residues: 1765 sheet: -0.21 (0.28), residues: 356 loop : -0.55 (0.17), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 92 TYR 0.015 0.002 TYR T 232 PHE 0.023 0.002 PHE L 259 HIS 0.018 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.15 (34066) covalent geometry : angle 0.60421 / 0.33 (47270) hydrogen bonds : bond 0.04833 / 3.32 ( 1711) hydrogen bonds : angle 4.27650 / 3.12 ( 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 151 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.9072 (mp10) cc_final: 0.8845 (mm-40) REVERT: B 97 LEU cc_start: 0.9497 (tp) cc_final: 0.9293 (tp) REVERT: D 62 MET cc_start: 0.9420 (mmm) cc_final: 0.9140 (mmm) REVERT: E 110 CYS cc_start: 0.9557 (m) cc_final: 0.9263 (p) REVERT: E 119 ILE cc_start: 0.9231 (pt) cc_final: 0.8889 (pt) REVERT: E 120 MET cc_start: 0.8249 (mpp) cc_final: 0.7909 (mpp) REVERT: F 84 MET cc_start: 0.9095 (mmt) cc_final: 0.8716 (mmt) REVERT: G 56 GLU cc_start: 0.8897 (tt0) cc_final: 0.8211 (mm-30) REVERT: H 59 MET cc_start: 0.8859 (ttm) cc_final: 0.8617 (tpp) REVERT: H 64 SER cc_start: 0.9449 (m) cc_final: 0.9152 (p) REVERT: H 71 GLU cc_start: 0.9364 (mp0) cc_final: 0.8890 (tt0) REVERT: K 210 MET cc_start: 0.7364 (ppp) cc_final: 0.7125 (ppp) REVERT: K 211 MET cc_start: 0.0053 (ttp) cc_final: -0.0262 (ttm) REVERT: K 326 MET cc_start: 0.5229 (tpt) cc_final: 0.4771 (tpp) REVERT: L 158 MET cc_start: 0.3623 (mmt) cc_final: 0.3303 (mmt) REVERT: M 30 GLN cc_start: 0.4628 (mp10) cc_final: 0.4070 (tm-30) REVERT: M 210 MET cc_start: 0.3544 (ppp) cc_final: 0.2701 (ptm) REVERT: M 211 MET cc_start: 0.2002 (mtm) cc_final: 0.1132 (ttm) REVERT: N 211 MET cc_start: -0.3870 (tpt) cc_final: -0.4110 (tpt) REVERT: P 326 MET cc_start: 0.6297 (mmp) cc_final: 0.6024 (mmp) REVERT: R 211 MET cc_start: 0.0392 (ttp) cc_final: -0.0088 (ptm) REVERT: S 243 MET cc_start: 0.6342 (mmt) cc_final: 0.5941 (ppp) REVERT: T 306 ARG cc_start: 0.2659 (mmm160) cc_final: 0.1980 (tpt170) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.2031 time to fit residues: 53.0533 Evaluate side-chains 122 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 1.177 ------------------------------------------------------------------------------- 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: 30.0000 chunk 316 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 309 optimal weight: 20.0000 chunk 211 optimal weight: 40.0000 chunk 229 optimal weight: 9.9990 chunk 53 optimal weight: 0.6980 chunk 79 optimal weight: 40.0000 chunk 297 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 92 optimal weight: 30.0000 overall best weight: 7.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 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** ** 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** ** 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** ** Q 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 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** ** S 145 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 = 0.3796 r_free = 0.3796 target = 0.059045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.043514 restraints weight = 377171.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.042817 restraints weight = 290028.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.042803 restraints weight = 221767.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.042932 restraints weight = 188742.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.042928 restraints weight = 176026.187| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.5851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 34066 Z= 0.204 Angle : 0.664 11.676 47270 Z= 0.362 Chirality : 0.044 0.245 5415 Planarity : 0.005 0.058 5012 Dihedral : 25.297 102.897 7175 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: 0.11 (0.14), residues: 3380 helix: 0.71 (0.12), residues: 1797 sheet: -0.32 (0.28), residues: 356 loop : -0.61 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 86 TYR 0.026 0.002 TYR L 216 PHE 0.019 0.002 PHE E 104 HIS 0.013 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.20 (34066) covalent geometry : angle 0.66362 / 0.36 (47270) hydrogen bonds : bond 0.06912 / 4.73 ( 1711) hydrogen bonds : angle 4.47064 / 3.25 ( 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 141 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.9295 (mt-10) cc_final: 0.8822 (mt-10) REVERT: B 97 LEU cc_start: 0.9539 (tp) cc_final: 0.9280 (tp) REVERT: D 62 MET cc_start: 0.9219 (mmm) cc_final: 0.9002 (mmm) REVERT: E 119 ILE cc_start: 0.9098 (pt) cc_final: 0.8727 (pt) REVERT: E 120 MET cc_start: 0.8430 (mpp) cc_final: 0.8197 (mpp) REVERT: F 84 MET cc_start: 0.8955 (mmt) cc_final: 0.8613 (mmt) REVERT: G 56 GLU cc_start: 0.8699 (tt0) cc_final: 0.8206 (mt-10) REVERT: H 64 SER cc_start: 0.9567 (m) cc_final: 0.9278 (p) REVERT: H 71 GLU cc_start: 0.9291 (mp0) cc_final: 0.9054 (mp0) REVERT: K 210 MET cc_start: 0.7130 (ppp) cc_final: 0.6855 (ppp) REVERT: K 211 MET cc_start: -0.0162 (ttp) cc_final: -0.0614 (ttm) REVERT: K 326 MET cc_start: 0.5138 (tpt) cc_final: 0.4707 (tpp) REVERT: L 158 MET cc_start: 0.3384 (mmt) cc_final: 0.3003 (mmt) REVERT: M 30 GLN cc_start: 0.4514 (mp10) cc_final: 0.3792 (tm-30) REVERT: M 158 MET cc_start: 0.7546 (mmp) cc_final: 0.6831 (mmm) REVERT: M 210 MET cc_start: 0.3214 (ppp) cc_final: 0.2287 (ptm) REVERT: O 125 MET cc_start: 0.6806 (ptp) cc_final: 0.6571 (ptp) REVERT: O 210 MET cc_start: 0.4011 (ppp) cc_final: 0.3726 (ppp) REVERT: O 326 MET cc_start: 0.5219 (tpt) cc_final: 0.4613 (tpp) REVERT: P 326 MET cc_start: 0.7155 (mmp) cc_final: 0.6678 (mmp) REVERT: S 243 MET cc_start: 0.6296 (mmt) cc_final: 0.5749 (ppp) REVERT: T 306 ARG cc_start: 0.2316 (mmm160) cc_final: 0.1649 (tpt170) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1990 time to fit residues: 48.3685 Evaluate side-chains 119 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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: 0.9990 chunk 353 optimal weight: 10.0000 chunk 303 optimal weight: 30.0000 chunk 173 optimal weight: 8.9990 chunk 326 optimal weight: 9.9990 chunk 206 optimal weight: 4.9990 chunk 351 optimal weight: 40.0000 chunk 254 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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** ** Q 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 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** ** S 145 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 = 0.3825 r_free = 0.3825 target = 0.059994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.043953 restraints weight = 372780.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.043465 restraints weight = 302811.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.043710 restraints weight = 231855.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.043354 restraints weight = 216232.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.043392 restraints weight = 208050.760| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.5940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 34066 Z= 0.130 Angle : 0.598 8.979 47270 Z= 0.327 Chirality : 0.043 0.225 5415 Planarity : 0.004 0.059 5012 Dihedral : 25.197 100.477 7175 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: 0.34 (0.14), residues: 3380 helix: 0.92 (0.12), residues: 1805 sheet: -0.31 (0.28), residues: 356 loop : -0.53 (0.18), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 92 TYR 0.018 0.002 TYR L 216 PHE 0.013 0.002 PHE K 327 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.13 (34066) covalent geometry : angle 0.59763 / 0.33 (47270) hydrogen bonds : bond 0.04582 / 3.15 ( 1711) hydrogen bonds : angle 4.17947 / 3.05 ( 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 148 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 62 MET cc_start: 0.9342 (mmm) cc_final: 0.9065 (mmm) REVERT: E 119 ILE cc_start: 0.9056 (pt) cc_final: 0.8688 (pt) REVERT: E 120 MET cc_start: 0.8421 (mpp) cc_final: 0.8185 (mpp) REVERT: F 84 MET cc_start: 0.8672 (mmt) cc_final: 0.8323 (mmt) REVERT: G 56 GLU cc_start: 0.8705 (tt0) cc_final: 0.8127 (mm-30) REVERT: H 64 SER cc_start: 0.9583 (m) cc_final: 0.9235 (p) REVERT: H 71 GLU cc_start: 0.9508 (mp0) cc_final: 0.9192 (mp0) REVERT: K 210 MET cc_start: 0.7241 (ppp) cc_final: 0.6954 (ppp) REVERT: K 211 MET cc_start: -0.0259 (ttp) cc_final: -0.0611 (ttm) REVERT: K 326 MET cc_start: 0.5496 (tpt) cc_final: 0.4969 (tpp) REVERT: L 158 MET cc_start: 0.3423 (mmt) cc_final: 0.2859 (mmt) REVERT: M 30 GLN cc_start: 0.4566 (mp10) cc_final: 0.3884 (tm-30) REVERT: M 158 MET cc_start: 0.7228 (mmp) cc_final: 0.6811 (mmm) REVERT: M 210 MET cc_start: 0.3180 (ppp) cc_final: 0.2006 (ptm) REVERT: M 211 MET cc_start: 0.0512 (mtm) cc_final: -0.0662 (ttm) REVERT: O 326 MET cc_start: 0.5389 (tpt) cc_final: 0.4759 (tpp) REVERT: P 326 MET cc_start: 0.6998 (mmp) cc_final: 0.6575 (mmp) REVERT: R 125 MET cc_start: 0.7773 (pmm) cc_final: 0.7573 (pmm) REVERT: S 243 MET cc_start: 0.6210 (mmt) cc_final: 0.5689 (ppp) REVERT: S 326 MET cc_start: 0.5454 (mpp) cc_final: 0.5247 (mpp) REVERT: T 306 ARG cc_start: 0.2245 (mmm160) cc_final: 0.1631 (tpt170) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2014 time to fit residues: 51.7356 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 : 1.180 ------------------------------------------------------------------------------- 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: 7.9990 chunk 244 optimal weight: 7.9990 chunk 192 optimal weight: 7.9990 chunk 82 optimal weight: 40.0000 chunk 23 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 296 optimal weight: 10.0000 chunk 118 optimal weight: 40.0000 chunk 138 optimal weight: 20.0000 overall best weight: 6.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 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** ** 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** ** Q 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 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** ** S 145 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 = 0.3790 r_free = 0.3790 target = 0.058788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.043538 restraints weight = 377784.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.043409 restraints weight = 326180.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.043107 restraints weight = 241235.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.043435 restraints weight = 210975.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.043323 restraints weight = 190745.293| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.6248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 34066 Z= 0.199 Angle : 0.650 10.193 47270 Z= 0.355 Chirality : 0.044 0.242 5415 Planarity : 0.005 0.059 5012 Dihedral : 25.241 103.663 7175 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % 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: 0.19 (0.14), residues: 3380 helix: 0.80 (0.12), residues: 1805 sheet: -0.39 (0.28), residues: 356 loop : -0.58 (0.18), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 92 TYR 0.031 0.002 TYR L 216 PHE 0.018 0.002 PHE E 104 HIS 0.010 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.20 (34066) covalent geometry : angle 0.64975 / 0.36 (47270) hydrogen bonds : bond 0.06594 / 4.51 ( 1711) hydrogen bonds : angle 4.38010 / 3.19 ( 4679) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7267.27 seconds wall clock time: 125 minutes 58.50 seconds (7558.50 seconds total)