Starting phenix.real_space_refine on Thu May 29 22:45:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jne_36443/05_2025/8jne_36443.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jne_36443/05_2025/8jne_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_36443/05_2025/8jne_36443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jne_36443/05_2025/8jne_36443.map" model { file = "/net/cci-nas-00/data/ceres_data/8jne_36443/05_2025/8jne_36443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jne_36443/05_2025/8jne_36443.cif" } resolution = 4.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 309 5.49 5 S 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 17.09, per 1000 atoms: 0.52 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: 8.51 Conformation dependent library (CDL) restraints added in 3.8 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: 12.98 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: 13.06 Time building geometry restraints manager: 9.78 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=" N MET N 243 " pdb=" CA MET N 243 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.28e-02 6.10e+03 5.52e+00 bond pdb=" C GLU E 73 " pdb=" O GLU E 73 " ideal model delta sigma weight residual 1.236 1.262 -0.026 1.15e-02 7.56e+03 5.07e+00 bond pdb=" CA VAL E 117 " pdb=" CB VAL E 117 " ideal model delta sigma weight residual 1.542 1.566 -0.024 1.08e-02 8.57e+03 4.88e+00 bond pdb=" P DT J 14 " pdb=" OP2 DT J 14 " ideal model delta sigma weight residual 1.480 1.521 -0.041 2.00e-02 2.50e+03 4.26e+00 bond pdb=" C GLU G 61 " pdb=" O GLU G 61 " ideal model delta sigma weight residual 1.237 1.261 -0.024 1.16e-02 7.43e+03 4.25e+00 ... (remaining 34061 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 45439 2.46 - 4.92: 1659 4.92 - 7.38: 136 7.38 - 9.83: 26 9.83 - 12.29: 10 Bond angle restraints: 47270 Sorted by residual: 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 angle pdb=" C HIS A 39 " pdb=" CA HIS A 39 " pdb=" CB HIS A 39 " ideal model delta sigma weight residual 109.51 117.71 -8.20 1.71e+00 3.42e-01 2.30e+01 angle pdb=" C HIS D 49 " pdb=" N PRO D 50 " pdb=" CA PRO D 50 " ideal model delta sigma weight residual 119.47 124.93 -5.46 1.16e+00 7.43e-01 2.22e+01 angle pdb=" N PHE T 195 " pdb=" CA PHE T 195 " pdb=" CB PHE T 195 " ideal model delta sigma weight residual 110.44 103.22 7.22 1.56e+00 4.11e-01 2.14e+01 angle pdb=" N PHE N 195 " pdb=" CA PHE N 195 " pdb=" CB PHE N 195 " ideal model delta sigma weight residual 110.44 103.23 7.21 1.56e+00 4.11e-01 2.14e+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 - 0.128: 5318 0.128 - 0.256: 67 0.256 - 0.384: 1 0.384 - 0.512: 8 0.512 - 0.640: 21 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 2.35 -2.99 -0.64 2.00e-01 2.50e+01 1.03e+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 2.35 -2.95 -0.60 2.00e-01 2.50e+01 9.06e+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 2.35 -2.94 -0.60 2.00e-01 2.50e+01 8.97e+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: 1.330 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: 0.020 Extract box with map and model: 1.270 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 75.850 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 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= 0.302 Angle : 1.093 12.292 47270 Z= 0.678 Chirality : 0.063 0.640 5415 Planarity : 0.006 0.089 5012 Dihedral : 20.643 94.338 13512 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 24.82 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (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 HIS 0.030 0.002 HIS T 294 PHE 0.096 0.003 PHE N 195 TYR 0.016 0.003 TYR F 51 ARG 0.021 0.002 ARG N 299 Details of bonding type rmsd hydrogen bonds : bond 0.20823 ( 1711) hydrogen bonds : angle 6.82401 ( 4679) covalent geometry : bond 0.00587 (34066) covalent geometry : angle 1.09304 (47270) *********************** 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 : 3.052 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: 0.7680 (mp) REVERT: A 61 LEU cc_start: 0.7677 (mt) cc_final: 0.7439 (mt) REVERT: A 74 ILE cc_start: 0.9526 (mt) cc_final: 0.9318 (mm) REVERT: A 106 ASP cc_start: 0.9045 (m-30) cc_final: 0.8500 (m-30) REVERT: B 46 ILE cc_start: 0.9438 (mt) cc_final: 0.9128 (tp) REVERT: B 68 ASP cc_start: 0.8931 (m-30) cc_final: 0.8660 (m-30) REVERT: B 81 VAL cc_start: 0.9020 (t) cc_final: 0.8771 (t) REVERT: B 96 THR cc_start: 0.9038 (m) cc_final: 0.8738 (p) REVERT: D 37 TYR cc_start: 0.8137 (m-80) cc_final: 0.7621 (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: 0.8121 (mmm) REVERT: D 106 LEU cc_start: 0.8866 (tp) cc_final: 0.8521 (mt) REVERT: E 54 TYR cc_start: 0.8426 (m-80) cc_final: 0.7960 (m-10) REVERT: E 94 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8184 (mm-30) REVERT: E 99 TYR cc_start: 0.8394 (t80) cc_final: 0.8139 (t80) REVERT: E 119 ILE cc_start: 0.9374 (pt) cc_final: 0.8873 (pt) REVERT: E 124 ILE cc_start: 0.9515 (mt) cc_final: 0.9176 (mm) REVERT: F 44 LYS cc_start: 0.9022 (tttt) cc_final: 0.8518 (mtpp) REVERT: F 46 ILE cc_start: 0.9154 (mt) cc_final: 0.8880 (tt) REVERT: F 81 VAL cc_start: 0.8462 (t) cc_final: 0.8070 (t) REVERT: F 85 ASP cc_start: 0.8538 (m-30) cc_final: 0.8298 (m-30) REVERT: G 114 VAL cc_start: 0.8434 (t) cc_final: 0.8091 (p) REVERT: G 115 LEU cc_start: 0.8884 (mt) cc_final: 0.8167 (mp) REVERT: H 37 TYR cc_start: 0.7981 (m-80) cc_final: 0.7710 (m-10) REVERT: H 61 ILE cc_start: 0.9678 (mt) cc_final: 0.9306 (mm) REVERT: H 65 PHE cc_start: 0.8983 (t80) cc_final: 0.8713 (t80) REVERT: H 73 ILE cc_start: 0.9790 (mt) cc_final: 0.9580 (tp) REVERT: H 100 LEU cc_start: 0.9236 (mt) cc_final: 0.9033 (mt) REVERT: K 326 MET cc_start: 0.3037 (tpt) cc_final: 0.2614 (tpt) REVERT: L 50 GLU cc_start: 0.7985 (tt0) cc_final: 0.7408 (tt0) REVERT: L 210 MET cc_start: 0.2391 (tmm) cc_final: 0.0943 (ppp) REVERT: L 211 MET cc_start: 0.2829 (ttm) cc_final: 0.2420 (ttm) REVERT: L 254 ARG cc_start: 0.1415 (ttm170) cc_final: 0.0887 (ptt-90) REVERT: L 326 MET cc_start: 0.2701 (tpt) cc_final: 0.1694 (ptm) REVERT: M 30 GLN cc_start: 0.4970 (mp10) cc_final: 0.4354 (tm-30) REVERT: M 235 ARG cc_start: -0.0296 (mmt180) cc_final: -0.0591 (mpt180) REVERT: N 210 MET cc_start: 0.2131 (tmm) cc_final: 0.1833 (tmm) REVERT: S 210 MET cc_start: 0.4584 (tmm) cc_final: 0.3221 (ppp) REVERT: S 243 MET cc_start: 0.6316 (mmt) cc_final: 0.5907 (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: 0.4707 time to fit residues: 259.2706 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 : 3.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 310 optimal weight: 5.9990 chunk 278 optimal weight: 6.9990 chunk 154 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 188 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 chunk 288 optimal weight: 10.0000 chunk 111 optimal weight: 20.0000 chunk 175 optimal weight: 30.0000 chunk 214 optimal weight: 0.7980 chunk 334 optimal weight: 8.9990 overall best weight: 6.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS B 93 GLN D 49 HIS E 39 HIS E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 244 HIS ** L 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 202 GLN ** N 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 294 HIS ** Q 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 114 GLN T 206 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.062626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.047368 restraints weight = 373362.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.046850 restraints weight = 307939.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.046886 restraints weight = 232669.759| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 34066 Z= 0.245 Angle : 0.712 10.845 47270 Z= 0.393 Chirality : 0.044 0.245 5415 Planarity : 0.006 0.079 5012 Dihedral : 25.103 97.425 7175 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.07 % Allowed : 3.64 % Favored : 96.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.14), residues: 3380 helix: 0.73 (0.12), residues: 1746 sheet: 0.83 (0.27), residues: 342 loop : -0.74 (0.16), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS K 244 PHE 0.022 0.002 PHE N 195 TYR 0.028 0.002 TYR O 54 ARG 0.008 0.001 ARG M 170 Details of bonding type rmsd hydrogen bonds : bond 0.06443 ( 1711) hydrogen bonds : angle 4.93675 ( 4679) covalent geometry : bond 0.00524 (34066) covalent geometry : angle 0.71175 (47270) *********************** 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 208 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 206 time to evaluate : 3.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 CYS cc_start: 0.9230 (m) cc_final: 0.8942 (t) REVERT: A 125 GLN cc_start: 0.9101 (mp10) cc_final: 0.8766 (mm-40) REVERT: B 68 ASP cc_start: 0.9028 (m-30) cc_final: 0.8718 (m-30) REVERT: C 101 THR cc_start: 0.9347 (m) cc_final: 0.9129 (p) REVERT: D 62 MET cc_start: 0.9196 (mmm) cc_final: 0.8811 (mmm) REVERT: D 68 ASP cc_start: 0.9366 (t70) cc_final: 0.8984 (t0) REVERT: D 69 ILE cc_start: 0.9589 (mm) cc_final: 0.9216 (tp) REVERT: E 54 TYR cc_start: 0.8600 (m-80) cc_final: 0.8249 (m-10) REVERT: E 94 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8761 (mm-30) REVERT: E 105 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8432 (tm-30) REVERT: E 119 ILE cc_start: 0.9363 (pt) cc_final: 0.8895 (pt) REVERT: E 120 MET cc_start: 0.7971 (mpp) cc_final: 0.7708 (mpp) REVERT: E 130 ILE cc_start: 0.9637 (mt) cc_final: 0.8961 (mt) REVERT: F 81 VAL cc_start: 0.8625 (t) cc_final: 0.8260 (t) REVERT: F 85 ASP cc_start: 0.8957 (m-30) cc_final: 0.8701 (m-30) REVERT: F 98 TYR cc_start: 0.8324 (m-80) cc_final: 0.8118 (m-80) REVERT: G 51 LEU cc_start: 0.9838 (tp) cc_final: 0.9530 (tp) REVERT: G 55 LEU cc_start: 0.9843 (mt) cc_final: 0.9566 (mt) REVERT: G 110 ASN cc_start: 0.9175 (m-40) cc_final: 0.8922 (m110) REVERT: G 112 GLN cc_start: 0.7296 (mm-40) cc_final: 0.7000 (tm-30) REVERT: G 114 VAL cc_start: 0.8463 (t) cc_final: 0.8182 (t) REVERT: H 61 ILE cc_start: 0.9738 (mt) cc_final: 0.9446 (mt) REVERT: K 158 MET cc_start: -0.1997 (mmm) cc_final: -0.2343 (mmm) REVERT: K 210 MET cc_start: 0.6660 (tmm) cc_final: 0.6246 (ppp) REVERT: K 326 MET cc_start: 0.4581 (tpt) cc_final: 0.4182 (tpt) REVERT: L 125 MET cc_start: 0.4655 (pmm) cc_final: 0.4160 (ptm) REVERT: L 326 MET cc_start: 0.1248 (tpt) cc_final: 0.0996 (ptp) REVERT: M 30 GLN cc_start: 0.5307 (mp10) cc_final: 0.4562 (tm-30) REVERT: M 210 MET cc_start: 0.1797 (ppp) cc_final: 0.1237 (ptm) REVERT: M 211 MET cc_start: -0.1416 (ttm) cc_final: -0.1757 (ttt) REVERT: P 326 MET cc_start: 0.7263 (mmp) cc_final: 0.6843 (mmp) REVERT: R 158 MET cc_start: 0.3156 (mmm) cc_final: 0.2728 (mmp) REVERT: R 210 MET cc_start: -0.1807 (tmm) cc_final: -0.2625 (tmm) REVERT: R 235 ARG cc_start: 0.1585 (mmt180) cc_final: -0.0930 (ptt180) REVERT: S 34 ASN cc_start: 0.6237 (p0) cc_final: 0.6034 (p0) REVERT: S 243 MET cc_start: 0.6231 (mmt) cc_final: 0.5668 (ppp) REVERT: S 326 MET cc_start: 0.5201 (mpp) cc_final: 0.4988 (mpp) REVERT: T 306 ARG cc_start: 0.2409 (mmm160) cc_final: 0.2201 (tpt170) outliers start: 2 outliers final: 0 residues processed: 208 average time/residue: 0.4367 time to fit residues: 148.1775 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 : 3.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 202 optimal weight: 40.0000 chunk 98 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 296 optimal weight: 7.9990 chunk 340 optimal weight: 40.0000 chunk 103 optimal weight: 0.9980 chunk 185 optimal weight: 6.9990 chunk 38 optimal weight: 0.0980 chunk 267 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** L 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 206 GLN ** P 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 62 ASN ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.062321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.043052 restraints weight = 396916.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.044467 restraints weight = 206243.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.045346 restraints weight = 132031.531| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34066 Z= 0.159 Angle : 0.566 7.254 47270 Z= 0.320 Chirality : 0.039 0.270 5415 Planarity : 0.004 0.054 5012 Dihedral : 24.929 101.581 7175 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.14), residues: 3380 helix: 1.04 (0.12), residues: 1804 sheet: 0.37 (0.23), residues: 480 loop : -0.46 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 75 PHE 0.028 0.002 PHE H 65 TYR 0.034 0.002 TYR H 40 ARG 0.009 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.04501 ( 1711) hydrogen bonds : angle 4.26248 ( 4679) covalent geometry : bond 0.00334 (34066) covalent geometry : angle 0.56640 (47270) *********************** 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 184 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 3.193 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.9307 (mmp) cc_final: 0.9102 (mmm) REVERT: A 120 MET cc_start: 0.8155 (mmm) cc_final: 0.7615 (mmm) REVERT: A 125 GLN cc_start: 0.9089 (mp10) cc_final: 0.8724 (mm-40) REVERT: B 68 ASP cc_start: 0.9322 (m-30) cc_final: 0.9007 (m-30) REVERT: C 101 THR cc_start: 0.9221 (m) cc_final: 0.8936 (p) REVERT: D 62 MET cc_start: 0.9530 (mmm) cc_final: 0.9182 (mmm) REVERT: D 69 ILE cc_start: 0.9816 (mm) cc_final: 0.9413 (tp) REVERT: E 54 TYR cc_start: 0.8655 (m-80) cc_final: 0.8260 (m-10) REVERT: E 105 GLU cc_start: 0.9197 (tm-30) cc_final: 0.8861 (tm-30) REVERT: E 110 CYS cc_start: 0.9610 (m) cc_final: 0.9244 (p) REVERT: E 119 ILE cc_start: 0.9329 (pt) cc_final: 0.8926 (pt) REVERT: E 120 MET cc_start: 0.8204 (mpp) cc_final: 0.7761 (mpp) REVERT: F 44 LYS cc_start: 0.8912 (ttmm) cc_final: 0.8646 (tppp) REVERT: F 81 VAL cc_start: 0.8836 (t) cc_final: 0.8534 (t) REVERT: F 84 MET cc_start: 0.8796 (mmt) cc_final: 0.8486 (mmt) REVERT: F 85 ASP cc_start: 0.8949 (m-30) cc_final: 0.8639 (m-30) REVERT: G 51 LEU cc_start: 0.9796 (tp) cc_final: 0.9446 (tp) REVERT: G 55 LEU cc_start: 0.9857 (mt) cc_final: 0.9545 (mt) REVERT: G 91 GLU cc_start: 0.8673 (pp20) cc_final: 0.8413 (tm-30) REVERT: G 110 ASN cc_start: 0.9282 (m-40) cc_final: 0.8981 (m110) REVERT: G 112 GLN cc_start: 0.7364 (mm-40) cc_final: 0.6901 (tm-30) REVERT: G 114 VAL cc_start: 0.8583 (t) cc_final: 0.8343 (t) REVERT: H 35 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7544 (pm20) REVERT: K 211 MET cc_start: -0.0673 (ttp) cc_final: -0.0940 (ttm) REVERT: K 326 MET cc_start: 0.4766 (tpt) cc_final: 0.4357 (tpp) REVERT: L 158 MET cc_start: 0.4484 (mmp) cc_final: 0.3790 (mmt) REVERT: M 30 GLN cc_start: 0.5841 (mp10) cc_final: 0.5320 (tm-30) REVERT: M 158 MET cc_start: 0.6104 (mmp) cc_final: 0.5870 (mmm) REVERT: M 210 MET cc_start: 0.3198 (ppp) cc_final: 0.2773 (ptm) REVERT: R 210 MET cc_start: -0.1203 (tmm) cc_final: -0.1945 (tmm) REVERT: S 243 MET cc_start: 0.6093 (mmt) cc_final: 0.5687 (ppp) REVERT: T 306 ARG cc_start: 0.2602 (mmm160) cc_final: 0.2234 (tpt170) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.4314 time to fit residues: 131.6103 Evaluate side-chains 138 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 3.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 175 optimal weight: 50.0000 chunk 295 optimal weight: 9.9990 chunk 259 optimal weight: 8.9990 chunk 179 optimal weight: 40.0000 chunk 227 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 273 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 348 optimal weight: 50.0000 chunk 275 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 24 GLN E 108 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** K 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 188 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 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** Q 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 267 ASN ** R 138 HIS ** 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 101 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.057442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.043125 restraints weight = 385965.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.042513 restraints weight = 320218.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.042489 restraints weight = 241492.391| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.6410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 34066 Z= 0.313 Angle : 0.750 13.857 47270 Z= 0.415 Chirality : 0.046 0.193 5415 Planarity : 0.006 0.070 5012 Dihedral : 25.804 107.860 7175 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 24.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.04 % Allowed : 2.48 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.14), residues: 3380 helix: 0.31 (0.12), residues: 1781 sheet: 0.07 (0.23), residues: 456 loop : -0.34 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS E 113 PHE 0.042 0.003 PHE E 104 TYR 0.050 0.003 TYR H 40 ARG 0.019 0.001 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.08784 ( 1711) hydrogen bonds : angle 4.98452 ( 4679) covalent geometry : bond 0.00672 (34066) covalent geometry : angle 0.75044 (47270) *********************** 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 156 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 3.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9261 (tp30) cc_final: 0.8871 (tp30) REVERT: A 125 GLN cc_start: 0.9217 (mp10) cc_final: 0.8874 (mm110) REVERT: B 68 ASP cc_start: 0.9280 (m-30) cc_final: 0.8687 (t70) REVERT: C 55 LEU cc_start: 0.9708 (mt) cc_final: 0.9499 (mm) REVERT: D 62 MET cc_start: 0.9428 (mmm) cc_final: 0.9044 (mmm) REVERT: E 54 TYR cc_start: 0.8637 (m-80) cc_final: 0.8290 (m-10) REVERT: E 119 ILE cc_start: 0.9061 (pt) cc_final: 0.8781 (pt) REVERT: F 44 LYS cc_start: 0.8943 (ttmm) cc_final: 0.8596 (tppt) REVERT: G 55 LEU cc_start: 0.9771 (mt) cc_final: 0.9546 (mm) REVERT: G 112 GLN cc_start: 0.7700 (mm-40) cc_final: 0.7168 (tm-30) REVERT: H 61 ILE cc_start: 0.9577 (mt) cc_final: 0.9354 (mt) REVERT: H 64 SER cc_start: 0.9605 (m) cc_final: 0.9353 (p) REVERT: K 210 MET cc_start: 0.7215 (ppp) cc_final: 0.6952 (ppp) REVERT: K 211 MET cc_start: 0.0197 (ttp) cc_final: -0.0456 (ttm) REVERT: K 326 MET cc_start: 0.5845 (tpt) cc_final: 0.5405 (tpp) REVERT: L 158 MET cc_start: 0.5240 (mmp) cc_final: 0.4818 (mmt) REVERT: M 158 MET cc_start: 0.7505 (mmp) cc_final: 0.6951 (mmm) REVERT: M 210 MET cc_start: 0.2527 (ppp) cc_final: 0.1547 (ptm) REVERT: M 211 MET cc_start: -0.1946 (ttt) cc_final: -0.2395 (ttt) REVERT: P 326 MET cc_start: 0.7299 (mmp) cc_final: 0.7065 (mmp) REVERT: Q 243 MET cc_start: 0.4620 (ppp) cc_final: 0.4401 (ttt) REVERT: R 211 MET cc_start: 0.0284 (ttm) cc_final: -0.0113 (ptm) REVERT: S 34 ASN cc_start: 0.5533 (p0) cc_final: 0.5305 (p0) REVERT: S 243 MET cc_start: 0.6262 (mmt) cc_final: 0.5512 (tmm) REVERT: T 306 ARG cc_start: 0.1965 (mmm160) cc_final: 0.1595 (tpt170) outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 0.4297 time to fit residues: 112.5370 Evaluate side-chains 123 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 3.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 324 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 chunk 265 optimal weight: 20.0000 chunk 333 optimal weight: 20.0000 chunk 146 optimal weight: 50.0000 chunk 279 optimal weight: 6.9990 chunk 366 optimal weight: 8.9990 chunk 167 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN D 109 HIS E 108 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** K 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 244 HIS ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 188 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** O 206 GLN ** 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 267 ASN ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 101 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.058182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.041618 restraints weight = 377574.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.040720 restraints weight = 298507.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.040903 restraints weight = 210650.985| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.6751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 34066 Z= 0.206 Angle : 0.612 10.026 47270 Z= 0.341 Chirality : 0.040 0.183 5415 Planarity : 0.005 0.100 5012 Dihedral : 25.549 101.760 7175 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.14), residues: 3380 helix: 0.78 (0.12), residues: 1749 sheet: 0.13 (0.22), residues: 490 loop : -0.32 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS B 75 PHE 0.022 0.002 PHE L 259 TYR 0.024 0.002 TYR F 98 ARG 0.008 0.001 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.05287 ( 1711) hydrogen bonds : angle 4.36489 ( 4679) covalent geometry : bond 0.00442 (34066) covalent geometry : angle 0.61182 (47270) *********************** 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 151 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 3.093 Fit side-chains REVERT: A 50 GLU cc_start: 0.9187 (tp30) cc_final: 0.8807 (tp30) REVERT: A 125 GLN cc_start: 0.9075 (mp10) cc_final: 0.8697 (mm110) REVERT: D 62 MET cc_start: 0.9302 (mmm) cc_final: 0.8958 (mmm) REVERT: E 94 GLU cc_start: 0.9174 (tp30) cc_final: 0.8817 (tp30) REVERT: E 119 ILE cc_start: 0.8989 (pt) cc_final: 0.8606 (pt) REVERT: F 44 LYS cc_start: 0.8913 (ttmm) cc_final: 0.8609 (tppt) REVERT: F 81 VAL cc_start: 0.8595 (t) cc_final: 0.8386 (t) REVERT: F 84 MET cc_start: 0.9256 (mmm) cc_final: 0.8597 (mmt) REVERT: G 55 LEU cc_start: 0.9821 (mt) cc_final: 0.9593 (mm) REVERT: G 56 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8552 (mm-30) REVERT: G 91 GLU cc_start: 0.9284 (pm20) cc_final: 0.8957 (tm-30) REVERT: H 61 ILE cc_start: 0.9701 (mt) cc_final: 0.9456 (mt) REVERT: H 71 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8768 (mm-30) REVERT: K 211 MET cc_start: -0.0010 (ttp) cc_final: -0.0435 (ttm) REVERT: K 326 MET cc_start: 0.6227 (tpt) cc_final: 0.5702 (tpp) REVERT: L 158 MET cc_start: 0.5264 (mmp) cc_final: 0.4756 (mmm) REVERT: M 158 MET cc_start: 0.6356 (mmp) cc_final: 0.5740 (mmm) REVERT: M 210 MET cc_start: 0.3162 (ppp) cc_final: 0.2684 (ptm) REVERT: P 326 MET cc_start: 0.6397 (mmp) cc_final: 0.6077 (mmp) REVERT: S 34 ASN cc_start: 0.5934 (p0) cc_final: 0.5714 (p0) REVERT: S 243 MET cc_start: 0.6213 (mmt) cc_final: 0.5578 (tmm) REVERT: T 306 ARG cc_start: 0.2254 (mmm160) cc_final: 0.1673 (tpt170) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.4216 time to fit residues: 107.3322 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 : 3.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 308 optimal weight: 20.0000 chunk 118 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 310 optimal weight: 20.0000 chunk 250 optimal weight: 4.9990 chunk 130 optimal weight: 30.0000 chunk 207 optimal weight: 10.0000 chunk 315 optimal weight: 30.0000 chunk 53 optimal weight: 0.0970 chunk 233 optimal weight: 50.0000 chunk 40 optimal weight: 3.9990 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN G 24 GLN ** 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 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 244 HIS ** M 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 244 HIS ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 294 HIS ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 101 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.058304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.042890 restraints weight = 374835.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.042093 restraints weight = 254203.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.042214 restraints weight = 194112.186| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.7153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 34066 Z= 0.180 Angle : 0.582 9.140 47270 Z= 0.324 Chirality : 0.039 0.152 5415 Planarity : 0.004 0.058 5012 Dihedral : 25.266 103.051 7175 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.14), residues: 3380 helix: 0.99 (0.12), residues: 1750 sheet: 0.18 (0.24), residues: 466 loop : -0.41 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 75 PHE 0.018 0.002 PHE H 65 TYR 0.028 0.002 TYR H 83 ARG 0.014 0.000 ARG E 128 Details of bonding type rmsd hydrogen bonds : bond 0.05086 ( 1711) hydrogen bonds : angle 4.17252 ( 4679) covalent geometry : bond 0.00385 (34066) covalent geometry : angle 0.58181 (47270) *********************** 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 144 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 3.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9177 (tp30) cc_final: 0.8775 (tp30) REVERT: A 120 MET cc_start: 0.8126 (mmm) cc_final: 0.7800 (mmm) REVERT: B 68 ASP cc_start: 0.8850 (m-30) cc_final: 0.8170 (t70) REVERT: D 62 MET cc_start: 0.9290 (mmm) cc_final: 0.8957 (mmm) REVERT: E 94 GLU cc_start: 0.9145 (tp30) cc_final: 0.8811 (tp30) REVERT: E 119 ILE cc_start: 0.9017 (pt) cc_final: 0.8696 (pt) REVERT: F 44 LYS cc_start: 0.9057 (ttmm) cc_final: 0.8751 (tppt) REVERT: F 84 MET cc_start: 0.8890 (mmm) cc_final: 0.8145 (mmt) REVERT: G 56 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8514 (mm-30) REVERT: G 91 GLU cc_start: 0.9283 (pm20) cc_final: 0.8942 (tm-30) REVERT: G 111 ILE cc_start: 0.9269 (mp) cc_final: 0.8733 (tp) REVERT: H 61 ILE cc_start: 0.9521 (mt) cc_final: 0.9297 (mt) REVERT: H 71 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8251 (tp30) REVERT: K 210 MET cc_start: 0.7212 (ppp) cc_final: 0.6956 (ppp) REVERT: K 211 MET cc_start: -0.0329 (ttp) cc_final: -0.0700 (ttm) REVERT: K 326 MET cc_start: 0.6696 (tpt) cc_final: 0.6227 (tpp) REVERT: M 158 MET cc_start: 0.6998 (mmp) cc_final: 0.6341 (mmm) REVERT: M 210 MET cc_start: 0.2674 (ppp) cc_final: 0.1879 (ptt) REVERT: N 125 MET cc_start: 0.8384 (pmm) cc_final: 0.8168 (pmm) REVERT: O 125 MET cc_start: 0.6758 (ptp) cc_final: 0.6537 (ptp) REVERT: O 326 MET cc_start: 0.6364 (tpt) cc_final: 0.5975 (tpp) REVERT: P 326 MET cc_start: 0.6753 (mmp) cc_final: 0.6396 (mmp) REVERT: Q 211 MET cc_start: 0.0504 (tpt) cc_final: -0.0049 (tpp) REVERT: S 34 ASN cc_start: 0.5468 (p0) cc_final: 0.5202 (p0) REVERT: S 243 MET cc_start: 0.6296 (mmt) cc_final: 0.5570 (tmm) REVERT: T 306 ARG cc_start: 0.2434 (mmm160) cc_final: 0.1683 (tpt170) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.4094 time to fit residues: 102.1471 Evaluate side-chains 118 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 3.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 77 optimal weight: 8.9990 chunk 242 optimal weight: 50.0000 chunk 197 optimal weight: 7.9990 chunk 221 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 270 optimal weight: 7.9990 chunk 213 optimal weight: 50.0000 chunk 41 optimal weight: 1.9990 chunk 289 optimal weight: 50.0000 chunk 44 optimal weight: 0.8980 chunk 284 optimal weight: 10.0000 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** 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 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 330 ASN ** M 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 101 GLN ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.057552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.042442 restraints weight = 379432.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.041785 restraints weight = 308120.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.041886 restraints weight = 226317.547| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.7607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 34066 Z= 0.200 Angle : 0.596 9.867 47270 Z= 0.332 Chirality : 0.040 0.148 5415 Planarity : 0.004 0.061 5012 Dihedral : 25.277 104.944 7175 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.14), residues: 3380 helix: 1.00 (0.12), residues: 1750 sheet: 0.10 (0.24), residues: 478 loop : -0.37 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS B 75 PHE 0.018 0.002 PHE H 65 TYR 0.024 0.002 TYR H 40 ARG 0.007 0.000 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.05423 ( 1711) hydrogen bonds : angle 4.19475 ( 4679) covalent geometry : bond 0.00431 (34066) covalent geometry : angle 0.59641 (47270) *********************** 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 141 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 2.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9158 (tp30) cc_final: 0.8813 (tp30) REVERT: A 120 MET cc_start: 0.8138 (mmm) cc_final: 0.7768 (mmm) REVERT: B 68 ASP cc_start: 0.8995 (m-30) cc_final: 0.8455 (t0) REVERT: B 97 LEU cc_start: 0.9645 (tp) cc_final: 0.9424 (tp) REVERT: D 62 MET cc_start: 0.9314 (mmm) cc_final: 0.9020 (mmm) REVERT: D 100 LEU cc_start: 0.9377 (mt) cc_final: 0.8866 (mt) REVERT: E 94 GLU cc_start: 0.8937 (tp30) cc_final: 0.8626 (tp30) REVERT: E 119 ILE cc_start: 0.8965 (pt) cc_final: 0.8715 (pt) REVERT: F 84 MET cc_start: 0.9256 (mmm) cc_final: 0.8525 (tpp) REVERT: G 56 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8545 (mm-30) REVERT: G 91 GLU cc_start: 0.9274 (pm20) cc_final: 0.8953 (tm-30) REVERT: G 111 ILE cc_start: 0.9272 (mp) cc_final: 0.8728 (tp) REVERT: H 71 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8403 (tp30) REVERT: K 210 MET cc_start: 0.7377 (ppp) cc_final: 0.7088 (ppp) REVERT: K 211 MET cc_start: -0.0121 (ttp) cc_final: -0.0566 (ttm) REVERT: K 326 MET cc_start: 0.6673 (tpt) cc_final: 0.6262 (tpp) REVERT: M 158 MET cc_start: 0.7191 (mmp) cc_final: 0.6467 (mmm) REVERT: M 210 MET cc_start: 0.3169 (ppp) cc_final: 0.2547 (ptt) REVERT: O 125 MET cc_start: 0.6754 (ptp) cc_final: 0.6533 (ptp) REVERT: O 326 MET cc_start: 0.6318 (tpt) cc_final: 0.5883 (tpp) REVERT: P 326 MET cc_start: 0.6798 (mmp) cc_final: 0.6409 (mmp) REVERT: S 243 MET cc_start: 0.6360 (mmt) cc_final: 0.5547 (tmm) REVERT: T 306 ARG cc_start: 0.2568 (mmm160) cc_final: 0.1591 (tpt170) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.3926 time to fit residues: 94.8974 Evaluate side-chains 115 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 3.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 42 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 321 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 200 optimal weight: 5.9990 chunk 179 optimal weight: 7.9990 chunk 299 optimal weight: 6.9990 chunk 162 optimal weight: 40.0000 chunk 211 optimal weight: 7.9990 chunk 220 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** G 24 GLN ** 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 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 200 GLN ** O 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 206 GLN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.057526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.042345 restraints weight = 375653.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.041679 restraints weight = 293345.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.041683 restraints weight = 226288.319| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.8010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 34066 Z= 0.188 Angle : 0.588 9.088 47270 Z= 0.327 Chirality : 0.039 0.162 5415 Planarity : 0.004 0.061 5012 Dihedral : 25.196 105.504 7175 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.14), residues: 3380 helix: 1.09 (0.12), residues: 1733 sheet: 0.03 (0.24), residues: 466 loop : -0.40 (0.18), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS B 75 PHE 0.026 0.002 PHE E 104 TYR 0.022 0.002 TYR H 40 ARG 0.006 0.000 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.05088 ( 1711) hydrogen bonds : angle 4.15535 ( 4679) covalent geometry : bond 0.00401 (34066) covalent geometry : angle 0.58823 (47270) *********************** 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 138 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 3.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8244 (mmm) cc_final: 0.7848 (mmm) REVERT: B 68 ASP cc_start: 0.9056 (m-30) cc_final: 0.8669 (t70) REVERT: D 62 MET cc_start: 0.9283 (mmm) cc_final: 0.8982 (mmm) REVERT: E 94 GLU cc_start: 0.9040 (tp30) cc_final: 0.8773 (tp30) REVERT: F 84 MET cc_start: 0.9193 (mmm) cc_final: 0.8591 (tpp) REVERT: G 56 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8554 (mm-30) REVERT: G 91 GLU cc_start: 0.9305 (pm20) cc_final: 0.8977 (tm-30) REVERT: G 111 ILE cc_start: 0.9261 (mp) cc_final: 0.8728 (tp) REVERT: H 71 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8526 (tp30) REVERT: K 210 MET cc_start: 0.7677 (ppp) cc_final: 0.7450 (ppp) REVERT: K 211 MET cc_start: 0.0001 (ttp) cc_final: -0.0382 (ttm) REVERT: K 326 MET cc_start: 0.6601 (tpt) cc_final: 0.6248 (tpp) REVERT: L 158 MET cc_start: 0.5294 (mmp) cc_final: 0.4702 (mmm) REVERT: M 158 MET cc_start: 0.7136 (mmp) cc_final: 0.6496 (mmm) REVERT: M 210 MET cc_start: 0.3472 (ppp) cc_final: 0.2868 (ptt) REVERT: O 158 MET cc_start: -0.2032 (mmp) cc_final: -0.3091 (mmm) REVERT: O 326 MET cc_start: 0.6413 (tpt) cc_final: 0.6054 (tpp) REVERT: P 326 MET cc_start: 0.6864 (mmp) cc_final: 0.6487 (mmp) REVERT: R 125 MET cc_start: 0.7587 (pmm) cc_final: 0.7350 (pmm) REVERT: R 211 MET cc_start: -0.0507 (ttt) cc_final: -0.0942 (ttp) REVERT: S 243 MET cc_start: 0.6490 (mmt) cc_final: 0.5667 (tmm) REVERT: T 306 ARG cc_start: 0.2565 (mmm160) cc_final: 0.1642 (tpt170) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.3962 time to fit residues: 95.4520 Evaluate side-chains 117 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 3.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 95 optimal weight: 7.9990 chunk 145 optimal weight: 20.0000 chunk 244 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 203 optimal weight: 30.0000 chunk 199 optimal weight: 8.9990 chunk 300 optimal weight: 50.0000 chunk 29 optimal weight: 0.9990 chunk 237 optimal weight: 0.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** G 24 GLN ** 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 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 206 GLN ** 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 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** ** S 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 188 ASN ** 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 = 0.3763 r_free = 0.3763 target = 0.057317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.041612 restraints weight = 376714.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.040942 restraints weight = 292554.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.041034 restraints weight = 221639.830| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.8280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 34066 Z= 0.190 Angle : 0.596 9.068 47270 Z= 0.330 Chirality : 0.040 0.195 5415 Planarity : 0.004 0.063 5012 Dihedral : 25.204 106.198 7175 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.14), residues: 3380 helix: 1.07 (0.12), residues: 1746 sheet: -0.10 (0.24), residues: 468 loop : -0.39 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS B 75 PHE 0.018 0.002 PHE H 65 TYR 0.048 0.002 TYR E 54 ARG 0.006 0.000 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.05221 ( 1711) hydrogen bonds : angle 4.17392 ( 4679) covalent geometry : bond 0.00408 (34066) covalent geometry : angle 0.59613 (47270) *********************** 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 134 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 3.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9178 (tp30) cc_final: 0.8834 (tp30) REVERT: A 120 MET cc_start: 0.8183 (mmm) cc_final: 0.7809 (mmm) REVERT: B 68 ASP cc_start: 0.9012 (m-30) cc_final: 0.8611 (t70) REVERT: D 62 MET cc_start: 0.9257 (mmm) cc_final: 0.8945 (mmm) REVERT: D 100 LEU cc_start: 0.9360 (mt) cc_final: 0.8932 (mt) REVERT: E 94 GLU cc_start: 0.9078 (tp30) cc_final: 0.8782 (tp30) REVERT: E 120 MET cc_start: 0.8377 (mpp) cc_final: 0.8164 (mpp) REVERT: F 84 MET cc_start: 0.9116 (mmm) cc_final: 0.8479 (mmt) REVERT: G 56 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8524 (mm-30) REVERT: G 91 GLU cc_start: 0.9289 (pm20) cc_final: 0.8969 (tm-30) REVERT: G 111 ILE cc_start: 0.9322 (mp) cc_final: 0.8797 (tp) REVERT: H 71 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8443 (tp30) REVERT: K 210 MET cc_start: 0.7552 (ppp) cc_final: 0.7281 (ppp) REVERT: K 211 MET cc_start: 0.0177 (ttp) cc_final: -0.0248 (ttm) REVERT: K 326 MET cc_start: 0.6599 (tpt) cc_final: 0.6204 (tpp) REVERT: M 158 MET cc_start: 0.7135 (mmp) cc_final: 0.6524 (mmm) REVERT: M 210 MET cc_start: 0.3619 (ppp) cc_final: 0.2973 (ptt) REVERT: M 211 MET cc_start: -0.1393 (ttt) cc_final: -0.1751 (ttt) REVERT: O 326 MET cc_start: 0.6752 (tpt) cc_final: 0.6521 (tpp) REVERT: P 326 MET cc_start: 0.6675 (mmp) cc_final: 0.6359 (mmp) REVERT: Q 211 MET cc_start: 0.1805 (tpp) cc_final: 0.1161 (tpp) REVERT: R 125 MET cc_start: 0.7585 (pmm) cc_final: 0.7324 (pmm) REVERT: S 243 MET cc_start: 0.6485 (mmt) cc_final: 0.5703 (tmm) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.3812 time to fit residues: 89.7304 Evaluate side-chains 113 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 3.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 33 optimal weight: 0.9990 chunk 258 optimal weight: 30.0000 chunk 77 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 56 optimal weight: 20.0000 chunk 362 optimal weight: 50.0000 chunk 123 optimal weight: 30.0000 chunk 166 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 163 optimal weight: 40.0000 overall best weight: 6.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 101 GLN N 114 GLN ** O 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 206 GLN ** 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 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 138 HIS ** R 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 188 ASN ** 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 = 0.3743 r_free = 0.3743 target = 0.056640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.042098 restraints weight = 384119.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.040921 restraints weight = 310326.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.041084 restraints weight = 257768.083| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.8804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 34066 Z= 0.234 Angle : 0.653 10.640 47270 Z= 0.360 Chirality : 0.041 0.142 5415 Planarity : 0.004 0.066 5012 Dihedral : 25.432 108.965 7175 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 21.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.14), residues: 3380 helix: 0.81 (0.12), residues: 1746 sheet: -0.14 (0.30), residues: 318 loop : -0.83 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS B 75 PHE 0.025 0.002 PHE E 104 TYR 0.038 0.002 TYR L 205 ARG 0.006 0.001 ARG M 170 Details of bonding type rmsd hydrogen bonds : bond 0.06315 ( 1711) hydrogen bonds : angle 4.45519 ( 4679) covalent geometry : bond 0.00504 (34066) covalent geometry : angle 0.65291 (47270) ********************** 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 136 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 3.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9049 (tp30) cc_final: 0.8812 (tp30) REVERT: A 120 MET cc_start: 0.8280 (mmm) cc_final: 0.7906 (mmm) REVERT: B 97 LEU cc_start: 0.9640 (tp) cc_final: 0.9436 (tp) REVERT: D 62 MET cc_start: 0.9261 (mmm) cc_final: 0.8920 (mmm) REVERT: E 94 GLU cc_start: 0.9067 (tp30) cc_final: 0.8782 (tp30) REVERT: E 119 ILE cc_start: 0.8544 (pt) cc_final: 0.8340 (pt) REVERT: E 120 MET cc_start: 0.8298 (mpp) cc_final: 0.7989 (mpp) REVERT: F 84 MET cc_start: 0.8956 (mmm) cc_final: 0.8723 (tpp) REVERT: G 56 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8339 (mm-30) REVERT: G 91 GLU cc_start: 0.9289 (pm20) cc_final: 0.8994 (tm-30) REVERT: G 111 ILE cc_start: 0.9322 (mp) cc_final: 0.8774 (tp) REVERT: H 59 MET cc_start: 0.8835 (ttm) cc_final: 0.8450 (tpp) REVERT: H 71 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8490 (tp30) REVERT: K 210 MET cc_start: 0.7729 (ppp) cc_final: 0.7411 (ppp) REVERT: K 211 MET cc_start: 0.0607 (ttp) cc_final: 0.0102 (ttm) REVERT: K 326 MET cc_start: 0.6761 (tpt) cc_final: 0.6391 (tpp) REVERT: K 338 LYS cc_start: 0.6143 (mppt) cc_final: 0.5865 (pttm) REVERT: M 158 MET cc_start: 0.7357 (mmp) cc_final: 0.6642 (mmm) REVERT: M 210 MET cc_start: 0.3588 (ppp) cc_final: 0.2934 (ptt) REVERT: M 211 MET cc_start: -0.1586 (ttt) cc_final: -0.1837 (ttt) REVERT: O 158 MET cc_start: -0.1351 (mmm) cc_final: -0.2617 (mmm) REVERT: O 326 MET cc_start: 0.6454 (tpt) cc_final: 0.6143 (tpp) REVERT: P 326 MET cc_start: 0.6836 (mmp) cc_final: 0.6278 (mmp) REVERT: P 339 ASP cc_start: 0.6897 (p0) cc_final: 0.6549 (m-30) REVERT: Q 211 MET cc_start: 0.1940 (tpp) cc_final: 0.1371 (tpp) REVERT: R 125 MET cc_start: 0.7626 (pmm) cc_final: 0.7311 (pmm) REVERT: S 243 MET cc_start: 0.6446 (mmt) cc_final: 0.5663 (tmm) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.3844 time to fit residues: 91.9338 Evaluate side-chains 113 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 3.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 148 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 272 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 131 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 306 optimal weight: 20.0000 chunk 309 optimal weight: 0.0170 chunk 318 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 overall best weight: 2.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** 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** K 330 ASN ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 145 GLN P 188 ASN ** Q 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 188 ASN ** 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 = 0.3777 r_free = 0.3777 target = 0.057845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.043382 restraints weight = 375707.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.042631 restraints weight = 257738.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.042816 restraints weight = 199502.812| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.8794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 34066 Z= 0.144 Angle : 0.578 8.725 47270 Z= 0.318 Chirality : 0.039 0.167 5415 Planarity : 0.004 0.064 5012 Dihedral : 25.101 104.334 7175 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.14), residues: 3380 helix: 1.22 (0.12), residues: 1736 sheet: 0.35 (0.31), residues: 290 loop : -0.69 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 113 PHE 0.021 0.002 PHE H 65 TYR 0.019 0.001 TYR F 98 ARG 0.005 0.000 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.04258 ( 1711) hydrogen bonds : angle 4.00926 ( 4679) covalent geometry : bond 0.00305 (34066) covalent geometry : angle 0.57826 (47270) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9028.69 seconds wall clock time: 160 minutes 20.07 seconds (9620.07 seconds total)