Starting phenix.real_space_refine on Tue Aug 26 02:44:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jne_36443/08_2025/8jne_36443.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jne_36443/08_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_36443/08_2025/8jne_36443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jne_36443/08_2025/8jne_36443.map" model { file = "/net/cci-nas-00/data/ceres_data/8jne_36443/08_2025/8jne_36443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jne_36443/08_2025/8jne_36443.cif" } resolution = 4.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 309 5.49 5 S 132 5.16 5 C 19680 2.51 5 N 5946 2.21 5 O 6889 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 259 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 7.26, per 1000 atoms: 0.22 Number of scatterers: 32956 At special positions: 0 Unit cell: (204.58, 163.24, 136.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 132 16.00 P 309 15.00 O 6889 8.00 N 5946 7.00 C 19680 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.95 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6318 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 20 sheets defined 57.8% alpha, 13.8% beta 142 base pairs and 288 stacking pairs defined. Time for finding SS restraints: 4.58 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: 7.03 Time building geometry restraints manager: 3.79 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: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 33.150 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.580 ------------------------------------------------------------------------------- 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 : 24.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Rotamer: Outliers : 0.14 % Allowed : 0.79 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.13), residues: 3380 helix: 0.03 (0.11), residues: 1697 sheet: 0.30 (0.20), residues: 542 loop : -0.25 (0.17), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG N 299 TYR 0.016 0.003 TYR F 51 PHE 0.096 0.003 PHE N 195 HIS 0.030 0.002 HIS T 294 Details of bonding type rmsd covalent geometry : bond 0.00587 (34066) covalent geometry : angle 1.09304 (47270) hydrogen bonds : bond 0.20823 ( 1711) hydrogen bonds : angle 6.82401 ( 4679) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 352 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8059 (mt) cc_final: 0.7688 (mp) REVERT: A 61 LEU cc_start: 0.7677 (mt) cc_final: 0.7470 (mt) REVERT: A 74 ILE cc_start: 0.9526 (mt) cc_final: 0.9321 (mm) REVERT: A 106 ASP cc_start: 0.9045 (m-30) cc_final: 0.8491 (m-30) REVERT: B 46 ILE cc_start: 0.9438 (mt) cc_final: 0.9129 (tp) REVERT: B 68 ASP cc_start: 0.8931 (m-30) cc_final: 0.8668 (m-30) REVERT: B 81 VAL cc_start: 0.9020 (t) cc_final: 0.8771 (t) REVERT: B 96 THR cc_start: 0.9038 (m) cc_final: 0.8750 (p) REVERT: D 37 TYR cc_start: 0.8137 (m-80) cc_final: 0.7619 (m-80) REVERT: D 54 ILE cc_start: 0.8586 (tt) cc_final: 0.8329 (tt) REVERT: D 62 MET cc_start: 0.8330 (mmm) cc_final: 0.8121 (mmm) REVERT: D 106 LEU cc_start: 0.8866 (tp) cc_final: 0.8527 (mt) REVERT: E 54 TYR cc_start: 0.8426 (m-80) cc_final: 0.7956 (m-10) REVERT: E 94 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8182 (mm-30) REVERT: E 99 TYR cc_start: 0.8394 (t80) cc_final: 0.8141 (t80) REVERT: E 119 ILE cc_start: 0.9374 (pt) cc_final: 0.8872 (pt) REVERT: E 124 ILE cc_start: 0.9515 (mt) cc_final: 0.9176 (mm) REVERT: F 44 LYS cc_start: 0.9022 (tttt) cc_final: 0.8519 (mtpp) REVERT: F 46 ILE cc_start: 0.9154 (mt) cc_final: 0.8880 (tt) REVERT: F 81 VAL cc_start: 0.8462 (t) cc_final: 0.8074 (t) REVERT: F 85 ASP cc_start: 0.8538 (m-30) cc_final: 0.8300 (m-30) REVERT: G 114 VAL cc_start: 0.8434 (t) cc_final: 0.8099 (p) REVERT: G 115 LEU cc_start: 0.8884 (mt) cc_final: 0.8138 (mp) REVERT: H 37 TYR cc_start: 0.7981 (m-80) cc_final: 0.7715 (m-10) REVERT: H 61 ILE cc_start: 0.9678 (mt) cc_final: 0.9301 (mm) REVERT: H 65 PHE cc_start: 0.8983 (t80) cc_final: 0.8738 (t80) REVERT: H 73 ILE cc_start: 0.9790 (mt) cc_final: 0.9582 (tp) REVERT: H 100 LEU cc_start: 0.9236 (mt) cc_final: 0.9024 (mt) REVERT: K 326 MET cc_start: 0.3037 (tpt) cc_final: 0.2619 (tpt) REVERT: L 50 GLU cc_start: 0.7985 (tt0) cc_final: 0.7410 (tt0) REVERT: L 210 MET cc_start: 0.2391 (tmm) cc_final: 0.0946 (ppp) REVERT: L 211 MET cc_start: 0.2829 (ttm) cc_final: 0.2417 (ttm) REVERT: L 254 ARG cc_start: 0.1415 (ttm170) cc_final: 0.0891 (ptt-90) REVERT: L 326 MET cc_start: 0.2701 (tpt) cc_final: 0.1685 (ptm) REVERT: M 30 GLN cc_start: 0.4970 (mp10) cc_final: 0.4350 (tm-30) REVERT: M 235 ARG cc_start: -0.0296 (mmt180) cc_final: -0.0589 (mpt180) REVERT: N 210 MET cc_start: 0.2131 (tmm) cc_final: 0.1826 (tmm) REVERT: S 210 MET cc_start: 0.4584 (tmm) cc_final: 0.3226 (ppp) REVERT: S 243 MET cc_start: 0.6316 (mmt) cc_final: 0.5909 (ppp) REVERT: T 306 ARG cc_start: 0.2747 (mmm160) cc_final: 0.1926 (tpt170) outliers start: 4 outliers final: 1 residues processed: 353 average time/residue: 0.2236 time to fit residues: 124.1256 Evaluate side-chains 184 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 197 optimal weight: 40.0000 chunk 215 optimal weight: 50.0000 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 108 ASN B 93 GLN D 49 HIS E 39 HIS E 108 ASN ** F 25 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 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** 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 = 0.3882 r_free = 0.3882 target = 0.062314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.047951 restraints weight = 375310.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.047334 restraints weight = 329643.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.047325 restraints weight = 256516.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.047384 restraints weight = 218778.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.047417 restraints weight = 197627.941| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 34066 Z= 0.249 Angle : 0.712 10.851 47270 Z= 0.395 Chirality : 0.044 0.163 5415 Planarity : 0.006 0.085 5012 Dihedral : 25.115 98.135 7175 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.18 % Allowed : 3.71 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.14), residues: 3380 helix: 0.74 (0.12), residues: 1748 sheet: 0.79 (0.26), residues: 340 loop : -0.74 (0.16), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 99 TYR 0.030 0.002 TYR B 98 PHE 0.030 0.002 PHE K 248 HIS 0.013 0.002 HIS K 244 Details of bonding type rmsd covalent geometry : bond 0.00528 (34066) covalent geometry : angle 0.71247 (47270) hydrogen bonds : bond 0.06498 ( 1711) hydrogen bonds : angle 4.92356 ( 4679) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 204 time to evaluate : 1.176 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: A 110 CYS cc_start: 0.9170 (m) cc_final: 0.8949 (t) REVERT: A 125 GLN cc_start: 0.9230 (mp10) cc_final: 0.9009 (mm-40) REVERT: B 68 ASP cc_start: 0.9144 (m-30) cc_final: 0.8735 (m-30) REVERT: B 84 MET cc_start: 0.8762 (mmm) cc_final: 0.8446 (tpp) REVERT: C 101 THR cc_start: 0.9371 (m) cc_final: 0.9168 (p) REVERT: D 62 MET cc_start: 0.9263 (mmm) cc_final: 0.8848 (mmm) REVERT: D 68 ASP cc_start: 0.9268 (t70) cc_final: 0.8926 (t0) REVERT: D 69 ILE cc_start: 0.9572 (mm) cc_final: 0.9181 (tp) REVERT: E 54 TYR cc_start: 0.8608 (m-80) cc_final: 0.8284 (m-10) REVERT: E 56 LYS cc_start: 0.9332 (ttmt) cc_final: 0.9062 (tptp) REVERT: E 105 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8395 (tm-30) REVERT: E 119 ILE cc_start: 0.9301 (pt) cc_final: 0.8832 (pt) REVERT: E 120 MET cc_start: 0.8007 (mpp) cc_final: 0.7775 (mpp) REVERT: E 130 ILE cc_start: 0.9622 (mt) cc_final: 0.8900 (mt) REVERT: F 81 VAL cc_start: 0.8739 (t) cc_final: 0.8360 (t) REVERT: F 85 ASP cc_start: 0.8736 (m-30) cc_final: 0.8515 (m-30) REVERT: F 98 TYR cc_start: 0.8349 (m-80) cc_final: 0.8102 (m-80) REVERT: G 51 LEU cc_start: 0.9808 (tp) cc_final: 0.9490 (tp) REVERT: G 55 LEU cc_start: 0.9834 (mt) cc_final: 0.9582 (mt) REVERT: G 112 GLN cc_start: 0.7295 (mm-40) cc_final: 0.6807 (tm-30) REVERT: G 114 VAL cc_start: 0.8563 (t) cc_final: 0.8290 (t) REVERT: G 115 LEU cc_start: 0.8342 (mt) cc_final: 0.7916 (mt) REVERT: H 61 ILE cc_start: 0.9721 (mt) cc_final: 0.9448 (mt) REVERT: H 62 MET cc_start: 0.9407 (mmm) cc_final: 0.9200 (tpp) REVERT: K 158 MET cc_start: -0.1887 (mmm) cc_final: -0.2224 (mmm) REVERT: K 210 MET cc_start: 0.6574 (tmm) cc_final: 0.6103 (ppp) REVERT: K 326 MET cc_start: 0.4748 (tpt) cc_final: 0.4403 (tpt) REVERT: L 34 ASN cc_start: 0.5963 (OUTLIER) cc_final: 0.5316 (p0) REVERT: L 125 MET cc_start: 0.4759 (pmm) cc_final: 0.4278 (ptm) REVERT: M 30 GLN cc_start: 0.5186 (mp10) cc_final: 0.4417 (tm-30) REVERT: M 210 MET cc_start: 0.1948 (ppp) cc_final: 0.1403 (ptm) REVERT: M 211 MET cc_start: -0.1497 (ttm) cc_final: -0.1885 (ttt) REVERT: P 326 MET cc_start: 0.7459 (mmp) cc_final: 0.6998 (mmp) REVERT: R 210 MET cc_start: -0.2283 (tmm) cc_final: -0.2775 (tmm) REVERT: R 235 ARG cc_start: 0.1653 (mmt180) cc_final: -0.0944 (ptt180) REVERT: S 34 ASN cc_start: 0.6168 (p0) cc_final: 0.5959 (p0) REVERT: S 243 MET cc_start: 0.6235 (mmt) cc_final: 0.5631 (ppp) REVERT: S 326 MET cc_start: 0.5243 (mpp) cc_final: 0.5002 (mpp) outliers start: 5 outliers final: 1 residues processed: 209 average time/residue: 0.2216 time to fit residues: 75.6619 Evaluate side-chains 148 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 146 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 342 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 212 optimal weight: 50.0000 chunk 9 optimal weight: 7.9990 chunk 311 optimal weight: 7.9990 chunk 295 optimal weight: 8.9990 chunk 116 optimal weight: 7.9990 chunk 132 optimal weight: 30.0000 chunk 29 optimal weight: 2.9990 chunk 310 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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** A 108 ASN E 108 ASN K 244 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.061574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.042111 restraints weight = 407868.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.043517 restraints weight = 205648.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.044383 restraints weight = 129590.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.044921 restraints weight = 94227.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.045257 restraints weight = 76105.764| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 34066 Z= 0.188 Angle : 0.592 7.708 47270 Z= 0.334 Chirality : 0.040 0.271 5415 Planarity : 0.004 0.055 5012 Dihedral : 25.108 100.018 7175 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 0.04 % Allowed : 1.80 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.14), residues: 3380 helix: 1.03 (0.12), residues: 1748 sheet: 0.49 (0.23), residues: 482 loop : -0.15 (0.18), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 42 TYR 0.028 0.002 TYR H 40 PHE 0.022 0.002 PHE E 104 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00394 (34066) covalent geometry : angle 0.59200 (47270) hydrogen bonds : bond 0.05053 ( 1711) hydrogen bonds : angle 4.41236 ( 4679) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 1.106 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: A 120 MET cc_start: 0.8211 (mmm) cc_final: 0.7724 (mmm) REVERT: A 125 GLN cc_start: 0.9131 (mp10) cc_final: 0.8828 (mm-40) REVERT: B 68 ASP cc_start: 0.9356 (m-30) cc_final: 0.9032 (m-30) REVERT: C 101 THR cc_start: 0.9273 (m) cc_final: 0.8987 (p) REVERT: D 62 MET cc_start: 0.9519 (mmm) cc_final: 0.9131 (mmm) REVERT: E 54 TYR cc_start: 0.8760 (m-80) cc_final: 0.8335 (m-10) REVERT: E 56 LYS cc_start: 0.9389 (ttmt) cc_final: 0.9027 (tptp) REVERT: E 105 GLU cc_start: 0.9144 (tm-30) cc_final: 0.8767 (tm-30) REVERT: E 110 CYS cc_start: 0.9565 (m) cc_final: 0.9222 (p) REVERT: E 119 ILE cc_start: 0.9386 (pt) cc_final: 0.8973 (mm) REVERT: E 120 MET cc_start: 0.8307 (mpp) cc_final: 0.7729 (mpp) REVERT: F 81 VAL cc_start: 0.8833 (t) cc_final: 0.8550 (t) REVERT: F 84 MET cc_start: 0.8739 (mmt) cc_final: 0.8439 (mmt) REVERT: F 85 ASP cc_start: 0.8948 (m-30) cc_final: 0.8740 (m-30) REVERT: G 114 VAL cc_start: 0.8506 (t) cc_final: 0.8253 (t) REVERT: H 61 ILE cc_start: 0.9776 (mt) cc_final: 0.9500 (mt) REVERT: H 64 SER cc_start: 0.9499 (m) cc_final: 0.9264 (p) REVERT: K 211 MET cc_start: -0.0580 (ttp) cc_final: -0.0864 (ttm) REVERT: K 326 MET cc_start: 0.5076 (tpt) cc_final: 0.4710 (tpp) REVERT: L 158 MET cc_start: 0.4419 (mmp) cc_final: 0.3696 (mmt) REVERT: M 30 GLN cc_start: 0.5789 (mp10) cc_final: 0.5291 (tm-30) REVERT: M 158 MET cc_start: 0.5992 (mmp) cc_final: 0.5639 (tpp) REVERT: M 210 MET cc_start: 0.3472 (ppp) cc_final: 0.2546 (ptm) REVERT: M 211 MET cc_start: 0.1331 (ttm) cc_final: 0.0418 (ttt) REVERT: P 210 MET cc_start: -0.0092 (ppp) cc_final: -0.0506 (ppp) REVERT: R 211 MET cc_start: 0.0946 (ttm) cc_final: 0.0086 (ptp) REVERT: S 243 MET cc_start: 0.6233 (mmt) cc_final: 0.5877 (ppp) outliers start: 1 outliers final: 0 residues processed: 178 average time/residue: 0.2176 time to fit residues: 64.1148 Evaluate side-chains 131 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 106 optimal weight: 9.9990 chunk 162 optimal weight: 40.0000 chunk 276 optimal weight: 0.9980 chunk 119 optimal weight: 40.0000 chunk 92 optimal weight: 8.9990 chunk 137 optimal weight: 50.0000 chunk 166 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 217 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 overall best weight: 6.7988 ------------------------------------------------------------------------------- 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** A 108 ASN B 93 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 206 GLN ** 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 202 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** ** P 202 GLN ** 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 ** S 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.058352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.043206 restraints weight = 377009.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.041328 restraints weight = 359083.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.041687 restraints weight = 236845.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.041434 restraints weight = 212631.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.041543 restraints weight = 202071.248| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.6267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 34066 Z= 0.246 Angle : 0.661 11.546 47270 Z= 0.369 Chirality : 0.042 0.221 5415 Planarity : 0.005 0.057 5012 Dihedral : 25.486 104.880 7175 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.04 % Allowed : 1.98 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.14), residues: 3380 helix: 0.75 (0.12), residues: 1749 sheet: 0.41 (0.22), residues: 490 loop : -0.26 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG B 92 TYR 0.026 0.002 TYR H 40 PHE 0.023 0.002 PHE E 104 HIS 0.012 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00523 (34066) covalent geometry : angle 0.66123 (47270) hydrogen bonds : bond 0.06786 ( 1711) hydrogen bonds : angle 4.55477 ( 4679) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9558 (mmm) cc_final: 0.9334 (mmp) REVERT: A 120 MET cc_start: 0.8262 (mmm) cc_final: 0.7798 (mmm) REVERT: B 68 ASP cc_start: 0.8955 (m-30) cc_final: 0.8731 (t70) REVERT: D 62 MET cc_start: 0.9355 (mmm) cc_final: 0.9001 (mmm) REVERT: E 54 TYR cc_start: 0.8597 (m-80) cc_final: 0.8159 (m-10) REVERT: H 100 LEU cc_start: 0.9481 (mt) cc_final: 0.9267 (mt) REVERT: K 210 MET cc_start: 0.7317 (ppp) cc_final: 0.7062 (ppp) REVERT: K 211 MET cc_start: -0.0097 (ttp) cc_final: -0.0513 (ttm) REVERT: K 326 MET cc_start: 0.5949 (tpt) cc_final: 0.5488 (tpp) REVERT: M 158 MET cc_start: 0.6958 (mmp) cc_final: 0.6395 (mmm) REVERT: M 210 MET cc_start: 0.2729 (ppp) cc_final: 0.1943 (ptm) REVERT: M 211 MET cc_start: -0.0429 (ttm) cc_final: -0.0786 (ttt) REVERT: N 210 MET cc_start: 0.1308 (ppp) cc_final: 0.1093 (ppp) REVERT: O 210 MET cc_start: 0.3665 (ppp) cc_final: 0.3277 (ppp) REVERT: P 326 MET cc_start: 0.7010 (mmp) cc_final: 0.6808 (mmp) REVERT: S 158 MET cc_start: 0.2759 (mmp) cc_final: 0.2466 (mmm) REVERT: S 243 MET cc_start: 0.6294 (mmt) cc_final: 0.5677 (tmm) outliers start: 1 outliers final: 0 residues processed: 153 average time/residue: 0.1982 time to fit residues: 51.1435 Evaluate side-chains 116 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 204 optimal weight: 10.0000 chunk 178 optimal weight: 5.9990 chunk 184 optimal weight: 20.0000 chunk 237 optimal weight: 10.0000 chunk 230 optimal weight: 40.0000 chunk 331 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 355 optimal weight: 40.0000 chunk 31 optimal weight: 5.9990 chunk 353 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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** A 108 ASN A 125 GLN B 25 ASN 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 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 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 244 HIS ** 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** Q 267 ASN ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 101 GLN ** S 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.058004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.043975 restraints weight = 378695.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.043546 restraints weight = 334244.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.043532 restraints weight = 213749.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.043552 restraints weight = 196855.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.043085 restraints weight = 187977.569| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.6932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 34066 Z= 0.216 Angle : 0.614 9.475 47270 Z= 0.344 Chirality : 0.040 0.164 5415 Planarity : 0.005 0.064 5012 Dihedral : 25.482 107.014 7175 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.04 % Allowed : 1.84 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.14), residues: 3380 helix: 0.81 (0.12), residues: 1757 sheet: 0.26 (0.23), residues: 468 loop : -0.37 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 79 TYR 0.031 0.002 TYR H 40 PHE 0.018 0.002 PHE E 104 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00461 (34066) covalent geometry : angle 0.61363 (47270) hydrogen bonds : bond 0.05427 ( 1711) hydrogen bonds : angle 4.37377 ( 4679) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 68 ASP cc_start: 0.9104 (m-30) cc_final: 0.8720 (t70) REVERT: D 62 MET cc_start: 0.9192 (mmm) cc_final: 0.8874 (mmm) REVERT: E 119 ILE cc_start: 0.8979 (pt) cc_final: 0.8684 (pt) REVERT: F 84 MET cc_start: 0.9255 (mmm) cc_final: 0.8481 (mmt) REVERT: G 56 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8463 (mm-30) REVERT: G 111 ILE cc_start: 0.9267 (mp) cc_final: 0.8897 (mm) REVERT: K 211 MET cc_start: -0.0138 (ttp) cc_final: -0.0599 (ttm) REVERT: K 326 MET cc_start: 0.6145 (tpt) cc_final: 0.5757 (tpp) REVERT: M 158 MET cc_start: 0.6548 (mmp) cc_final: 0.5974 (mmm) REVERT: M 210 MET cc_start: 0.2835 (ppp) cc_final: 0.2190 (ptm) REVERT: M 211 MET cc_start: -0.0050 (ttm) cc_final: -0.0298 (ttt) REVERT: O 125 MET cc_start: 0.6682 (ptp) cc_final: 0.6468 (ptp) REVERT: P 210 MET cc_start: -0.0493 (ppp) cc_final: -0.0739 (ppp) REVERT: P 326 MET cc_start: 0.6622 (mmp) cc_final: 0.6202 (mmp) REVERT: S 34 ASN cc_start: 0.5012 (p0) cc_final: 0.4723 (p0) REVERT: S 243 MET cc_start: 0.6264 (mmt) cc_final: 0.5445 (tmm) outliers start: 1 outliers final: 0 residues processed: 144 average time/residue: 0.1759 time to fit residues: 43.8395 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 : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 150 optimal weight: 2.9990 chunk 109 optimal weight: 9.9990 chunk 296 optimal weight: 0.9990 chunk 337 optimal weight: 7.9990 chunk 350 optimal weight: 30.0000 chunk 126 optimal weight: 20.0000 chunk 216 optimal weight: 50.0000 chunk 252 optimal weight: 40.0000 chunk 65 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 318 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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** A 108 ASN D 109 HIS 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** K 206 GLN ** 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** N 244 HIS ** 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** ** P 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.057803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.043684 restraints weight = 377523.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.043152 restraints weight = 318460.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.043205 restraints weight = 204615.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.043637 restraints weight = 183936.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.043060 restraints weight = 172211.962| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.7369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 34066 Z= 0.203 Angle : 0.601 9.370 47270 Z= 0.335 Chirality : 0.040 0.197 5415 Planarity : 0.004 0.071 5012 Dihedral : 25.381 106.532 7175 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.04 % Allowed : 1.04 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.14), residues: 3380 helix: 0.91 (0.12), residues: 1749 sheet: 0.42 (0.26), residues: 388 loop : -0.59 (0.17), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 79 TYR 0.035 0.002 TYR H 40 PHE 0.021 0.002 PHE K 248 HIS 0.013 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00437 (34066) covalent geometry : angle 0.60143 (47270) hydrogen bonds : bond 0.05541 ( 1711) hydrogen bonds : angle 4.29514 ( 4679) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9109 (tp30) cc_final: 0.8791 (tp30) REVERT: A 120 MET cc_start: 0.8080 (mmm) cc_final: 0.7767 (mmm) REVERT: B 68 ASP cc_start: 0.8965 (m-30) cc_final: 0.7978 (t70) REVERT: D 62 MET cc_start: 0.9207 (mmm) cc_final: 0.8867 (mmm) REVERT: E 119 ILE cc_start: 0.8951 (pt) cc_final: 0.8750 (pt) REVERT: F 81 VAL cc_start: 0.8699 (t) cc_final: 0.8498 (t) REVERT: F 84 MET cc_start: 0.9107 (mmm) cc_final: 0.8223 (mmt) REVERT: H 71 GLU cc_start: 0.9145 (mp0) cc_final: 0.8939 (mp0) REVERT: K 210 MET cc_start: 0.7301 (ppp) cc_final: 0.7033 (ppp) REVERT: K 211 MET cc_start: -0.0038 (ttp) cc_final: -0.0479 (ttm) REVERT: K 326 MET cc_start: 0.6242 (tpt) cc_final: 0.5845 (tpp) REVERT: L 158 MET cc_start: 0.5749 (mmp) cc_final: 0.4877 (mmt) REVERT: M 158 MET cc_start: 0.6914 (mmp) cc_final: 0.6309 (mmm) REVERT: M 210 MET cc_start: 0.2700 (ppp) cc_final: 0.2067 (ptm) REVERT: M 211 MET cc_start: -0.0178 (ttm) cc_final: -0.0519 (ttm) REVERT: O 326 MET cc_start: 0.6347 (tpt) cc_final: 0.5991 (tpp) REVERT: P 210 MET cc_start: 0.0114 (ppp) cc_final: -0.0090 (ppp) REVERT: P 326 MET cc_start: 0.6742 (mmp) cc_final: 0.6380 (mmp) REVERT: R 211 MET cc_start: 0.0131 (ttp) cc_final: -0.0692 (ptm) REVERT: S 34 ASN cc_start: 0.5097 (p0) cc_final: 0.4860 (p0) REVERT: S 243 MET cc_start: 0.6268 (mmt) cc_final: 0.5486 (tmm) outliers start: 1 outliers final: 0 residues processed: 145 average time/residue: 0.1796 time to fit residues: 45.3001 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 : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 136 optimal weight: 0.1980 chunk 12 optimal weight: 5.9990 chunk 294 optimal weight: 0.9990 chunk 307 optimal weight: 20.0000 chunk 59 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 192 optimal weight: 50.0000 chunk 237 optimal weight: 3.9990 chunk 141 optimal weight: 20.0000 chunk 56 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- 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** A 108 ASN 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 62 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** ** O 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 202 GLN ** 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** ** S 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 145 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 = 0.3787 r_free = 0.3787 target = 0.058306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.042942 restraints weight = 378046.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.042535 restraints weight = 309749.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.042584 restraints weight = 223385.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.042469 restraints weight = 213176.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.042516 restraints weight = 185306.588| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.7588 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= 0.161 Angle : 0.562 8.497 47270 Z= 0.314 Chirality : 0.039 0.151 5415 Planarity : 0.004 0.062 5012 Dihedral : 25.154 109.571 7175 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.04 % Allowed : 0.94 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.14), residues: 3380 helix: 1.09 (0.12), residues: 1759 sheet: 0.42 (0.27), residues: 388 loop : -0.53 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 92 TYR 0.038 0.002 TYR H 83 PHE 0.024 0.002 PHE K 248 HIS 0.009 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00341 (34066) covalent geometry : angle 0.56153 (47270) hydrogen bonds : bond 0.04448 ( 1711) hydrogen bonds : angle 4.05793 ( 4679) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8089 (mmm) cc_final: 0.7752 (mmm) REVERT: B 68 ASP cc_start: 0.9040 (m-30) cc_final: 0.8647 (t70) REVERT: D 62 MET cc_start: 0.9260 (mmm) cc_final: 0.8928 (mmm) REVERT: E 119 ILE cc_start: 0.8949 (pt) cc_final: 0.8744 (pt) REVERT: F 84 MET cc_start: 0.8470 (mmm) cc_final: 0.7626 (mmt) REVERT: G 56 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8239 (mm-30) REVERT: K 210 MET cc_start: 0.7399 (ppp) cc_final: 0.7107 (ppp) REVERT: K 211 MET cc_start: -0.0120 (ttp) cc_final: -0.0513 (ttm) REVERT: K 326 MET cc_start: 0.6306 (tpt) cc_final: 0.5893 (tpp) REVERT: M 158 MET cc_start: 0.7096 (mmp) cc_final: 0.6348 (mmm) REVERT: M 210 MET cc_start: 0.2583 (ppp) cc_final: 0.1988 (ptm) REVERT: M 243 MET cc_start: 0.0930 (ptt) cc_final: 0.0641 (ppp) REVERT: O 125 MET cc_start: 0.6778 (ptp) cc_final: 0.6566 (ptp) REVERT: O 158 MET cc_start: -0.2115 (mmm) cc_final: -0.2354 (mmm) REVERT: P 210 MET cc_start: 0.0910 (ppp) cc_final: 0.0668 (ppp) REVERT: P 326 MET cc_start: 0.6900 (mmp) cc_final: 0.6521 (mmp) REVERT: R 211 MET cc_start: 0.0326 (ttp) cc_final: -0.0479 (ptm) REVERT: S 34 ASN cc_start: 0.5333 (p0) cc_final: 0.5103 (p0) REVERT: S 243 MET cc_start: 0.6473 (mmt) cc_final: 0.5657 (tmm) outliers start: 1 outliers final: 0 residues processed: 139 average time/residue: 0.1869 time to fit residues: 46.0044 Evaluate side-chains 112 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 262 optimal weight: 30.0000 chunk 87 optimal weight: 10.0000 chunk 8 optimal weight: 0.0370 chunk 231 optimal weight: 20.0000 chunk 116 optimal weight: 3.9990 chunk 145 optimal weight: 20.0000 chunk 321 optimal weight: 9.9990 chunk 135 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 286 optimal weight: 50.0000 chunk 20 optimal weight: 1.9990 overall best weight: 3.6066 ------------------------------------------------------------------------------- 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** A 108 ASN 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** ** M 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 188 ASN ** 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** ** S 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 145 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 = 0.3788 r_free = 0.3788 target = 0.058227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.043033 restraints weight = 376094.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.042325 restraints weight = 296953.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.042372 restraints weight = 234925.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.042285 restraints weight = 207522.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.042331 restraints weight = 185805.902| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.7842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34066 Z= 0.156 Angle : 0.556 8.702 47270 Z= 0.310 Chirality : 0.038 0.220 5415 Planarity : 0.004 0.060 5012 Dihedral : 25.020 109.180 7175 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.04 % Allowed : 1.01 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.14), residues: 3380 helix: 1.26 (0.12), residues: 1748 sheet: 0.13 (0.24), residues: 478 loop : -0.27 (0.18), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 92 TYR 0.029 0.002 TYR H 83 PHE 0.022 0.002 PHE K 248 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00333 (34066) covalent geometry : angle 0.55631 (47270) hydrogen bonds : bond 0.04434 ( 1711) hydrogen bonds : angle 3.97604 ( 4679) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8126 (mmm) cc_final: 0.7760 (mmm) REVERT: E 120 MET cc_start: 0.8371 (mpp) cc_final: 0.8002 (mpp) REVERT: F 84 MET cc_start: 0.8747 (mmm) cc_final: 0.7886 (mmt) REVERT: G 56 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8193 (mm-30) REVERT: H 59 MET cc_start: 0.8924 (tpt) cc_final: 0.8442 (tpp) REVERT: K 210 MET cc_start: 0.7532 (ppp) cc_final: 0.7266 (ppp) REVERT: K 211 MET cc_start: -0.0194 (ttp) cc_final: -0.0545 (ttm) REVERT: K 326 MET cc_start: 0.6306 (tpt) cc_final: 0.5883 (tpp) REVERT: L 158 MET cc_start: 0.5932 (mmp) cc_final: 0.5235 (mmm) REVERT: M 158 MET cc_start: 0.7070 (mmp) cc_final: 0.6312 (mmm) REVERT: M 210 MET cc_start: 0.2780 (ppp) cc_final: 0.2248 (ptm) REVERT: M 243 MET cc_start: 0.0962 (ptt) cc_final: 0.0635 (ppp) REVERT: O 326 MET cc_start: 0.6595 (tpt) cc_final: 0.6261 (tpp) REVERT: P 326 MET cc_start: 0.6972 (mmp) cc_final: 0.6606 (mmp) REVERT: R 125 MET cc_start: 0.7584 (pmm) cc_final: 0.7378 (pmm) REVERT: R 211 MET cc_start: 0.0386 (ttp) cc_final: -0.0379 (ptm) REVERT: S 34 ASN cc_start: 0.5403 (p0) cc_final: 0.5203 (p0) REVERT: S 243 MET cc_start: 0.6469 (mmt) cc_final: 0.5675 (tmm) outliers start: 1 outliers final: 1 residues processed: 139 average time/residue: 0.1873 time to fit residues: 46.1359 Evaluate side-chains 115 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 236 optimal weight: 9.9990 chunk 316 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 309 optimal weight: 6.9990 chunk 211 optimal weight: 6.9990 chunk 229 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 297 optimal weight: 20.0000 chunk 142 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN 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 62 ASN ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 330 ASN ** M 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 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 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 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.057128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.042645 restraints weight = 382742.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.041865 restraints weight = 269828.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.041941 restraints weight = 213325.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.041836 restraints weight = 188002.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.041909 restraints weight = 172589.013| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.8287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 34066 Z= 0.219 Angle : 0.627 9.133 47270 Z= 0.346 Chirality : 0.041 0.220 5415 Planarity : 0.004 0.063 5012 Dihedral : 25.284 113.883 7175 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.14), residues: 3380 helix: 1.01 (0.12), residues: 1751 sheet: 0.29 (0.27), residues: 390 loop : -0.55 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 92 TYR 0.054 0.002 TYR E 54 PHE 0.036 0.002 PHE E 104 HIS 0.011 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00473 (34066) covalent geometry : angle 0.62682 (47270) hydrogen bonds : bond 0.06006 ( 1711) hydrogen bonds : angle 4.27703 ( 4679) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8198 (mmm) cc_final: 0.7887 (mmm) REVERT: E 73 GLU cc_start: 0.8943 (pp20) cc_final: 0.8661 (mt-10) REVERT: F 84 MET cc_start: 0.8833 (mmm) cc_final: 0.8022 (mmt) REVERT: G 56 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8285 (mm-30) REVERT: H 59 MET cc_start: 0.8983 (tpt) cc_final: 0.8570 (tpp) REVERT: H 62 MET cc_start: 0.9268 (mmp) cc_final: 0.9026 (mmp) REVERT: K 210 MET cc_start: 0.7607 (ppp) cc_final: 0.7307 (ppp) REVERT: K 211 MET cc_start: 0.0196 (ttp) cc_final: -0.0273 (ttm) REVERT: K 326 MET cc_start: 0.6553 (tpt) cc_final: 0.6037 (tpp) REVERT: M 210 MET cc_start: 0.3917 (ppp) cc_final: 0.3278 (ptt) REVERT: O 158 MET cc_start: -0.2110 (mmm) cc_final: -0.2320 (mmm) REVERT: O 326 MET cc_start: 0.6375 (tpt) cc_final: 0.5852 (tpp) REVERT: P 326 MET cc_start: 0.6992 (mmp) cc_final: 0.6589 (mmp) REVERT: R 125 MET cc_start: 0.7518 (pmm) cc_final: 0.7283 (pmm) REVERT: S 243 MET cc_start: 0.6467 (mmt) cc_final: 0.5615 (tmm) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1859 time to fit residues: 42.3513 Evaluate side-chains 109 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 18 optimal weight: 2.9990 chunk 353 optimal weight: 9.9990 chunk 303 optimal weight: 20.0000 chunk 173 optimal weight: 0.8980 chunk 326 optimal weight: 7.9990 chunk 206 optimal weight: 6.9990 chunk 351 optimal weight: 2.9990 chunk 254 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 133 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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** ** C 84 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 62 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 P 145 GLN P 188 ASN ** Q 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 294 HIS R 138 HIS ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 145 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.058499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.043249 restraints weight = 378217.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.042183 restraints weight = 320671.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.042571 restraints weight = 237623.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.042301 restraints weight = 221823.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.042364 restraints weight = 197082.322| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.8357 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= 0.138 Angle : 0.565 10.947 47270 Z= 0.312 Chirality : 0.039 0.302 5415 Planarity : 0.004 0.061 5012 Dihedral : 24.962 112.269 7175 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.15), residues: 3380 helix: 1.24 (0.12), residues: 1760 sheet: 0.31 (0.27), residues: 390 loop : -0.49 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 92 TYR 0.028 0.001 TYR H 83 PHE 0.019 0.002 PHE E 104 HIS 0.006 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00293 (34066) covalent geometry : angle 0.56522 (47270) hydrogen bonds : bond 0.03898 ( 1711) hydrogen bonds : angle 3.91921 ( 4679) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8177 (mmm) cc_final: 0.7841 (mmm) REVERT: B 68 ASP cc_start: 0.9090 (m-30) cc_final: 0.8613 (t70) REVERT: F 84 MET cc_start: 0.8423 (mmm) cc_final: 0.7800 (mmt) REVERT: G 56 GLU cc_start: 0.8984 (mt-10) cc_final: 0.8158 (mm-30) REVERT: H 59 MET cc_start: 0.9150 (tpt) cc_final: 0.8606 (tpp) REVERT: H 61 ILE cc_start: 0.9529 (mt) cc_final: 0.9320 (mt) REVERT: K 210 MET cc_start: 0.7758 (ppp) cc_final: 0.7496 (ppp) REVERT: K 211 MET cc_start: -0.0053 (ttp) cc_final: -0.0364 (ttm) REVERT: K 326 MET cc_start: 0.6440 (tpt) cc_final: 0.5933 (tpp) REVERT: M 158 MET cc_start: 0.7423 (mmp) cc_final: 0.6981 (mmm) REVERT: M 210 MET cc_start: 0.4054 (ppp) cc_final: 0.3458 (ptt) REVERT: O 326 MET cc_start: 0.6548 (tpt) cc_final: 0.6150 (tpp) REVERT: P 326 MET cc_start: 0.6867 (mmp) cc_final: 0.6500 (mmp) REVERT: R 125 MET cc_start: 0.7508 (pmm) cc_final: 0.7296 (pmm) REVERT: R 211 MET cc_start: -0.0618 (ttt) cc_final: -0.1807 (ptp) REVERT: S 243 MET cc_start: 0.6431 (mmt) cc_final: 0.5699 (tmm) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1863 time to fit residues: 46.1912 Evaluate side-chains 111 residues out of total 2777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 151 optimal weight: 20.0000 chunk 37 optimal weight: 8.9990 chunk 244 optimal weight: 30.0000 chunk 192 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 123 optimal weight: 50.0000 chunk 296 optimal weight: 0.9990 chunk 118 optimal weight: 30.0000 chunk 138 optimal weight: 9.9990 overall best weight: 6.1992 ------------------------------------------------------------------------------- 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 108 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 62 ASN ** 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 114 GLN ** P 34 ASN ** 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 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 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.057076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.042152 restraints weight = 381894.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.041209 restraints weight = 299145.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.041174 restraints weight = 234475.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.041231 restraints weight = 203744.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.041236 restraints weight = 194964.014| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.8674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 34066 Z= 0.212 Angle : 0.615 11.088 47270 Z= 0.339 Chirality : 0.040 0.301 5415 Planarity : 0.004 0.063 5012 Dihedral : 25.201 115.265 7175 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.14), residues: 3380 helix: 1.05 (0.12), residues: 1769 sheet: 0.49 (0.27), residues: 372 loop : -0.60 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 92 TYR 0.029 0.002 TYR H 83 PHE 0.018 0.002 PHE K 248 HIS 0.010 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00457 (34066) covalent geometry : angle 0.61476 (47270) hydrogen bonds : bond 0.05430 ( 1711) hydrogen bonds : angle 4.19361 ( 4679) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5388.82 seconds wall clock time: 94 minutes 36.57 seconds (5676.57 seconds total)