Starting phenix.real_space_refine on Sat Aug 8 20:06:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jnd_36442/08_2026/8jnd_36442.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jnd_36442/08_2026/8jnd_36442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jnd_36442/08_2026/8jnd_36442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jnd_36442/08_2026/8jnd_36442.map" model { file = "/net/cci-nas-00/data/ceres_data/8jnd_36442/08_2026/8jnd_36442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jnd_36442/08_2026/8jnd_36442.cif" } resolution = 3.66 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 119 5.16 5 C 18079 2.51 5 N 5506 2.21 5 O 6391 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 243 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30404 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 819 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 805 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 714 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 3189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3189 Classifications: {'DNA': 156} Link IDs: {'rna3p': 155} Chain: "J" Number of atoms: 3143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3143 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Chain: "K" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2163 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Chain: "L" Number of atoms: 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: "M" 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: "N" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2163 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Chain: "O" Number of atoms: 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: 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: "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 Time building chain proxies: 6.65, per 1000 atoms: 0.22 Number of scatterers: 30404 At special positions: 0 Unit cell: (180.2, 153.7, 138.86, 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 119 16.00 P 309 15.00 O 6391 8.00 N 5506 7.00 C 18079 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: 2.87 Conformation dependent library (CDL) restraints added in 1.1 seconds 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5702 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 19 sheets defined 57.7% alpha, 14.1% beta 156 base pairs and 269 stacking pairs defined. Time for finding SS restraints: 4.33 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.698A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.595A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.579A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.739A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.486A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 123 Processing helix chain 'K' and resid 25 through 31 removed outlier: 3.775A pdb=" N GLU K 29 " --> pdb=" O ILE K 25 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN K 30 " --> pdb=" O SER K 26 " (cutoff:3.500A) removed outlier: 3.604A 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 63 removed outlier: 4.313A pdb=" N LEU K 60 " --> pdb=" O PRO K 56 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE K 63 " --> pdb=" O GLU K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 82 removed outlier: 3.584A pdb=" N LYS K 80 " --> pdb=" O ALA K 76 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU K 81 " --> pdb=" O GLU K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 113 Processing helix chain 'K' and resid 132 through 144 removed outlier: 3.739A 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: 3.909A pdb=" N LEU K 204 " --> pdb=" O GLN K 200 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR K 205 " --> pdb=" O THR K 201 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN K 206 " --> pdb=" O GLN K 202 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA K 209 " --> pdb=" O TYR K 205 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL K 212 " --> pdb=" O SER K 208 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU K 213 " --> pdb=" O ALA K 209 " (cutoff:3.500A) removed outlier: 3.655A 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 removed outlier: 3.519A pdb=" N ARG K 241 " --> pdb=" O GLU K 237 " (cutoff:3.500A) Processing helix chain 'K' and resid 290 through 296 removed outlier: 4.329A pdb=" N HIS K 294 " --> pdb=" O ASN K 290 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA K 295 " --> pdb=" O ILE K 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 113 Processing helix chain 'L' and resid 132 through 144 removed outlier: 3.644A pdb=" N VAL L 142 " --> pdb=" O HIS L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 146 No H-bonds generated for 'chain 'L' and resid 145 through 146' Processing helix chain 'L' and resid 147 through 151 Processing helix chain 'L' and resid 167 through 178 Processing helix chain 'L' and resid 181 through 188 Processing helix chain 'L' and resid 196 through 214 removed outlier: 4.023A pdb=" N LEU L 204 " --> pdb=" O GLN L 200 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR L 205 " --> pdb=" O THR L 201 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN L 206 " --> pdb=" O GLN L 202 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA L 209 " --> pdb=" O TYR L 205 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL L 212 " --> pdb=" O SER L 208 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU L 213 " --> pdb=" O ALA L 209 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER L 214 " --> pdb=" O MET L 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 231 removed outlier: 3.523A pdb=" N ARG L 229 " --> pdb=" O THR L 225 " (cutoff:3.500A) Processing helix chain 'L' and resid 237 through 260 Processing helix chain 'L' and resid 290 through 295 removed outlier: 4.074A pdb=" N HIS L 294 " --> pdb=" O ASN L 290 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA L 295 " --> pdb=" O ILE L 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 290 through 295' Processing helix chain 'M' and resid 106 through 113 Processing helix chain 'M' and resid 132 through 144 removed outlier: 3.629A pdb=" N VAL M 142 " --> pdb=" O HIS M 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 146 No H-bonds generated for 'chain 'M' and resid 145 through 146' Processing helix chain 'M' and resid 147 through 151 Processing helix chain 'M' and resid 167 through 178 Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'M' and resid 196 through 214 removed outlier: 4.018A pdb=" N LEU M 204 " --> pdb=" O GLN M 200 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TYR M 205 " --> pdb=" O THR M 201 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN M 206 " --> pdb=" O GLN M 202 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA M 209 " --> pdb=" O TYR M 205 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL M 212 " --> pdb=" O SER M 208 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU M 213 " --> pdb=" O ALA M 209 " (cutoff:3.500A) removed outlier: 3.703A 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: 4.330A pdb=" N HIS M 294 " --> pdb=" O ASN M 290 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA M 295 " --> pdb=" O ILE M 291 " (cutoff:3.500A) Processing helix chain 'N' and resid 25 through 31 removed outlier: 3.766A pdb=" N GLU N 29 " --> pdb=" O ILE N 25 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN N 30 " --> pdb=" O SER N 26 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS N 31 " --> pdb=" O ARG N 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 25 through 31' Processing helix chain 'N' and resid 34 through 45 Processing helix chain 'N' and resid 48 through 54 Processing helix chain 'N' and resid 56 through 63 removed outlier: 4.259A pdb=" N LEU N 60 " --> pdb=" O PRO N 56 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE N 63 " --> pdb=" O GLU N 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 82 removed outlier: 3.545A pdb=" N LYS N 80 " --> pdb=" O ALA N 76 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU N 81 " --> pdb=" O GLU N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 113 Processing helix chain 'N' and resid 132 through 144 removed outlier: 3.642A 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 removed outlier: 3.538A pdb=" N LEU N 171 " --> pdb=" O ARG N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 181 through 188 Processing helix chain 'N' and resid 196 through 214 removed outlier: 4.032A pdb=" N LEU N 204 " --> pdb=" O GLN N 200 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR N 205 " --> pdb=" O THR N 201 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN N 206 " --> pdb=" O GLN N 202 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA N 209 " --> pdb=" O TYR N 205 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL N 212 " --> pdb=" O SER N 208 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU N 213 " --> pdb=" O ALA N 209 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER N 214 " --> pdb=" O MET N 210 " (cutoff:3.500A) Processing helix chain 'N' and resid 225 through 231 Processing helix chain 'N' and resid 237 through 260 Processing helix chain 'N' and resid 290 through 296 removed outlier: 4.207A pdb=" N HIS N 294 " --> pdb=" O ASN N 290 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA N 295 " --> pdb=" O ILE N 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 25 through 31 removed outlier: 3.765A pdb=" N GLU O 29 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN O 30 " --> pdb=" O SER O 26 " (cutoff:3.500A) removed outlier: 3.522A 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 63 removed outlier: 4.279A pdb=" N LEU O 60 " --> pdb=" O PRO O 56 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE O 63 " --> pdb=" O GLU O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 82 removed outlier: 3.619A pdb=" N LYS O 80 " --> pdb=" O ALA O 76 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU O 81 " --> pdb=" O GLU O 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 113 Processing helix chain 'O' and resid 132 through 144 removed outlier: 3.674A 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: 3.934A pdb=" N LEU O 204 " --> pdb=" O GLN O 200 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR O 205 " --> pdb=" O THR O 201 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN O 206 " --> pdb=" O GLN O 202 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA O 209 " --> pdb=" O TYR O 205 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL O 212 " --> pdb=" O SER O 208 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU O 213 " --> pdb=" O ALA O 209 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER O 214 " --> pdb=" O MET O 210 " (cutoff:3.500A) Processing helix chain 'O' and resid 225 through 231 removed outlier: 3.533A pdb=" N ARG O 229 " --> pdb=" O THR O 225 " (cutoff:3.500A) Processing helix chain 'O' and resid 237 through 260 Processing helix chain 'O' and resid 291 through 296 removed outlier: 3.880A pdb=" N ALA O 295 " --> pdb=" O ILE O 291 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 31 removed outlier: 3.850A pdb=" N GLU P 29 " --> pdb=" O ILE P 25 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN P 30 " --> pdb=" O SER P 26 " (cutoff:3.500A) removed outlier: 3.543A 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: 4.225A pdb=" N LEU P 60 " --> pdb=" O PRO P 56 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 82 removed outlier: 3.714A pdb=" N LYS P 80 " --> pdb=" O ALA P 76 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU P 81 " --> pdb=" O GLU P 77 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 113 Processing helix chain 'P' and resid 132 through 144 removed outlier: 3.738A 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: 3.951A pdb=" N LEU P 204 " --> pdb=" O GLN P 200 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR P 205 " --> pdb=" O THR P 201 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN P 206 " --> pdb=" O GLN P 202 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA P 209 " --> pdb=" O TYR P 205 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL P 212 " --> pdb=" O SER P 208 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU P 213 " --> pdb=" O ALA P 209 " (cutoff:3.500A) removed outlier: 3.669A 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 291 through 296 removed outlier: 4.114A pdb=" N ALA P 295 " --> pdb=" O ILE P 291 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 31 removed outlier: 3.778A pdb=" N GLU Q 29 " --> pdb=" O ILE Q 25 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN Q 30 " --> pdb=" O SER Q 26 " (cutoff:3.500A) removed outlier: 3.627A 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: 4.241A pdb=" N LEU Q 60 " --> pdb=" O PRO Q 56 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 82 removed outlier: 3.523A pdb=" N LYS Q 80 " --> pdb=" O ALA Q 76 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU Q 81 " --> pdb=" O GLU Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 113 Processing helix chain 'Q' and resid 132 through 144 removed outlier: 3.669A 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: 3.974A pdb=" N LEU Q 204 " --> pdb=" O GLN Q 200 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR Q 205 " --> pdb=" O THR Q 201 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN Q 206 " --> pdb=" O GLN Q 202 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA Q 209 " --> pdb=" O TYR Q 205 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL Q 212 " --> pdb=" O SER Q 208 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU Q 213 " --> pdb=" O ALA Q 209 " (cutoff:3.500A) removed outlier: 3.679A 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: 4.296A pdb=" N HIS Q 294 " --> pdb=" O ASN Q 290 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA Q 295 " --> pdb=" O ILE Q 291 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 113 Processing helix chain 'R' and resid 132 through 144 removed outlier: 3.686A 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: 3.955A pdb=" N LEU R 204 " --> pdb=" O GLN R 200 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR R 205 " --> pdb=" O THR R 201 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN R 206 " --> pdb=" O GLN R 202 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA R 209 " --> pdb=" O TYR R 205 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL R 212 " --> pdb=" O SER R 208 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU R 213 " --> pdb=" O ALA R 209 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER R 214 " --> pdb=" O MET R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 231 removed outlier: 3.513A pdb=" N ARG R 229 " --> pdb=" O THR R 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 260 Processing helix chain 'R' and resid 290 through 296 removed outlier: 4.233A pdb=" N HIS R 294 " --> pdb=" O ASN R 290 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA R 295 " --> pdb=" O ILE R 291 " (cutoff:3.500A) Processing helix chain 'S' and resid 25 through 31 removed outlier: 3.799A pdb=" N GLU S 29 " --> pdb=" O ILE S 25 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN S 30 " --> pdb=" O SER S 26 " (cutoff:3.500A) removed outlier: 3.642A 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 63 removed outlier: 4.164A pdb=" N LEU S 60 " --> pdb=" O PRO S 56 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE S 63 " --> pdb=" O GLU S 59 " (cutoff:3.500A) Processing helix chain 'S' and resid 67 through 82 removed outlier: 3.598A pdb=" N LYS S 80 " --> pdb=" O ALA S 76 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU S 81 " --> pdb=" O GLU S 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 113 Processing helix chain 'S' and resid 132 through 144 removed outlier: 3.687A pdb=" N VAL S 142 " --> pdb=" O HIS S 138 " (cutoff:3.500A) Processing helix chain 'S' and resid 145 through 146 No H-bonds generated for 'chain 'S' and resid 145 through 146' Processing helix chain 'S' and resid 147 through 151 Processing helix chain 'S' and resid 167 through 178 Processing helix chain 'S' and resid 181 through 188 Processing helix chain 'S' and resid 196 through 214 removed outlier: 4.015A pdb=" N LEU S 204 " --> pdb=" O GLN S 200 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR S 205 " --> pdb=" O THR S 201 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN S 206 " --> pdb=" O GLN S 202 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL S 212 " --> pdb=" O SER S 208 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU S 213 " --> pdb=" O ALA S 209 " (cutoff:3.500A) removed outlier: 3.599A 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: 4.365A pdb=" N HIS S 294 " --> pdb=" O ASN S 290 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA S 295 " --> pdb=" O ILE S 291 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.076A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.827A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.243A 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: 6.824A 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: 4.996A pdb=" N LYS K 156 " --> pdb=" O TYR K 216 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA K 217 " --> pdb=" O ALA K 262 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N VAL K 264 " --> pdb=" O ALA K 217 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEU K 219 " --> pdb=" O VAL K 264 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N THR K 266 " --> pdb=" O LEU K 219 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL K 221 " --> pdb=" O THR K 266 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N GLN K 268 " --> pdb=" O VAL K 221 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE K 265 " --> pdb=" O THR K 123 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET K 125 " --> pdb=" O ILE K 265 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN K 267 " --> pdb=" O MET K 125 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY K 127 " --> pdb=" O ASN K 267 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE K 122 " --> pdb=" O THR K 298 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N LEU K 300 " --> pdb=" O ILE K 122 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLU K 124 " --> pdb=" O LEU K 300 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU K 302 " --> pdb=" O GLU K 124 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N PHE K 126 " --> pdb=" O LEU K 302 " (cutoff:3.500A) removed outlier: 9.081A pdb=" N LYS K 304 " --> pdb=" O PHE K 126 " (cutoff:3.500A) removed outlier: 6.676A 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: 5.068A pdb=" N LYS L 156 " --> pdb=" O TYR L 216 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA L 217 " --> pdb=" O ALA L 262 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N VAL L 264 " --> pdb=" O ALA L 217 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU L 219 " --> pdb=" O VAL L 264 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N THR L 266 " --> pdb=" O LEU L 219 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL L 221 " --> pdb=" O THR L 266 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N GLN L 268 " --> pdb=" O VAL L 221 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE L 265 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N MET L 125 " --> pdb=" O ILE L 265 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN L 267 " --> pdb=" O MET L 125 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY L 127 " --> pdb=" O ASN L 267 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ILE L 122 " --> pdb=" O THR L 297 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ARG L 299 " --> pdb=" O ILE L 122 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU L 124 " --> pdb=" O ARG L 299 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N TYR L 301 " --> pdb=" O GLU L 124 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N PHE L 126 " --> pdb=" O TYR L 301 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ARG L 303 " --> pdb=" O PHE L 126 " (cutoff:3.500A) removed outlier: 6.659A 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: 5.020A pdb=" N LYS M 156 " --> pdb=" O TYR M 216 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU M 218 " --> pdb=" O LYS M 156 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA M 217 " --> pdb=" O ALA M 262 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N VAL M 264 " --> pdb=" O ALA M 217 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU M 219 " --> pdb=" O VAL M 264 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N THR M 266 " --> pdb=" O LEU M 219 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N VAL M 221 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N GLN M 268 " --> pdb=" O VAL M 221 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE M 265 " --> pdb=" O THR M 123 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET M 125 " --> pdb=" O ILE M 265 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN M 267 " --> pdb=" O MET M 125 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY M 127 " --> pdb=" O ASN M 267 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ILE M 122 " --> pdb=" O THR M 298 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N LEU M 300 " --> pdb=" O ILE M 122 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLU M 124 " --> pdb=" O LEU M 300 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N LEU M 302 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N PHE M 126 " --> pdb=" O LEU M 302 " (cutoff:3.500A) removed outlier: 8.983A pdb=" N LYS M 304 " --> pdb=" O PHE M 126 " (cutoff:3.500A) removed outlier: 6.560A 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: 4.954A pdb=" N LYS N 156 " --> pdb=" O TYR N 216 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA N 217 " --> pdb=" O ALA N 262 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N VAL N 264 " --> pdb=" O ALA N 217 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU N 219 " --> pdb=" O VAL N 264 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N THR N 266 " --> pdb=" O LEU N 219 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N VAL N 221 " --> pdb=" O THR N 266 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N GLN N 268 " --> pdb=" O VAL N 221 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE N 265 " --> pdb=" O THR N 123 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET N 125 " --> pdb=" O ILE N 265 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN N 267 " --> pdb=" O MET N 125 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY N 127 " --> pdb=" O ASN N 267 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ILE N 122 " --> pdb=" O THR N 298 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N LEU N 300 " --> pdb=" O ILE N 122 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLU N 124 " --> pdb=" O LEU N 300 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU N 302 " --> pdb=" O GLU N 124 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE N 126 " --> pdb=" O LEU N 302 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N LYS N 304 " --> pdb=" O PHE N 126 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ARG N 299 " --> pdb=" O TYR N 315 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 189 through 193 removed outlier: 5.370A pdb=" N LYS O 156 " --> pdb=" O TYR O 216 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU O 218 " --> pdb=" O LYS O 156 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ALA O 217 " --> pdb=" O ALA O 262 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N VAL O 264 " --> pdb=" O ALA O 217 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU O 219 " --> pdb=" O VAL O 264 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N THR O 266 " --> pdb=" O LEU O 219 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL O 221 " --> pdb=" O THR O 266 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N GLN O 268 " --> pdb=" O VAL O 221 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE O 265 " --> pdb=" O THR O 123 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N MET O 125 " --> pdb=" O ILE O 265 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN O 267 " --> pdb=" O MET O 125 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY O 127 " --> pdb=" O ASN O 267 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ILE O 122 " --> pdb=" O THR O 298 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N LEU O 300 " --> pdb=" O ILE O 122 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLU O 124 " --> pdb=" O LEU O 300 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LEU O 302 " --> pdb=" O GLU O 124 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N PHE O 126 " --> pdb=" O LEU O 302 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N LYS O 304 " --> pdb=" O PHE O 126 " (cutoff:3.500A) removed outlier: 6.742A 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: 3.507A pdb=" N ALA P 190 " --> pdb=" O ALA P 157 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA P 192 " --> pdb=" O TYR P 159 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LYS P 156 " --> pdb=" O LEU P 218 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ILE P 220 " --> pdb=" O LYS P 156 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N MET P 158 " --> pdb=" O ILE P 220 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ASP P 222 " --> pdb=" O MET P 158 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ILE P 160 " --> pdb=" O ASP P 222 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA P 217 " --> pdb=" O ALA P 262 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N VAL P 264 " --> pdb=" O ALA P 217 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU P 219 " --> pdb=" O VAL P 264 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N THR P 266 " --> pdb=" O LEU P 219 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL P 221 " --> pdb=" O THR P 266 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N GLN P 268 " --> pdb=" O VAL P 221 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE P 265 " --> pdb=" O THR P 123 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N MET P 125 " --> pdb=" O ILE P 265 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN P 267 " --> pdb=" O MET P 125 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY P 127 " --> pdb=" O ASN P 267 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ILE P 122 " --> pdb=" O THR P 298 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N LEU P 300 " --> pdb=" O ILE P 122 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLU P 124 " --> pdb=" O LEU P 300 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU P 302 " --> pdb=" O GLU P 124 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE P 126 " --> pdb=" O LEU P 302 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N LYS P 304 " --> pdb=" O PHE P 126 " (cutoff:3.500A) removed outlier: 6.552A 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: 6.642A pdb=" N LYS Q 156 " --> pdb=" O LEU Q 218 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ILE Q 220 " --> pdb=" O LYS Q 156 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N MET Q 158 " --> pdb=" O ILE Q 220 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ASP Q 222 " --> pdb=" O MET Q 158 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE Q 160 " --> pdb=" O ASP Q 222 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA Q 217 " --> pdb=" O ALA Q 262 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N VAL Q 264 " --> pdb=" O ALA Q 217 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU Q 219 " --> pdb=" O VAL Q 264 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N THR Q 266 " --> pdb=" O LEU Q 219 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL Q 221 " --> pdb=" O THR Q 266 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N GLN Q 268 " --> pdb=" O VAL Q 221 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE Q 265 " --> pdb=" O THR Q 123 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET Q 125 " --> pdb=" O ILE Q 265 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN Q 267 " --> pdb=" O MET Q 125 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY Q 127 " --> pdb=" O ASN Q 267 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR Q 298 " --> pdb=" O ILE Q 122 " (cutoff:3.500A) removed outlier: 6.525A 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: 6.653A pdb=" N LYS R 156 " --> pdb=" O LEU R 218 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N ILE R 220 " --> pdb=" O LYS R 156 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N MET R 158 " --> pdb=" O ILE R 220 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ASP R 222 " --> pdb=" O MET R 158 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ILE R 160 " --> pdb=" O ASP R 222 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA R 217 " --> pdb=" O ALA R 262 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL R 264 " --> pdb=" O ALA R 217 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU R 219 " --> pdb=" O VAL R 264 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N THR R 266 " --> pdb=" O LEU R 219 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL R 221 " --> pdb=" O THR R 266 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N GLN R 268 " --> pdb=" O VAL R 221 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE R 265 " --> pdb=" O THR R 123 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET R 125 " --> pdb=" O ILE R 265 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN R 267 " --> pdb=" O MET R 125 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR R 298 " --> pdb=" O ILE R 122 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N TYR R 301 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ILE R 314 " --> pdb=" O TYR R 301 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ARG R 303 " --> pdb=" O CYS R 312 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N CYS R 312 " --> pdb=" O ARG R 303 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'S' and resid 189 through 193 removed outlier: 5.116A pdb=" N LYS S 156 " --> pdb=" O TYR S 216 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU S 218 " --> pdb=" O LYS S 156 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA S 217 " --> pdb=" O ALA S 262 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL S 264 " --> pdb=" O ALA S 217 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU S 219 " --> pdb=" O VAL S 264 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N THR S 266 " --> pdb=" O LEU S 219 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL S 221 " --> pdb=" O THR S 266 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N GLN S 268 " --> pdb=" O VAL S 221 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE S 265 " --> pdb=" O THR S 123 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N MET S 125 " --> pdb=" O ILE S 265 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN S 267 " --> pdb=" O MET S 125 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY S 127 " --> pdb=" O ASN S 267 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ILE S 122 " --> pdb=" O THR S 298 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N LEU S 300 " --> pdb=" O ILE S 122 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLU S 124 " --> pdb=" O LEU S 300 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU S 302 " --> pdb=" O GLU S 124 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N PHE S 126 " --> pdb=" O LEU S 302 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N LYS S 304 " --> pdb=" O PHE S 126 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N TYR S 301 " --> pdb=" O ILE S 314 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ILE S 314 " --> pdb=" O TYR S 301 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ARG S 303 " --> pdb=" O CYS S 312 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N CYS S 312 " --> pdb=" O ARG S 303 " (cutoff:3.500A) 1245 hydrogen bonds defined for protein. 3654 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 397 hydrogen bonds 786 hydrogen bond angles 0 basepair planarities 156 basepair parallelities 269 stacking parallelities Total time for adding SS restraints: 7.24 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5963 1.33 - 1.45: 8379 1.45 - 1.57: 16333 1.57 - 1.69: 616 1.69 - 1.81: 192 Bond restraints: 31483 Sorted by residual: bond pdb=" C3' DA I 138 " pdb=" C2' DA I 138 " ideal model delta sigma weight residual 1.516 1.557 -0.041 8.00e-03 1.56e+04 2.64e+01 bond pdb=" C3' DC I 142 " pdb=" C2' DC I 142 " ideal model delta sigma weight residual 1.516 1.554 -0.038 8.00e-03 1.56e+04 2.28e+01 bond pdb=" C3' DA J 67 " pdb=" O3' DA J 67 " ideal model delta sigma weight residual 1.435 1.382 0.053 1.30e-02 5.92e+03 1.63e+01 bond pdb=" C3' DG I 49 " pdb=" O3' DG I 49 " ideal model delta sigma weight residual 1.435 1.383 0.052 1.30e-02 5.92e+03 1.62e+01 bond pdb=" C3' DG J 12 " pdb=" C2' DG J 12 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.61e+01 ... (remaining 31478 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 42832 2.53 - 5.07: 863 5.07 - 7.60: 71 7.60 - 10.13: 19 10.13 - 12.67: 2 Bond angle restraints: 43787 Sorted by residual: angle pdb=" O4' DG I 143 " pdb=" C1' DG I 143 " pdb=" N9 DG I 143 " ideal model delta sigma weight residual 108.00 112.64 -4.64 7.00e-01 2.04e+00 4.39e+01 angle pdb=" C4' DG I 150 " pdb=" O4' DG I 150 " pdb=" C1' DG I 150 " ideal model delta sigma weight residual 110.10 104.24 5.86 1.00e+00 1.00e+00 3.43e+01 angle pdb=" O4' DT J 17 " pdb=" C1' DT J 17 " pdb=" N1 DT J 17 " ideal model delta sigma weight residual 108.00 111.88 -3.88 7.00e-01 2.04e+00 3.06e+01 angle pdb=" O5' DC I 155 " pdb=" C5' DC I 155 " pdb=" C4' DC I 155 " ideal model delta sigma weight residual 109.40 113.74 -4.34 8.00e-01 1.56e+00 2.95e+01 angle pdb=" O4' DA I 28 " pdb=" C4' DA I 28 " pdb=" C3' DA I 28 " ideal model delta sigma weight residual 106.00 102.75 3.25 6.00e-01 2.78e+00 2.93e+01 ... (remaining 43782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.41: 15239 20.41 - 40.83: 1661 40.83 - 61.24: 1271 61.24 - 81.65: 76 81.65 - 102.06: 4 Dihedral angle restraints: 18251 sinusoidal: 9349 harmonic: 8902 Sorted by residual: dihedral pdb=" CA VAL Q 334 " pdb=" C VAL Q 334 " pdb=" N GLY Q 335 " pdb=" CA GLY Q 335 " ideal model delta harmonic sigma weight residual -180.00 -152.00 -28.00 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA VAL M 334 " pdb=" C VAL M 334 " pdb=" N GLY M 335 " pdb=" CA GLY M 335 " ideal model delta harmonic sigma weight residual -180.00 -152.19 -27.81 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA VAL O 334 " pdb=" C VAL O 334 " pdb=" N GLY O 335 " pdb=" CA GLY O 335 " ideal model delta harmonic sigma weight residual 180.00 -152.22 -27.78 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 18248 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 4762 0.115 - 0.230: 240 0.230 - 0.344: 3 0.344 - 0.459: 0 0.459 - 0.574: 6 Chirality restraints: 5011 Sorted by residual: chirality pdb=" P DA I 146 " pdb=" OP1 DA I 146 " pdb=" OP2 DA I 146 " pdb=" O5' DA I 146 " both_signs ideal model delta sigma weight residual True 2.34 -2.91 -0.57 2.00e-01 2.50e+01 8.23e+00 chirality pdb=" P DT J 14 " pdb=" OP1 DT J 14 " pdb=" OP2 DT J 14 " pdb=" O5' DT J 14 " both_signs ideal model delta sigma weight residual True 2.34 -2.91 -0.57 2.00e-01 2.50e+01 8.13e+00 chirality pdb=" P DA J 97 " pdb=" OP1 DA J 97 " pdb=" OP2 DA J 97 " pdb=" O5' DA J 97 " both_signs ideal model delta sigma weight residual True 2.34 -2.90 -0.57 2.00e-01 2.50e+01 8.05e+00 ... (remaining 5008 not shown) Planarity restraints: 4558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I 142 " -0.050 2.00e-02 2.50e+03 3.04e-02 2.07e+01 pdb=" N1 DC I 142 " 0.070 2.00e-02 2.50e+03 pdb=" C2 DC I 142 " -0.021 2.00e-02 2.50e+03 pdb=" O2 DC I 142 " 0.013 2.00e-02 2.50e+03 pdb=" N3 DC I 142 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DC I 142 " -0.010 2.00e-02 2.50e+03 pdb=" N4 DC I 142 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DC I 142 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DC I 142 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 143 " 0.030 2.00e-02 2.50e+03 1.82e-02 9.94e+00 pdb=" N9 DG I 143 " -0.052 2.00e-02 2.50e+03 pdb=" C8 DG I 143 " 0.017 2.00e-02 2.50e+03 pdb=" N7 DG I 143 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG I 143 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG I 143 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 143 " 0.004 2.00e-02 2.50e+03 pdb=" N1 DG I 143 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 143 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 143 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DG I 143 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG I 143 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 118 " 0.030 2.00e-02 2.50e+03 1.93e-02 8.37e+00 pdb=" N1 DC I 118 " -0.048 2.00e-02 2.50e+03 pdb=" C2 DC I 118 " 0.008 2.00e-02 2.50e+03 pdb=" O2 DC I 118 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DC I 118 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 118 " 0.005 2.00e-02 2.50e+03 pdb=" N4 DC I 118 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DC I 118 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DC I 118 " 0.002 2.00e-02 2.50e+03 ... (remaining 4555 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3272 2.74 - 3.28: 30952 3.28 - 3.82: 55589 3.82 - 4.36: 66620 4.36 - 4.90: 101755 Nonbonded interactions: 258188 Sorted by model distance: nonbonded pdb=" N THR Q 103 " pdb=" O GLY Q 151 " model vdw 2.205 3.120 nonbonded pdb=" NH1 ARG P 170 " pdb=" O ALA P 331 " model vdw 2.213 3.120 nonbonded pdb=" OG SER S 106 " pdb=" OD1 ASP S 336 " model vdw 2.222 3.040 nonbonded pdb=" N THR R 103 " pdb=" O GLY R 151 " model vdw 2.231 3.120 nonbonded pdb=" N THR M 103 " pdb=" O GLY M 151 " model vdw 2.238 3.120 ... (remaining 258183 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 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 32.540 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 37.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 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 0.053 31483 Z= 0.512 Angle : 0.860 12.666 43787 Z= 0.612 Chirality : 0.056 0.574 5011 Planarity : 0.006 0.064 4558 Dihedral : 21.262 102.065 12549 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.04 % Allowed : 1.31 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.14), residues: 3051 helix: -0.03 (0.12), residues: 1569 sheet: 0.77 (0.21), residues: 480 loop : -0.83 (0.17), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG R 299 TYR 0.025 0.002 TYR S 54 PHE 0.027 0.002 PHE E 78 HIS 0.011 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.51 (31483) covalent geometry : angle 0.85962 / 0.61 (43787) hydrogen bonds : bond 0.14945 / 10.19 ( 1642) hydrogen bonds : angle 5.89333 / 4.22 ( 4440) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 299 time to evaluate : 1.058 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 50 GLU cc_start: 0.9342 (mt-10) cc_final: 0.9137 (mm-30) REVERT: A 76 GLN cc_start: 0.9732 (tp40) cc_final: 0.9524 (tp-100) REVERT: A 81 ASP cc_start: 0.8637 (t0) cc_final: 0.7928 (t70) REVERT: A 119 ILE cc_start: 0.9254 (pt) cc_final: 0.8842 (pt) REVERT: B 59 LYS cc_start: 0.9347 (tttm) cc_final: 0.9136 (tttp) REVERT: B 63 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8870 (mt-10) REVERT: B 84 MET cc_start: 0.9025 (mmm) cc_final: 0.8643 (mmm) REVERT: B 92 ARG cc_start: 0.9196 (ptm-80) cc_final: 0.8767 (ttp80) REVERT: C 56 GLU cc_start: 0.9124 (tt0) cc_final: 0.8522 (tt0) REVERT: D 62 MET cc_start: 0.9575 (mmm) cc_final: 0.9250 (mmp) REVERT: D 64 SER cc_start: 0.8915 (m) cc_final: 0.8456 (t) REVERT: D 94 ILE cc_start: 0.9603 (mm) cc_final: 0.9376 (tp) REVERT: E 93 GLN cc_start: 0.9289 (tt0) cc_final: 0.8921 (tp40) REVERT: E 94 GLU cc_start: 0.9434 (mm-30) cc_final: 0.9022 (mm-30) REVERT: E 123 ASP cc_start: 0.8775 (m-30) cc_final: 0.7841 (m-30) REVERT: F 44 LYS cc_start: 0.8940 (tttt) cc_final: 0.8671 (tttt) REVERT: G 64 GLU cc_start: 0.9304 (tp30) cc_final: 0.8766 (tp30) REVERT: G 71 ARG cc_start: 0.9420 (ttm170) cc_final: 0.9184 (tmm-80) REVERT: H 62 MET cc_start: 0.9609 (mmm) cc_final: 0.9312 (mmm) REVERT: K 294 HIS cc_start: 0.4607 (t-90) cc_final: 0.4059 (t70) REVERT: L 158 MET cc_start: -0.0447 (mmm) cc_final: -0.0677 (mmm) REVERT: L 326 MET cc_start: 0.2790 (tpt) cc_final: 0.2468 (tpt) REVERT: M 125 MET cc_start: -0.1932 (pmm) cc_final: -0.2550 (ptp) REVERT: P 247 ARG cc_start: 0.9440 (ttp-170) cc_final: 0.9214 (tpp-160) REVERT: Q 149 ASP cc_start: 0.9411 (t70) cc_final: 0.9187 (p0) REVERT: Q 210 MET cc_start: 0.7215 (tmm) cc_final: 0.6377 (ptt) REVERT: Q 248 PHE cc_start: 0.9258 (t80) cc_final: 0.8917 (t80) outliers start: 1 outliers final: 0 residues processed: 299 average time/residue: 0.2077 time to fit residues: 97.8016 Evaluate side-chains 152 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 197 optimal weight: 40.0000 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 40.0000 chunk 207 optimal weight: 0.3980 chunk 155 optimal weight: 40.0000 chunk 244 optimal weight: 50.0000 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 8.9990 overall best weight: 8.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS E 68 GLN K 23 GLN K 47 HIS ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 GLN N 47 HIS O 47 HIS P 47 HIS Q 23 GLN Q 47 HIS Q 62 ASN R 206 GLN S 47 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.078941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.047032 restraints weight = 214912.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.048404 restraints weight = 74911.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.049103 restraints weight = 40398.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.049527 restraints weight = 28222.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.049705 restraints weight = 22739.163| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 31483 Z= 0.288 Angle : 0.770 14.961 43787 Z= 0.419 Chirality : 0.048 0.267 5011 Planarity : 0.005 0.079 4558 Dihedral : 26.029 93.112 6814 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 1.07 % Allowed : 6.09 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.14), residues: 3051 helix: 0.84 (0.13), residues: 1613 sheet: 0.66 (0.22), residues: 456 loop : -0.77 (0.18), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 150 TYR 0.033 0.002 TYR S 232 PHE 0.021 0.002 PHE P 248 HIS 0.016 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.29 (31483) covalent geometry : angle 0.76985 / 0.42 (43787) hydrogen bonds : bond 0.07393 / 5.02 ( 1642) hydrogen bonds : angle 5.16462 / 3.73 ( 4440) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8691 (t0) cc_final: 0.7896 (t70) REVERT: A 119 ILE cc_start: 0.8972 (pt) cc_final: 0.8628 (pt) REVERT: B 63 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8662 (mt-10) REVERT: C 56 GLU cc_start: 0.9105 (tt0) cc_final: 0.8413 (tt0) REVERT: D 59 MET cc_start: 0.9411 (tpp) cc_final: 0.9204 (tpp) REVERT: D 62 MET cc_start: 0.9573 (mmm) cc_final: 0.9310 (mmp) REVERT: D 64 SER cc_start: 0.8963 (m) cc_final: 0.8649 (t) REVERT: D 71 GLU cc_start: 0.9249 (mm-30) cc_final: 0.8810 (mm-30) REVERT: D 106 LEU cc_start: 0.9632 (mt) cc_final: 0.9322 (mt) REVERT: E 39 HIS cc_start: 0.7244 (OUTLIER) cc_final: 0.6764 (t70) REVERT: F 44 LYS cc_start: 0.8878 (tttt) cc_final: 0.8660 (tttt) REVERT: H 62 MET cc_start: 0.9682 (mmm) cc_final: 0.9436 (mmm) REVERT: K 294 HIS cc_start: 0.4918 (t70) cc_final: 0.4453 (t70) REVERT: M 125 MET cc_start: -0.2194 (pmm) cc_final: -0.2741 (ptp) REVERT: M 158 MET cc_start: 0.5110 (mmm) cc_final: 0.4222 (ttt) REVERT: M 243 MET cc_start: 0.3768 (ptt) cc_final: 0.3446 (mtt) REVERT: N 211 MET cc_start: 0.4170 (mmt) cc_final: 0.3587 (mmm) REVERT: O 210 MET cc_start: 0.1653 (ptt) cc_final: 0.1070 (ptt) REVERT: O 243 MET cc_start: 0.8609 (mmt) cc_final: 0.7733 (tpt) REVERT: P 211 MET cc_start: -0.1995 (mmm) cc_final: -0.2248 (tmm) REVERT: Q 248 PHE cc_start: 0.9311 (t80) cc_final: 0.9009 (t80) REVERT: S 210 MET cc_start: 0.2728 (ptt) cc_final: 0.2525 (ppp) REVERT: S 211 MET cc_start: -0.1309 (ttm) cc_final: -0.2785 (tpt) outliers start: 27 outliers final: 16 residues processed: 169 average time/residue: 0.1776 time to fit residues: 50.6582 Evaluate side-chains 141 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain M residue 237 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 24 optimal weight: 0.9990 chunk 301 optimal weight: 30.0000 chunk 142 optimal weight: 10.0000 chunk 134 optimal weight: 50.0000 chunk 281 optimal weight: 40.0000 chunk 63 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 253 optimal weight: 0.4980 chunk 296 optimal weight: 1.9990 chunk 234 optimal weight: 5.9990 chunk 85 optimal weight: 30.0000 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 73 ASN H 84 ASN ** K 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 GLN O 23 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.080244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.048337 restraints weight = 213394.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.049792 restraints weight = 73817.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.050505 restraints weight = 39572.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.050901 restraints weight = 27254.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.051156 restraints weight = 22389.360| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.139 31483 Z= 0.144 Angle : 0.605 11.964 43787 Z= 0.341 Chirality : 0.044 0.271 5011 Planarity : 0.004 0.050 4558 Dihedral : 25.914 89.643 6814 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.80 % Allowed : 7.80 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.15), residues: 3051 helix: 1.32 (0.13), residues: 1581 sheet: 0.83 (0.24), residues: 390 loop : -0.77 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 129 TYR 0.031 0.002 TYR S 232 PHE 0.009 0.001 PHE P 248 HIS 0.010 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 (31483) covalent geometry : angle 0.60545 / 0.34 (43787) hydrogen bonds : bond 0.05492 / 3.68 ( 1642) hydrogen bonds : angle 4.39135 / 3.16 ( 4440) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8476 (tp30) REVERT: A 81 ASP cc_start: 0.8717 (t0) cc_final: 0.7832 (t70) REVERT: A 119 ILE cc_start: 0.9028 (pt) cc_final: 0.8803 (pt) REVERT: A 120 MET cc_start: 0.8573 (mmm) cc_final: 0.7956 (mmm) REVERT: B 63 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8589 (mt-10) REVERT: B 84 MET cc_start: 0.8988 (tpp) cc_final: 0.8394 (tpp) REVERT: C 56 GLU cc_start: 0.9114 (tt0) cc_final: 0.8467 (tt0) REVERT: D 59 MET cc_start: 0.9372 (tpp) cc_final: 0.9135 (tpp) REVERT: D 62 MET cc_start: 0.9541 (mmm) cc_final: 0.9169 (mmp) REVERT: D 64 SER cc_start: 0.8971 (m) cc_final: 0.8645 (t) REVERT: D 71 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8823 (mm-30) REVERT: D 94 ILE cc_start: 0.9576 (mm) cc_final: 0.9311 (tt) REVERT: H 62 MET cc_start: 0.9684 (mmm) cc_final: 0.9342 (mmm) REVERT: H 94 ILE cc_start: 0.9544 (mm) cc_final: 0.9332 (tt) REVERT: K 294 HIS cc_start: 0.4913 (t70) cc_final: 0.4589 (t70) REVERT: M 125 MET cc_start: -0.2527 (pmm) cc_final: -0.3015 (ptp) REVERT: M 158 MET cc_start: 0.5153 (mmm) cc_final: 0.4264 (ttp) REVERT: M 210 MET cc_start: 0.0681 (ppp) cc_final: 0.0123 (ppp) REVERT: M 243 MET cc_start: 0.3973 (ptt) cc_final: 0.3681 (mtt) REVERT: N 211 MET cc_start: 0.4566 (mmt) cc_final: 0.4267 (mmm) REVERT: O 210 MET cc_start: 0.1541 (ptt) cc_final: 0.1196 (ptt) REVERT: O 211 MET cc_start: -0.2722 (mmt) cc_final: -0.3007 (mmt) REVERT: Q 248 PHE cc_start: 0.9316 (t80) cc_final: 0.9031 (t80) REVERT: R 158 MET cc_start: 0.2860 (mmm) cc_final: 0.2582 (mmm) REVERT: S 210 MET cc_start: 0.3043 (ptt) cc_final: 0.2802 (ppp) REVERT: S 211 MET cc_start: -0.0743 (ttm) cc_final: -0.2094 (tpt) outliers start: 20 outliers final: 11 residues processed: 162 average time/residue: 0.1743 time to fit residues: 47.7639 Evaluate side-chains 138 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 17 ARG Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain M residue 150 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 151 optimal weight: 20.0000 chunk 168 optimal weight: 0.1980 chunk 50 optimal weight: 4.9990 chunk 303 optimal weight: 10.0000 chunk 292 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 312 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 165 optimal weight: 20.0000 chunk 277 optimal weight: 10.0000 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 294 HIS ** N 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.079930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.047986 restraints weight = 213364.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.049460 restraints weight = 74248.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.050155 restraints weight = 40185.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.050546 restraints weight = 27674.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.050738 restraints weight = 22501.565| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31483 Z= 0.143 Angle : 0.593 11.340 43787 Z= 0.330 Chirality : 0.043 0.267 5011 Planarity : 0.003 0.041 4558 Dihedral : 25.741 91.837 6814 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 1.00 % Allowed : 8.56 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.15), residues: 3051 helix: 1.50 (0.13), residues: 1583 sheet: 1.05 (0.23), residues: 378 loop : -0.83 (0.17), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 303 TYR 0.032 0.001 TYR S 232 PHE 0.010 0.001 PHE S 248 HIS 0.013 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.14 (31483) covalent geometry : angle 0.59340 / 0.33 (43787) hydrogen bonds : bond 0.05020 / 3.38 ( 1642) hydrogen bonds : angle 4.11245 / 2.95 ( 4440) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.855 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: 0.8869 (mm-30) cc_final: 0.8528 (tp30) REVERT: A 81 ASP cc_start: 0.8723 (t0) cc_final: 0.7846 (t70) REVERT: A 120 MET cc_start: 0.8432 (mmm) cc_final: 0.7964 (mmm) REVERT: B 63 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8546 (mt-10) REVERT: B 84 MET cc_start: 0.8964 (tpp) cc_final: 0.8270 (tpp) REVERT: C 56 GLU cc_start: 0.9038 (tt0) cc_final: 0.8276 (mt-10) REVERT: D 64 SER cc_start: 0.8959 (m) cc_final: 0.8637 (t) REVERT: D 71 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8810 (mm-30) REVERT: D 94 ILE cc_start: 0.9599 (mm) cc_final: 0.9348 (tt) REVERT: E 90 MET cc_start: 0.9131 (mmm) cc_final: 0.8777 (mmp) REVERT: E 93 GLN cc_start: 0.9061 (tt0) cc_final: 0.8829 (tp40) REVERT: H 62 MET cc_start: 0.9683 (mmm) cc_final: 0.9426 (mmm) REVERT: H 71 GLU cc_start: 0.9305 (tp30) cc_final: 0.8802 (tm-30) REVERT: H 94 ILE cc_start: 0.9541 (mm) cc_final: 0.9296 (tt) REVERT: K 211 MET cc_start: 0.4419 (OUTLIER) cc_final: 0.4127 (ttm) REVERT: K 243 MET cc_start: 0.8839 (ptm) cc_final: 0.8254 (mmp) REVERT: M 125 MET cc_start: -0.2416 (pmm) cc_final: -0.2874 (ptp) REVERT: M 158 MET cc_start: 0.5116 (mmm) cc_final: 0.4337 (ttp) REVERT: M 210 MET cc_start: 0.0695 (ppp) cc_final: 0.0001 (ppp) REVERT: M 243 MET cc_start: 0.4572 (ptt) cc_final: 0.4324 (mtt) REVERT: N 211 MET cc_start: 0.4651 (mmt) cc_final: 0.4412 (tpt) REVERT: O 210 MET cc_start: 0.1615 (ptt) cc_final: 0.1264 (ptt) REVERT: O 211 MET cc_start: -0.2041 (mmt) cc_final: -0.2329 (mmt) REVERT: O 243 MET cc_start: 0.8635 (mmt) cc_final: 0.7907 (tpt) REVERT: Q 248 PHE cc_start: 0.9286 (t80) cc_final: 0.8997 (t80) REVERT: R 158 MET cc_start: 0.2374 (mmm) cc_final: 0.2059 (mmm) REVERT: S 210 MET cc_start: 0.3163 (ptt) cc_final: 0.2777 (ppp) REVERT: S 211 MET cc_start: -0.0682 (ttm) cc_final: -0.2189 (tpt) REVERT: S 252 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7779 (mm) outliers start: 25 outliers final: 15 residues processed: 151 average time/residue: 0.1704 time to fit residues: 44.4623 Evaluate side-chains 135 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 17 ARG Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 211 MET Chi-restraints excluded: chain Q residue 213 GLU Chi-restraints excluded: chain R residue 309 THR Chi-restraints excluded: chain S residue 252 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 248 optimal weight: 7.9990 chunk 128 optimal weight: 6.9990 chunk 83 optimal weight: 30.0000 chunk 250 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 chunk 280 optimal weight: 8.9990 chunk 99 optimal weight: 50.0000 chunk 104 optimal weight: 7.9990 chunk 189 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 31 HIS K 206 GLN M 206 GLN ** N 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 206 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.078311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.045052 restraints weight = 221505.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.046525 restraints weight = 79790.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.047273 restraints weight = 43900.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.047668 restraints weight = 30759.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.047843 restraints weight = 25030.753| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 31483 Z= 0.216 Angle : 0.647 12.904 43787 Z= 0.355 Chirality : 0.044 0.281 5011 Planarity : 0.004 0.041 4558 Dihedral : 25.721 95.974 6814 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 1.71 % Allowed : 8.68 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.15), residues: 3051 helix: 1.38 (0.13), residues: 1590 sheet: 1.09 (0.24), residues: 378 loop : -0.81 (0.17), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 129 TYR 0.024 0.002 TYR S 216 PHE 0.011 0.001 PHE A 78 HIS 0.010 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.22 (31483) covalent geometry : angle 0.64716 / 0.35 (43787) hydrogen bonds : bond 0.05966 / 4.05 ( 1642) hydrogen bonds : angle 4.21535 / 3.03 ( 4440) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 119 time to evaluate : 1.051 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: 0.9027 (mm-30) cc_final: 0.8406 (tp30) REVERT: A 81 ASP cc_start: 0.8752 (t0) cc_final: 0.7843 (t70) REVERT: A 120 MET cc_start: 0.8488 (mmm) cc_final: 0.8151 (mmm) REVERT: B 63 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8564 (mt-10) REVERT: B 84 MET cc_start: 0.9139 (tpp) cc_final: 0.8566 (tpp) REVERT: B 92 ARG cc_start: 0.9227 (OUTLIER) cc_final: 0.8881 (ttp80) REVERT: C 56 GLU cc_start: 0.9038 (tt0) cc_final: 0.8548 (mt-10) REVERT: D 64 SER cc_start: 0.9019 (m) cc_final: 0.8696 (t) REVERT: D 71 GLU cc_start: 0.9248 (mm-30) cc_final: 0.9012 (mm-30) REVERT: E 120 MET cc_start: 0.8505 (mtm) cc_final: 0.8292 (mtm) REVERT: H 62 MET cc_start: 0.9675 (mmm) cc_final: 0.9417 (mmm) REVERT: H 94 ILE cc_start: 0.9546 (OUTLIER) cc_final: 0.9299 (tt) REVERT: K 161 ASP cc_start: 0.4254 (OUTLIER) cc_final: 0.4031 (t70) REVERT: K 211 MET cc_start: 0.4536 (OUTLIER) cc_final: 0.4251 (ttm) REVERT: K 243 MET cc_start: 0.8825 (ptm) cc_final: 0.8250 (mmp) REVERT: M 125 MET cc_start: -0.2356 (pmm) cc_final: -0.2739 (ptp) REVERT: M 158 MET cc_start: 0.5178 (mmm) cc_final: 0.4427 (ttt) REVERT: M 210 MET cc_start: 0.0580 (ppp) cc_final: -0.0300 (ppp) REVERT: M 243 MET cc_start: 0.4521 (ptt) cc_final: 0.4296 (mtt) REVERT: O 210 MET cc_start: 0.1939 (ptt) cc_final: 0.1450 (ppp) REVERT: O 211 MET cc_start: -0.1560 (mmt) cc_final: -0.2107 (mmt) REVERT: Q 125 MET cc_start: 0.8576 (ptt) cc_final: 0.8355 (ppp) REVERT: Q 248 PHE cc_start: 0.9279 (t80) cc_final: 0.8984 (t80) REVERT: S 210 MET cc_start: 0.3507 (ptt) cc_final: 0.2985 (ppp) REVERT: S 211 MET cc_start: -0.1163 (ttm) cc_final: -0.2298 (tpt) REVERT: S 243 MET cc_start: 0.8214 (mmm) cc_final: 0.7509 (tpt) REVERT: S 252 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7716 (mm) outliers start: 43 outliers final: 22 residues processed: 155 average time/residue: 0.1681 time to fit residues: 44.5586 Evaluate side-chains 140 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 17 ARG Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain K residue 161 ASP Chi-restraints excluded: chain K residue 211 MET Chi-restraints excluded: chain O residue 34 ASN Chi-restraints excluded: chain Q residue 213 GLU Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 252 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 263 optimal weight: 40.0000 chunk 145 optimal weight: 50.0000 chunk 138 optimal weight: 30.0000 chunk 150 optimal weight: 6.9990 chunk 173 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 322 optimal weight: 50.0000 chunk 246 optimal weight: 50.0000 chunk 331 optimal weight: 0.4980 chunk 157 optimal weight: 40.0000 chunk 325 optimal weight: 30.0000 overall best weight: 9.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 206 GLN ** N 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.076511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.043194 restraints weight = 221497.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.044617 restraints weight = 81011.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.045311 restraints weight = 45091.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.045676 restraints weight = 31745.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.045928 restraints weight = 26268.215| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 31483 Z= 0.323 Angle : 0.773 18.761 43787 Z= 0.419 Chirality : 0.048 0.303 5011 Planarity : 0.005 0.055 4558 Dihedral : 25.852 100.750 6814 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.31 % Allowed : 9.55 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.15), residues: 3051 helix: 0.93 (0.13), residues: 1584 sheet: 1.22 (0.25), residues: 372 loop : -0.64 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 215 TYR 0.022 0.002 TYR S 216 PHE 0.022 0.002 PHE A 84 HIS 0.012 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.32 (31483) covalent geometry : angle 0.77310 / 0.42 (43787) hydrogen bonds : bond 0.07563 / 5.14 ( 1642) hydrogen bonds : angle 4.70672 / 3.36 ( 4440) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 115 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8385 (tp30) REVERT: A 81 ASP cc_start: 0.8867 (OUTLIER) cc_final: 0.7961 (t70) REVERT: A 120 MET cc_start: 0.8474 (mmm) cc_final: 0.7827 (mmm) REVERT: B 84 MET cc_start: 0.9268 (tpp) cc_final: 0.8799 (tpp) REVERT: B 92 ARG cc_start: 0.9248 (OUTLIER) cc_final: 0.8929 (ttp80) REVERT: D 64 SER cc_start: 0.9069 (m) cc_final: 0.8724 (t) REVERT: D 71 GLU cc_start: 0.9293 (mm-30) cc_final: 0.9050 (mm-30) REVERT: D 94 ILE cc_start: 0.9583 (OUTLIER) cc_final: 0.9339 (tt) REVERT: D 109 HIS cc_start: 0.9338 (OUTLIER) cc_final: 0.9060 (m-70) REVERT: E 39 HIS cc_start: 0.7987 (OUTLIER) cc_final: 0.7552 (t70) REVERT: E 93 GLN cc_start: 0.9260 (tt0) cc_final: 0.8990 (tp40) REVERT: F 63 GLU cc_start: 0.9385 (tt0) cc_final: 0.8901 (tm-30) REVERT: H 62 MET cc_start: 0.9652 (mmm) cc_final: 0.9365 (mmm) REVERT: H 94 ILE cc_start: 0.9571 (OUTLIER) cc_final: 0.9334 (tt) REVERT: K 161 ASP cc_start: 0.3871 (OUTLIER) cc_final: 0.3534 (t70) REVERT: K 211 MET cc_start: 0.4397 (OUTLIER) cc_final: 0.4124 (ttm) REVERT: K 243 MET cc_start: 0.8844 (ptm) cc_final: 0.8250 (mmp) REVERT: M 125 MET cc_start: -0.2332 (pmm) cc_final: -0.2591 (ptp) REVERT: M 158 MET cc_start: 0.4594 (mmm) cc_final: 0.3970 (ttt) REVERT: M 210 MET cc_start: 0.0059 (ppp) cc_final: -0.0650 (ppp) REVERT: M 243 MET cc_start: 0.4222 (ptt) cc_final: 0.3976 (mtt) REVERT: N 211 MET cc_start: 0.4457 (OUTLIER) cc_final: 0.3981 (tpt) REVERT: O 210 MET cc_start: 0.1962 (ptt) cc_final: 0.1627 (ptt) REVERT: O 211 MET cc_start: -0.1215 (mmt) cc_final: -0.1540 (mmt) REVERT: O 243 MET cc_start: 0.8767 (mmt) cc_final: 0.7833 (tpt) REVERT: P 205 TYR cc_start: 0.9025 (t80) cc_final: 0.8535 (t80) REVERT: Q 161 ASP cc_start: 0.4405 (OUTLIER) cc_final: 0.3118 (t0) REVERT: Q 211 MET cc_start: -0.1140 (ttp) cc_final: -0.2302 (tmm) REVERT: Q 213 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7693 (pm20) REVERT: Q 248 PHE cc_start: 0.9270 (t80) cc_final: 0.8998 (t80) REVERT: R 125 MET cc_start: 0.8949 (ttp) cc_final: 0.8643 (ppp) REVERT: R 211 MET cc_start: 0.2589 (mmm) cc_final: 0.2301 (mmm) REVERT: S 210 MET cc_start: 0.3975 (ptt) cc_final: 0.3448 (ppp) REVERT: S 243 MET cc_start: 0.8355 (mmm) cc_final: 0.7675 (tpt) REVERT: S 252 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7802 (mm) outliers start: 58 outliers final: 35 residues processed: 160 average time/residue: 0.1714 time to fit residues: 47.0190 Evaluate side-chains 159 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 112 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 109 HIS Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 17 ARG Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 161 ASP Chi-restraints excluded: chain K residue 211 MET Chi-restraints excluded: chain K residue 223 SER Chi-restraints excluded: chain L residue 223 SER Chi-restraints excluded: chain L residue 243 MET Chi-restraints excluded: chain N residue 211 MET Chi-restraints excluded: chain O residue 34 ASN Chi-restraints excluded: chain O residue 37 ASP Chi-restraints excluded: chain O residue 158 MET Chi-restraints excluded: chain Q residue 46 PHE Chi-restraints excluded: chain Q residue 161 ASP Chi-restraints excluded: chain Q residue 213 GLU Chi-restraints excluded: chain Q residue 223 SER Chi-restraints excluded: chain R residue 309 THR Chi-restraints excluded: chain S residue 34 ASN Chi-restraints excluded: chain S residue 37 ASP Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 252 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 312 optimal weight: 5.9990 chunk 178 optimal weight: 50.0000 chunk 90 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 chunk 325 optimal weight: 10.0000 chunk 228 optimal weight: 50.0000 chunk 327 optimal weight: 30.0000 chunk 195 optimal weight: 50.0000 chunk 80 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 0.0060 overall best weight: 9.2010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.077123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.044907 restraints weight = 217135.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.046110 restraints weight = 74510.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.046737 restraints weight = 40610.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.047142 restraints weight = 28781.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.047297 restraints weight = 23687.870| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 31483 Z= 0.285 Angle : 0.720 16.696 43787 Z= 0.392 Chirality : 0.046 0.308 5011 Planarity : 0.004 0.052 4558 Dihedral : 25.937 103.534 6814 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.63 % Allowed : 9.75 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.15), residues: 3051 helix: 0.94 (0.13), residues: 1578 sheet: 1.10 (0.23), residues: 438 loop : -0.58 (0.18), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 310 TYR 0.022 0.002 TYR N 216 PHE 0.033 0.002 PHE S 259 HIS 0.011 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.28 (31483) covalent geometry : angle 0.72039 / 0.39 (43787) hydrogen bonds : bond 0.06433 / 4.38 ( 1642) hydrogen bonds : angle 4.59455 / 3.28 ( 4440) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 112 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8573 (tp30) REVERT: A 81 ASP cc_start: 0.8846 (OUTLIER) cc_final: 0.7942 (t70) REVERT: A 94 GLU cc_start: 0.9307 (OUTLIER) cc_final: 0.8803 (tp30) REVERT: A 120 MET cc_start: 0.8361 (mmm) cc_final: 0.7996 (mmm) REVERT: B 84 MET cc_start: 0.9269 (tpp) cc_final: 0.8803 (tpp) REVERT: B 92 ARG cc_start: 0.9310 (OUTLIER) cc_final: 0.8964 (ttp80) REVERT: D 64 SER cc_start: 0.9100 (m) cc_final: 0.8789 (t) REVERT: D 71 GLU cc_start: 0.9293 (mm-30) cc_final: 0.9049 (mm-30) REVERT: E 39 HIS cc_start: 0.8001 (OUTLIER) cc_final: 0.7550 (t70) REVERT: F 63 GLU cc_start: 0.9384 (tt0) cc_final: 0.8881 (tm-30) REVERT: H 62 MET cc_start: 0.9673 (mmm) cc_final: 0.9288 (mmm) REVERT: H 94 ILE cc_start: 0.9555 (OUTLIER) cc_final: 0.9312 (tt) REVERT: K 161 ASP cc_start: 0.3834 (OUTLIER) cc_final: 0.3461 (t70) REVERT: K 211 MET cc_start: 0.4472 (OUTLIER) cc_final: 0.4178 (ttm) REVERT: K 243 MET cc_start: 0.8823 (ptm) cc_final: 0.8251 (mmp) REVERT: M 125 MET cc_start: -0.2381 (pmm) cc_final: -0.2655 (ptp) REVERT: M 158 MET cc_start: 0.4476 (mmm) cc_final: 0.3995 (ttt) REVERT: M 210 MET cc_start: 0.0249 (ppp) cc_final: -0.0614 (ppp) REVERT: M 243 MET cc_start: 0.4327 (ptt) cc_final: 0.4105 (mtt) REVERT: O 210 MET cc_start: 0.2100 (ptt) cc_final: 0.1627 (ppp) REVERT: O 211 MET cc_start: -0.0406 (mmt) cc_final: -0.0835 (mmt) REVERT: Q 125 MET cc_start: 0.8621 (ptt) cc_final: 0.8417 (ppp) REVERT: Q 161 ASP cc_start: 0.3950 (OUTLIER) cc_final: 0.3077 (t0) REVERT: Q 211 MET cc_start: -0.0207 (ttp) cc_final: -0.1741 (ttp) REVERT: Q 213 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7777 (pm20) REVERT: Q 248 PHE cc_start: 0.9244 (t80) cc_final: 0.8936 (t80) REVERT: R 125 MET cc_start: 0.8887 (ttp) cc_final: 0.8514 (ppp) REVERT: S 57 LYS cc_start: 0.4302 (OUTLIER) cc_final: 0.3818 (mmmt) REVERT: S 211 MET cc_start: -0.2213 (ttp) cc_final: -0.2437 (tmm) REVERT: S 243 MET cc_start: 0.8369 (mmm) cc_final: 0.7699 (tpt) REVERT: S 252 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7870 (mm) REVERT: S 326 MET cc_start: 0.6791 (tpt) cc_final: 0.6299 (pmm) outliers start: 66 outliers final: 42 residues processed: 162 average time/residue: 0.1770 time to fit residues: 49.6841 Evaluate side-chains 165 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 112 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 17 ARG Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 161 ASP Chi-restraints excluded: chain K residue 211 MET Chi-restraints excluded: chain K residue 223 SER Chi-restraints excluded: chain K residue 248 PHE Chi-restraints excluded: chain L residue 223 SER Chi-restraints excluded: chain L residue 248 PHE Chi-restraints excluded: chain L residue 326 MET Chi-restraints excluded: chain N residue 211 MET Chi-restraints excluded: chain O residue 34 ASN Chi-restraints excluded: chain O residue 37 ASP Chi-restraints excluded: chain O residue 158 MET Chi-restraints excluded: chain P residue 34 ASN Chi-restraints excluded: chain P residue 37 ASP Chi-restraints excluded: chain P residue 326 MET Chi-restraints excluded: chain Q residue 46 PHE Chi-restraints excluded: chain Q residue 161 ASP Chi-restraints excluded: chain Q residue 213 GLU Chi-restraints excluded: chain Q residue 223 SER Chi-restraints excluded: chain S residue 34 ASN Chi-restraints excluded: chain S residue 37 ASP Chi-restraints excluded: chain S residue 57 LYS Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 252 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 193 optimal weight: 6.9990 chunk 289 optimal weight: 7.9990 chunk 226 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 170 optimal weight: 7.9990 chunk 214 optimal weight: 7.9990 chunk 175 optimal weight: 50.0000 chunk 326 optimal weight: 2.9990 chunk 325 optimal weight: 40.0000 chunk 13 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 114 GLN N 23 GLN ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 206 GLN ** Q 206 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 = 0.4253 r_free = 0.4253 target = 0.095498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.063110 restraints weight = 239614.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.063467 restraints weight = 94652.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.063555 restraints weight = 48314.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.063786 restraints weight = 31274.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.063788 restraints weight = 24811.098| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31483 Z= 0.170 Angle : 0.630 14.503 43787 Z= 0.346 Chirality : 0.044 0.300 5011 Planarity : 0.003 0.038 4558 Dihedral : 25.892 103.642 6814 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.99 % Allowed : 10.51 % Favored : 87.50 % 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 are not related in a simple way. whole: 1.01 (0.15), residues: 3051 helix: 1.29 (0.13), residues: 1587 sheet: 1.19 (0.24), residues: 435 loop : -0.46 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 229 TYR 0.016 0.001 TYR R 216 PHE 0.010 0.001 PHE F 61 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.17 (31483) covalent geometry : angle 0.63013 / 0.35 (43787) hydrogen bonds : bond 0.05280 / 3.59 ( 1642) hydrogen bonds : angle 4.17080 / 2.98 ( 4440) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 130 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8514 (tp30) REVERT: A 120 MET cc_start: 0.8363 (mmm) cc_final: 0.7973 (mmm) REVERT: B 84 MET cc_start: 0.9136 (tpp) cc_final: 0.8655 (tpp) REVERT: B 85 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8313 (m-30) REVERT: B 92 ARG cc_start: 0.9266 (OUTLIER) cc_final: 0.8959 (ttp80) REVERT: D 64 SER cc_start: 0.9066 (m) cc_final: 0.8732 (t) REVERT: D 71 GLU cc_start: 0.9257 (mm-30) cc_final: 0.8988 (mm-30) REVERT: D 93 GLU cc_start: 0.9453 (mp0) cc_final: 0.9008 (mp0) REVERT: D 94 ILE cc_start: 0.9584 (mm) cc_final: 0.9309 (tt) REVERT: D 109 HIS cc_start: 0.9372 (OUTLIER) cc_final: 0.9105 (m-70) REVERT: E 39 HIS cc_start: 0.8086 (OUTLIER) cc_final: 0.7674 (t70) REVERT: F 63 GLU cc_start: 0.9298 (tt0) cc_final: 0.8732 (tm-30) REVERT: F 84 MET cc_start: 0.9232 (mmm) cc_final: 0.8631 (mmm) REVERT: H 59 MET cc_start: 0.9582 (tpp) cc_final: 0.9364 (tpp) REVERT: H 94 ILE cc_start: 0.9538 (mm) cc_final: 0.9300 (tt) REVERT: H 105 GLU cc_start: 0.9028 (mp0) cc_final: 0.8813 (pm20) REVERT: K 243 MET cc_start: 0.8454 (ptm) cc_final: 0.8095 (mmp) REVERT: M 125 MET cc_start: -0.2557 (pmm) cc_final: -0.2910 (ptp) REVERT: M 158 MET cc_start: 0.4260 (mmm) cc_final: 0.3794 (ttt) REVERT: M 210 MET cc_start: 0.1615 (ppp) cc_final: 0.0781 (ppp) REVERT: O 210 MET cc_start: 0.3434 (ptt) cc_final: 0.2997 (ppp) REVERT: Q 161 ASP cc_start: 0.2182 (OUTLIER) cc_final: 0.1864 (t70) REVERT: Q 211 MET cc_start: 0.6378 (ttp) cc_final: 0.4678 (ttp) REVERT: Q 248 PHE cc_start: 0.8762 (t80) cc_final: 0.8356 (t80) REVERT: R 125 MET cc_start: 0.8669 (ttp) cc_final: 0.8427 (ppp) REVERT: R 211 MET cc_start: 0.7774 (mmm) cc_final: 0.6662 (mmm) REVERT: S 243 MET cc_start: 0.7934 (mmm) cc_final: 0.7433 (tpt) outliers start: 50 outliers final: 34 residues processed: 168 average time/residue: 0.1639 time to fit residues: 47.5290 Evaluate side-chains 157 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 118 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 109 HIS Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 17 ARG Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain L residue 223 SER Chi-restraints excluded: chain L residue 248 PHE Chi-restraints excluded: chain L residue 326 MET Chi-restraints excluded: chain O residue 34 ASN Chi-restraints excluded: chain O residue 37 ASP Chi-restraints excluded: chain O residue 158 MET Chi-restraints excluded: chain P residue 34 ASN Chi-restraints excluded: chain P residue 326 MET Chi-restraints excluded: chain Q residue 161 ASP Chi-restraints excluded: chain Q residue 223 SER Chi-restraints excluded: chain R residue 210 MET Chi-restraints excluded: chain R residue 309 THR Chi-restraints excluded: chain S residue 34 ASN Chi-restraints excluded: chain S residue 37 ASP Chi-restraints excluded: chain S residue 162 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 236 optimal weight: 7.9990 chunk 167 optimal weight: 50.0000 chunk 120 optimal weight: 30.0000 chunk 320 optimal weight: 7.9990 chunk 65 optimal weight: 0.7980 chunk 126 optimal weight: 50.0000 chunk 258 optimal weight: 40.0000 chunk 7 optimal weight: 1.9990 chunk 154 optimal weight: 30.0000 chunk 283 optimal weight: 30.0000 chunk 284 optimal weight: 9.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 244 HIS ** Q 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.077482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.045526 restraints weight = 213315.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.046943 restraints weight = 75517.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.047612 restraints weight = 41266.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.047956 restraints weight = 28719.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.048207 restraints weight = 23698.436| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 31483 Z= 0.204 Angle : 0.660 14.823 43787 Z= 0.359 Chirality : 0.044 0.294 5011 Planarity : 0.004 0.039 4558 Dihedral : 25.833 104.606 6814 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.03 % Allowed : 10.75 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.15), residues: 3051 helix: 1.25 (0.13), residues: 1581 sheet: 1.25 (0.26), residues: 369 loop : -0.61 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 129 TYR 0.046 0.002 TYR H 83 PHE 0.023 0.002 PHE O 248 HIS 0.010 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.20 (31483) covalent geometry : angle 0.65952 / 0.36 (43787) hydrogen bonds : bond 0.05658 / 3.86 ( 1642) hydrogen bonds : angle 4.22793 / 3.02 ( 4440) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 122 time to evaluate : 0.837 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: A 50 GLU cc_start: 0.9222 (mm-30) cc_final: 0.8541 (tp30) REVERT: A 94 GLU cc_start: 0.9277 (OUTLIER) cc_final: 0.8746 (tp30) REVERT: A 120 MET cc_start: 0.8438 (mmm) cc_final: 0.8045 (mmm) REVERT: B 84 MET cc_start: 0.9168 (tpp) cc_final: 0.8704 (tpp) REVERT: B 85 ASP cc_start: 0.8765 (OUTLIER) cc_final: 0.8394 (m-30) REVERT: B 92 ARG cc_start: 0.9276 (OUTLIER) cc_final: 0.8956 (ttp80) REVERT: D 64 SER cc_start: 0.9068 (m) cc_final: 0.8730 (t) REVERT: D 71 GLU cc_start: 0.9251 (mm-30) cc_final: 0.8999 (mm-30) REVERT: D 93 GLU cc_start: 0.9438 (mp0) cc_final: 0.8972 (mp0) REVERT: D 94 ILE cc_start: 0.9617 (mm) cc_final: 0.9371 (tt) REVERT: D 109 HIS cc_start: 0.9356 (OUTLIER) cc_final: 0.9080 (m-70) REVERT: E 39 HIS cc_start: 0.7977 (OUTLIER) cc_final: 0.7583 (t70) REVERT: F 63 GLU cc_start: 0.9364 (tt0) cc_final: 0.8802 (tm-30) REVERT: H 94 ILE cc_start: 0.9561 (mm) cc_final: 0.9339 (tt) REVERT: H 105 GLU cc_start: 0.8949 (mp0) cc_final: 0.8732 (pm20) REVERT: K 243 MET cc_start: 0.8799 (ptm) cc_final: 0.8180 (mmp) REVERT: M 125 MET cc_start: -0.2105 (pmm) cc_final: -0.2360 (ptp) REVERT: M 158 MET cc_start: 0.4408 (mmm) cc_final: 0.3951 (ttt) REVERT: M 210 MET cc_start: -0.0098 (ppp) cc_final: -0.0896 (ppp) REVERT: N 211 MET cc_start: 0.4843 (OUTLIER) cc_final: 0.4500 (tpt) REVERT: O 210 MET cc_start: 0.2209 (ptt) cc_final: 0.1416 (ptt) REVERT: Q 161 ASP cc_start: 0.4197 (OUTLIER) cc_final: 0.3268 (t70) REVERT: Q 210 MET cc_start: 0.6026 (ppp) cc_final: 0.5641 (ppp) REVERT: Q 248 PHE cc_start: 0.9296 (t80) cc_final: 0.9011 (t80) REVERT: R 125 MET cc_start: 0.8795 (ttp) cc_final: 0.8396 (ppp) REVERT: R 211 MET cc_start: 0.3350 (mmm) cc_final: 0.1988 (mmm) REVERT: S 243 MET cc_start: 0.8467 (mmm) cc_final: 0.7819 (tpt) REVERT: S 326 MET cc_start: 0.6869 (tpt) cc_final: 0.6433 (pmm) outliers start: 51 outliers final: 41 residues processed: 162 average time/residue: 0.1683 time to fit residues: 47.2867 Evaluate side-chains 167 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 119 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 109 HIS Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 17 ARG Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 223 SER Chi-restraints excluded: chain K residue 266 THR Chi-restraints excluded: chain L residue 223 SER Chi-restraints excluded: chain L residue 248 PHE Chi-restraints excluded: chain L residue 326 MET Chi-restraints excluded: chain N residue 211 MET Chi-restraints excluded: chain O residue 34 ASN Chi-restraints excluded: chain O residue 37 ASP Chi-restraints excluded: chain P residue 34 ASN Chi-restraints excluded: chain P residue 326 MET Chi-restraints excluded: chain Q residue 161 ASP Chi-restraints excluded: chain Q residue 223 SER Chi-restraints excluded: chain R residue 309 THR Chi-restraints excluded: chain S residue 34 ASN Chi-restraints excluded: chain S residue 37 ASP Chi-restraints excluded: chain S residue 158 MET Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 153 optimal weight: 50.0000 chunk 262 optimal weight: 50.0000 chunk 309 optimal weight: 6.9990 chunk 167 optimal weight: 40.0000 chunk 70 optimal weight: 2.9990 chunk 273 optimal weight: 20.0000 chunk 139 optimal weight: 0.9990 chunk 166 optimal weight: 30.0000 chunk 137 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 93 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.077993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.046137 restraints weight = 211562.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.047443 restraints weight = 74328.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.048133 restraints weight = 40429.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.048485 restraints weight = 28192.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.048564 restraints weight = 23479.965| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 31483 Z= 0.167 Angle : 0.629 14.200 43787 Z= 0.344 Chirality : 0.043 0.297 5011 Planarity : 0.003 0.036 4558 Dihedral : 25.773 105.328 6814 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.83 % Allowed : 11.11 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.15), residues: 3051 helix: 1.37 (0.13), residues: 1581 sheet: 1.15 (0.25), residues: 435 loop : -0.38 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 215 TYR 0.059 0.001 TYR H 83 PHE 0.020 0.001 PHE O 248 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.17 (31483) covalent geometry : angle 0.62867 / 0.34 (43787) hydrogen bonds : bond 0.05064 / 3.45 ( 1642) hydrogen bonds : angle 4.06330 / 2.91 ( 4440) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 121 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8496 (tp30) REVERT: A 120 MET cc_start: 0.8420 (mmm) cc_final: 0.8022 (mmm) REVERT: B 84 MET cc_start: 0.9118 (tpp) cc_final: 0.8643 (tpp) REVERT: B 85 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8289 (m-30) REVERT: B 92 ARG cc_start: 0.9274 (OUTLIER) cc_final: 0.8968 (ttp80) REVERT: D 64 SER cc_start: 0.9055 (m) cc_final: 0.8726 (t) REVERT: D 71 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8948 (mm-30) REVERT: D 93 GLU cc_start: 0.9427 (mp0) cc_final: 0.8985 (mp0) REVERT: D 94 ILE cc_start: 0.9614 (mm) cc_final: 0.9371 (tt) REVERT: D 109 HIS cc_start: 0.9351 (OUTLIER) cc_final: 0.9040 (m-70) REVERT: E 39 HIS cc_start: 0.7998 (OUTLIER) cc_final: 0.7628 (t70) REVERT: E 90 MET cc_start: 0.9185 (mmm) cc_final: 0.8906 (mmp) REVERT: F 63 GLU cc_start: 0.9324 (tt0) cc_final: 0.8746 (tm-30) REVERT: H 59 MET cc_start: 0.9560 (tpp) cc_final: 0.9267 (tpp) REVERT: H 94 ILE cc_start: 0.9549 (mm) cc_final: 0.9324 (tt) REVERT: K 243 MET cc_start: 0.8788 (ptm) cc_final: 0.8168 (mmp) REVERT: M 125 MET cc_start: -0.2104 (pmm) cc_final: -0.2370 (ptp) REVERT: M 158 MET cc_start: 0.4275 (mmm) cc_final: 0.3858 (ttt) REVERT: M 210 MET cc_start: -0.0062 (ppp) cc_final: -0.0862 (ppp) REVERT: N 211 MET cc_start: 0.4815 (OUTLIER) cc_final: 0.4540 (tpt) REVERT: O 158 MET cc_start: 0.6277 (tmm) cc_final: 0.5872 (ppp) REVERT: O 210 MET cc_start: 0.1913 (ptt) cc_final: 0.1227 (ptt) REVERT: O 243 MET cc_start: 0.8725 (mmt) cc_final: 0.7822 (tpt) REVERT: Q 161 ASP cc_start: 0.3884 (OUTLIER) cc_final: 0.3048 (t70) REVERT: Q 210 MET cc_start: 0.6086 (ppp) cc_final: 0.5760 (ppp) REVERT: Q 248 PHE cc_start: 0.9291 (t80) cc_final: 0.8998 (t80) REVERT: R 125 MET cc_start: 0.8782 (ttp) cc_final: 0.8378 (ppp) REVERT: R 211 MET cc_start: 0.3538 (mmm) cc_final: 0.2273 (mmm) REVERT: S 243 MET cc_start: 0.8454 (mmm) cc_final: 0.7801 (tpt) REVERT: S 326 MET cc_start: 0.6817 (tpt) cc_final: 0.6401 (pmm) outliers start: 46 outliers final: 34 residues processed: 155 average time/residue: 0.1748 time to fit residues: 46.8152 Evaluate side-chains 156 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 116 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 109 HIS Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 17 ARG Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 223 SER Chi-restraints excluded: chain K residue 266 THR Chi-restraints excluded: chain L residue 223 SER Chi-restraints excluded: chain L residue 248 PHE Chi-restraints excluded: chain L residue 326 MET Chi-restraints excluded: chain N residue 211 MET Chi-restraints excluded: chain O residue 34 ASN Chi-restraints excluded: chain O residue 37 ASP Chi-restraints excluded: chain P residue 34 ASN Chi-restraints excluded: chain P residue 326 MET Chi-restraints excluded: chain Q residue 161 ASP Chi-restraints excluded: chain Q residue 223 SER Chi-restraints excluded: chain S residue 34 ASN Chi-restraints excluded: chain S residue 37 ASP Chi-restraints excluded: chain S residue 162 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 257 optimal weight: 8.9990 chunk 87 optimal weight: 30.0000 chunk 163 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 186 optimal weight: 20.0000 chunk 135 optimal weight: 0.7980 chunk 95 optimal weight: 20.0000 chunk 224 optimal weight: 50.0000 chunk 75 optimal weight: 20.0000 chunk 59 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.078520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.046832 restraints weight = 213235.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.048277 restraints weight = 75042.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.048992 restraints weight = 40931.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.049383 restraints weight = 28478.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.049619 restraints weight = 23505.768| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 31483 Z= 0.141 Angle : 0.616 13.578 43787 Z= 0.337 Chirality : 0.043 0.287 5011 Planarity : 0.003 0.040 4558 Dihedral : 25.672 105.379 6814 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 1.51 % Allowed : 11.39 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.15), residues: 3051 helix: 1.47 (0.13), residues: 1581 sheet: 1.24 (0.26), residues: 369 loop : -0.51 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 129 TYR 0.065 0.001 TYR H 83 PHE 0.021 0.001 PHE O 248 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 (31483) covalent geometry : angle 0.61576 / 0.34 (43787) hydrogen bonds : bond 0.04696 / 3.19 ( 1642) hydrogen bonds : angle 3.91694 / 2.80 ( 4440) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11202.87 seconds wall clock time: 191 minutes 15.28 seconds (11475.28 seconds total)