Starting phenix.real_space_refine on Sun Jul 5 20:17:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jnd_36442/07_2026/8jnd_36442.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jnd_36442/07_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_36442/07_2026/8jnd_36442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jnd_36442/07_2026/8jnd_36442.map" model { file = "/net/cci-nas-00/data/ceres_data/8jnd_36442/07_2026/8jnd_36442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jnd_36442/07_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-dev-6108/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: 6.05, per 1000 atoms: 0.20 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: 2.58 Conformation dependent library (CDL) restraints added in 950.6 milliseconds 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: 4.07 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: 6.98 Time building geometry restraints manager: 3.45 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: 42836 2.53 - 5.07: 859 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: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 30.240 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.640 ------------------------------------------------------------------------------- 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 : 0.858 12.666 43787 Z= 0.610 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 0.85814 / 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 : 1.029 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 30 THR cc_start: 0.9107 (p) cc_final: 0.8839 (t) 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: 0.8768 (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: 0.4058 (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: 0.6376 (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: 0.1994 time to fit residues: 93.4302 Evaluate side-chains 153 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 23 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.078907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.046844 restraints weight = 215016.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.048304 restraints weight = 74922.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.049007 restraints weight = 40479.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.049370 restraints weight = 27948.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.049612 restraints weight = 22907.873| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 31483 Z= 0.290 Angle : 0.762 14.952 43787 Z= 0.416 Chirality : 0.048 0.270 5011 Planarity : 0.005 0.080 4558 Dihedral : 26.098 92.483 6814 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 1.07 % Allowed : 6.21 % Favored : 92.71 % 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: 0.38 (0.14), residues: 3051 helix: 0.83 (0.13), residues: 1613 sheet: 0.65 (0.22), residues: 456 loop : -0.78 (0.18), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG M 150 TYR 0.042 0.002 TYR S 232 PHE 0.022 0.002 PHE P 248 HIS 0.017 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.29 (31483) covalent geometry : angle 0.76178 / 0.42 (43787) hydrogen bonds : bond 0.07292 / 4.95 ( 1642) hydrogen bonds : angle 5.14942 / 3.72 ( 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 177 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.759 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: 0.8709 (t0) cc_final: 0.7906 (t70) REVERT: A 119 ILE cc_start: 0.8978 (pt) cc_final: 0.8644 (pt) REVERT: B 63 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8677 (mt-10) REVERT: C 56 GLU cc_start: 0.9111 (tt0) cc_final: 0.8406 (tt0) REVERT: D 62 MET cc_start: 0.9581 (mmm) cc_final: 0.9320 (mmp) REVERT: D 64 SER cc_start: 0.8973 (m) cc_final: 0.8660 (t) REVERT: D 71 GLU cc_start: 0.9254 (mm-30) cc_final: 0.8856 (mm-30) REVERT: D 106 LEU cc_start: 0.9628 (mt) cc_final: 0.9328 (mt) REVERT: E 39 HIS cc_start: 0.7291 (OUTLIER) cc_final: 0.6793 (t70) REVERT: E 93 GLN cc_start: 0.9286 (tt0) cc_final: 0.9042 (tp40) REVERT: E 120 MET cc_start: 0.8241 (mtm) cc_final: 0.8011 (mtm) REVERT: H 62 MET cc_start: 0.9684 (mmm) cc_final: 0.9436 (mmm) REVERT: K 294 HIS cc_start: 0.4909 (t70) cc_final: 0.4448 (t70) REVERT: L 211 MET cc_start: -0.1893 (mtt) cc_final: -0.2108 (mtm) REVERT: M 125 MET cc_start: -0.2243 (pmm) cc_final: -0.2794 (ptp) REVERT: M 158 MET cc_start: 0.5083 (mmm) cc_final: 0.4242 (ttp) REVERT: M 243 MET cc_start: 0.3778 (ptt) cc_final: 0.3464 (mtt) REVERT: N 211 MET cc_start: 0.4318 (mmt) cc_final: 0.3749 (mmm) REVERT: O 210 MET cc_start: 0.1783 (ptt) cc_final: 0.0829 (ptt) REVERT: O 243 MET cc_start: 0.8627 (mmt) cc_final: 0.7783 (tpt) REVERT: O 326 MET cc_start: 0.8307 (tpp) cc_final: 0.8043 (tpp) REVERT: P 247 ARG cc_start: 0.9479 (ttp-170) cc_final: 0.9275 (ttp80) REVERT: Q 248 PHE cc_start: 0.9298 (t80) cc_final: 0.9012 (t80) REVERT: S 210 MET cc_start: 0.2778 (ptt) cc_final: 0.2556 (ppp) REVERT: S 211 MET cc_start: -0.1339 (ttm) cc_final: -0.2783 (tpt) outliers start: 27 outliers final: 16 residues processed: 172 average time/residue: 0.1697 time to fit residues: 48.8100 Evaluate side-chains 143 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.943 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 301 optimal weight: 20.0000 chunk 142 optimal weight: 7.9990 chunk 134 optimal weight: 50.0000 chunk 281 optimal weight: 30.0000 chunk 63 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 253 optimal weight: 10.0000 chunk 296 optimal weight: 10.0000 chunk 234 optimal weight: 6.9990 chunk 85 optimal weight: 30.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 73 ASN K 294 HIS O 23 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.079104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.047022 restraints weight = 214892.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.048500 restraints weight = 74796.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.049203 restraints weight = 40521.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.049586 restraints weight = 28058.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.049780 restraints weight = 22859.397| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 31483 Z= 0.207 Angle : 0.645 13.493 43787 Z= 0.360 Chirality : 0.045 0.280 5011 Planarity : 0.004 0.060 4558 Dihedral : 25.987 92.814 6814 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 1.04 % Allowed : 7.48 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.64 (0.15), residues: 3051 helix: 1.18 (0.13), residues: 1584 sheet: 0.82 (0.24), residues: 390 loop : -0.81 (0.17), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 129 TYR 0.035 0.002 TYR S 232 PHE 0.012 0.001 PHE G 25 HIS 0.011 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.21 (31483) covalent geometry : angle 0.64501 / 0.36 (43787) hydrogen bonds : bond 0.05892 / 3.96 ( 1642) hydrogen bonds : angle 4.53066 / 3.26 ( 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 167 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.934 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: 0.8799 (mm-30) cc_final: 0.8562 (tp30) REVERT: A 81 ASP cc_start: 0.8743 (t0) cc_final: 0.7868 (t70) REVERT: A 119 ILE cc_start: 0.9033 (pt) cc_final: 0.8759 (pt) REVERT: A 120 MET cc_start: 0.8528 (mmm) cc_final: 0.8020 (mmm) REVERT: B 63 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8596 (mt-10) REVERT: B 84 MET cc_start: 0.9015 (tpp) cc_final: 0.8505 (tpp) REVERT: C 56 GLU cc_start: 0.9020 (tt0) cc_final: 0.8348 (tt0) REVERT: D 64 SER cc_start: 0.9033 (m) cc_final: 0.8692 (t) REVERT: D 71 GLU cc_start: 0.9222 (mm-30) cc_final: 0.8847 (mm-30) REVERT: D 94 ILE cc_start: 0.9592 (mm) cc_final: 0.9346 (tt) REVERT: E 93 GLN cc_start: 0.9204 (tt0) cc_final: 0.8950 (tp40) REVERT: E 120 MET cc_start: 0.8334 (mtm) cc_final: 0.8092 (mtm) REVERT: H 62 MET cc_start: 0.9675 (mmm) cc_final: 0.9362 (mmm) REVERT: M 125 MET cc_start: -0.2194 (pmm) cc_final: -0.2674 (ptp) REVERT: M 158 MET cc_start: 0.5123 (mmm) cc_final: 0.4345 (ttp) REVERT: M 210 MET cc_start: 0.0477 (ppp) cc_final: -0.0076 (ppp) REVERT: M 243 MET cc_start: 0.3903 (ptt) cc_final: 0.3598 (mtt) REVERT: N 211 MET cc_start: 0.4244 (mmt) cc_final: 0.3708 (mmm) REVERT: O 210 MET cc_start: 0.1548 (ptt) cc_final: 0.0989 (ptt) REVERT: Q 248 PHE cc_start: 0.9304 (t80) cc_final: 0.9052 (t80) REVERT: R 158 MET cc_start: 0.3179 (mmm) cc_final: 0.2934 (mmm) REVERT: S 210 MET cc_start: 0.3143 (ptt) cc_final: 0.2551 (ppp) REVERT: S 211 MET cc_start: -0.0938 (ttm) cc_final: -0.2331 (tpt) REVERT: S 252 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7705 (mm) outliers start: 26 outliers final: 18 residues processed: 162 average time/residue: 0.1588 time to fit residues: 43.2698 Evaluate side-chains 142 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET 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 46 ILE Chi-restraints excluded: chain B residue 81 VAL 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 E residue 110 CYS 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 H residue 94 ILE Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain S residue 252 LEU 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: 10.0000 chunk 50 optimal weight: 1.9990 chunk 303 optimal weight: 0.6980 chunk 292 optimal weight: 40.0000 chunk 150 optimal weight: 50.0000 chunk 56 optimal weight: 3.9990 chunk 312 optimal weight: 8.9990 chunk 133 optimal weight: 7.9990 chunk 165 optimal weight: 20.0000 chunk 277 optimal weight: 40.0000 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 206 GLN P 23 GLN S 206 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.079100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.047133 restraints weight = 213930.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.048571 restraints weight = 74409.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.049264 restraints weight = 40011.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.049664 restraints weight = 27912.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.049844 restraints weight = 22594.495| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 31483 Z= 0.180 Angle : 0.618 12.793 43787 Z= 0.343 Chirality : 0.044 0.278 5011 Planarity : 0.004 0.037 4558 Dihedral : 25.898 95.258 6814 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.11 % Allowed : 8.72 % Favored : 90.17 % 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: 0.82 (0.15), residues: 3051 helix: 1.34 (0.13), residues: 1587 sheet: 1.12 (0.24), residues: 378 loop : -0.82 (0.17), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 247 TYR 0.020 0.002 TYR D 83 PHE 0.011 0.001 PHE A 104 HIS 0.013 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.18 (31483) covalent geometry : angle 0.61752 / 0.34 (43787) hydrogen bonds : bond 0.05450 / 3.69 ( 1642) hydrogen bonds : angle 4.29229 / 3.08 ( 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 160 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8615 (tp30) REVERT: A 81 ASP cc_start: 0.8747 (t0) cc_final: 0.7846 (t70) REVERT: A 120 MET cc_start: 0.8530 (mmm) cc_final: 0.8231 (mmm) REVERT: B 63 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8551 (mt-10) REVERT: B 84 MET cc_start: 0.9000 (tpp) cc_final: 0.8395 (tpp) REVERT: C 56 GLU cc_start: 0.9042 (tt0) cc_final: 0.8543 (mt-10) REVERT: D 64 SER cc_start: 0.9049 (m) cc_final: 0.8726 (t) REVERT: D 71 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8843 (mm-30) REVERT: E 37 LYS cc_start: 0.8854 (tppt) cc_final: 0.8622 (tppt) REVERT: E 93 GLN cc_start: 0.9208 (tt0) cc_final: 0.8981 (tp40) REVERT: E 120 MET cc_start: 0.8381 (mtm) cc_final: 0.8080 (mtm) REVERT: H 62 MET cc_start: 0.9679 (mmm) cc_final: 0.9335 (mmm) REVERT: H 94 ILE cc_start: 0.9552 (mm) cc_final: 0.9313 (tt) REVERT: K 211 MET cc_start: 0.4565 (OUTLIER) cc_final: 0.4276 (ttm) REVERT: K 243 MET cc_start: 0.8848 (ptm) cc_final: 0.8254 (mmp) REVERT: M 125 MET cc_start: -0.2315 (pmm) cc_final: -0.2747 (ptp) REVERT: M 158 MET cc_start: 0.5195 (mmm) cc_final: 0.4415 (ttp) REVERT: M 210 MET cc_start: 0.0428 (ppp) cc_final: -0.0268 (ppp) REVERT: M 243 MET cc_start: 0.4575 (ptt) cc_final: 0.4335 (mtt) REVERT: N 158 MET cc_start: 0.4477 (ttm) cc_final: 0.4206 (mtt) REVERT: N 211 MET cc_start: 0.4304 (mmt) cc_final: 0.3912 (tpt) REVERT: O 211 MET cc_start: 0.0119 (mmm) cc_final: -0.0151 (tpt) REVERT: O 243 MET cc_start: 0.8668 (mmt) cc_final: 0.7938 (tpt) REVERT: Q 248 PHE cc_start: 0.9298 (t80) cc_final: 0.9019 (t80) REVERT: S 211 MET cc_start: -0.1046 (ttm) cc_final: -0.1506 (ttp) outliers start: 28 outliers final: 17 residues processed: 155 average time/residue: 0.1574 time to fit residues: 42.1953 Evaluate side-chains 142 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 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 90 THR Chi-restraints excluded: chain E residue 110 CYS 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 O residue 34 ASN Chi-restraints excluded: chain Q residue 213 GLU Chi-restraints excluded: chain R residue 309 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 248 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 83 optimal weight: 20.0000 chunk 250 optimal weight: 20.0000 chunk 172 optimal weight: 30.0000 chunk 280 optimal weight: 20.0000 chunk 99 optimal weight: 40.0000 chunk 104 optimal weight: 7.9990 chunk 189 optimal weight: 40.0000 chunk 8 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 84 ASN L 206 GLN M 206 GLN ** P 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.078898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.045640 restraints weight = 220253.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.047161 restraints weight = 79269.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.047860 restraints weight = 43352.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.048243 restraints weight = 30305.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.048471 restraints weight = 24894.369| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 31483 Z= 0.157 Angle : 0.585 12.282 43787 Z= 0.328 Chirality : 0.043 0.279 5011 Planarity : 0.003 0.034 4558 Dihedral : 25.784 97.227 6814 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 1.55 % Allowed : 9.32 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.15), residues: 3051 helix: 1.46 (0.13), residues: 1596 sheet: 0.99 (0.23), residues: 444 loop : -0.71 (0.18), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 303 TYR 0.014 0.001 TYR D 83 PHE 0.010 0.001 PHE P 248 HIS 0.011 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.16 (31483) covalent geometry : angle 0.58501 / 0.33 (43787) hydrogen bonds : bond 0.04903 / 3.30 ( 1642) hydrogen bonds : angle 4.03647 / 2.90 ( 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 171 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 132 time to evaluate : 0.824 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: 0.9005 (mm-30) cc_final: 0.8600 (tp30) REVERT: A 81 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.7793 (t70) REVERT: A 119 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8870 (pp) REVERT: A 120 MET cc_start: 0.8526 (mmm) cc_final: 0.8020 (mmm) REVERT: B 63 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8460 (mt-10) REVERT: B 84 MET cc_start: 0.9000 (tpp) cc_final: 0.8377 (tpp) REVERT: B 92 ARG cc_start: 0.9205 (OUTLIER) cc_final: 0.8875 (ttp80) REVERT: C 56 GLU cc_start: 0.9080 (tt0) cc_final: 0.8407 (tt0) REVERT: D 64 SER cc_start: 0.9043 (m) cc_final: 0.8717 (t) REVERT: D 71 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8854 (mm-30) REVERT: D 94 ILE cc_start: 0.9588 (mm) cc_final: 0.9338 (tt) REVERT: E 90 MET cc_start: 0.9108 (mmm) cc_final: 0.8776 (mmp) REVERT: E 120 MET cc_start: 0.8411 (mtm) cc_final: 0.8137 (mtm) REVERT: F 84 MET cc_start: 0.9300 (tpp) cc_final: 0.8965 (mmm) REVERT: H 62 MET cc_start: 0.9652 (mmm) cc_final: 0.9426 (mmm) REVERT: H 71 GLU cc_start: 0.9237 (tp30) cc_final: 0.8809 (tm-30) REVERT: H 94 ILE cc_start: 0.9530 (OUTLIER) cc_final: 0.9286 (tt) REVERT: K 161 ASP cc_start: 0.4214 (OUTLIER) cc_final: 0.3981 (t70) REVERT: K 243 MET cc_start: 0.8818 (ptm) cc_final: 0.8244 (mmp) REVERT: M 125 MET cc_start: -0.2241 (pmm) cc_final: -0.2612 (ptp) REVERT: M 158 MET cc_start: 0.4967 (mmm) cc_final: 0.4365 (ttt) REVERT: M 210 MET cc_start: 0.0330 (ppp) cc_final: -0.0377 (ppp) REVERT: M 243 MET cc_start: 0.4410 (ptt) cc_final: 0.4181 (mtt) REVERT: N 158 MET cc_start: 0.4311 (ttm) cc_final: 0.4037 (mtt) REVERT: N 211 MET cc_start: 0.4338 (mmt) cc_final: 0.4050 (tpt) REVERT: O 211 MET cc_start: 0.0322 (mmm) cc_final: -0.0106 (tpt) REVERT: Q 161 ASP cc_start: 0.4778 (OUTLIER) cc_final: 0.3537 (t0) REVERT: Q 248 PHE cc_start: 0.9271 (t80) cc_final: 0.8961 (t80) REVERT: R 125 MET cc_start: 0.8930 (ttp) cc_final: 0.8692 (ppp) REVERT: R 158 MET cc_start: 0.2769 (mmm) cc_final: 0.2324 (mmm) REVERT: S 210 MET cc_start: 0.3564 (ppp) cc_final: 0.3323 (ppp) REVERT: S 211 MET cc_start: -0.0824 (ttm) cc_final: -0.1292 (ttp) REVERT: S 243 MET cc_start: 0.8218 (mmm) cc_final: 0.7532 (tpt) REVERT: S 252 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7846 (mm) outliers start: 39 outliers final: 28 residues processed: 163 average time/residue: 0.1551 time to fit residues: 43.3639 Evaluate side-chains 158 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 90 MET 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 A residue 119 ILE 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 102 LEU Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 34 ILE 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 H residue 94 ILE Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 161 ASP Chi-restraints excluded: chain L residue 223 SER Chi-restraints excluded: chain O residue 34 ASN Chi-restraints excluded: chain O residue 37 ASP Chi-restraints excluded: chain Q residue 161 ASP Chi-restraints excluded: chain Q residue 213 GLU Chi-restraints excluded: chain R residue 309 THR Chi-restraints excluded: chain S residue 34 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 263 optimal weight: 30.0000 chunk 145 optimal weight: 0.9990 chunk 138 optimal weight: 20.0000 chunk 150 optimal weight: 6.9990 chunk 173 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 322 optimal weight: 20.0000 chunk 246 optimal weight: 30.0000 chunk 331 optimal weight: 1.9990 chunk 157 optimal weight: 20.0000 chunk 325 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 31 HIS ** K 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 206 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.078975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.045900 restraints weight = 219612.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.047346 restraints weight = 78772.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.048083 restraints weight = 43310.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.048422 restraints weight = 30290.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.048650 restraints weight = 25025.194| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31483 Z= 0.142 Angle : 0.568 11.272 43787 Z= 0.319 Chirality : 0.042 0.275 5011 Planarity : 0.003 0.033 4558 Dihedral : 25.689 98.788 6814 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 1.71 % Allowed : 9.43 % Favored : 88.85 % 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: 1.06 (0.15), residues: 3051 helix: 1.55 (0.13), residues: 1619 sheet: 1.31 (0.25), residues: 375 loop : -0.86 (0.17), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 42 TYR 0.012 0.001 TYR R 216 PHE 0.013 0.001 PHE Q 259 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 (31483) covalent geometry : angle 0.56804 / 0.32 (43787) hydrogen bonds : bond 0.04629 / 3.12 ( 1642) hydrogen bonds : angle 3.87251 / 2.77 ( 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 177 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 134 time to evaluate : 0.744 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: 0.9060 (mm-30) cc_final: 0.8357 (tp30) REVERT: A 81 ASP cc_start: 0.8728 (OUTLIER) cc_final: 0.7800 (t70) REVERT: A 120 MET cc_start: 0.8501 (mmm) cc_final: 0.8156 (mmm) REVERT: B 63 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8456 (mt-10) REVERT: B 84 MET cc_start: 0.9008 (tpp) cc_final: 0.8516 (tpp) REVERT: B 92 ARG cc_start: 0.9210 (OUTLIER) cc_final: 0.8884 (ttp80) REVERT: C 56 GLU cc_start: 0.9062 (tt0) cc_final: 0.8391 (tt0) REVERT: D 64 SER cc_start: 0.9043 (m) cc_final: 0.8742 (t) REVERT: D 71 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8880 (mm-30) REVERT: D 93 GLU cc_start: 0.9432 (mp0) cc_final: 0.8964 (mp0) REVERT: D 94 ILE cc_start: 0.9580 (mm) cc_final: 0.9326 (tt) REVERT: D 109 HIS cc_start: 0.9406 (OUTLIER) cc_final: 0.9015 (m-70) REVERT: E 39 HIS cc_start: 0.7611 (OUTLIER) cc_final: 0.7209 (t70) REVERT: E 90 MET cc_start: 0.9012 (mmm) cc_final: 0.8701 (mmp) REVERT: E 120 MET cc_start: 0.8439 (mtm) cc_final: 0.8178 (mtm) REVERT: F 63 GLU cc_start: 0.9273 (tt0) cc_final: 0.8705 (tm-30) REVERT: F 84 MET cc_start: 0.9276 (tpp) cc_final: 0.8942 (mmm) REVERT: H 62 MET cc_start: 0.9678 (mmm) cc_final: 0.9340 (mmm) REVERT: H 71 GLU cc_start: 0.9220 (tp30) cc_final: 0.8787 (tm-30) REVERT: H 94 ILE cc_start: 0.9516 (OUTLIER) cc_final: 0.9269 (tt) REVERT: H 105 GLU cc_start: 0.9097 (mp0) cc_final: 0.8824 (pm20) REVERT: K 161 ASP cc_start: 0.3876 (OUTLIER) cc_final: 0.3577 (t70) REVERT: K 243 MET cc_start: 0.8782 (ptm) cc_final: 0.8202 (mmp) REVERT: M 125 MET cc_start: -0.2296 (pmm) cc_final: -0.2642 (ptp) REVERT: M 158 MET cc_start: 0.4951 (mmm) cc_final: 0.4344 (ttt) REVERT: M 210 MET cc_start: 0.0160 (ppp) cc_final: -0.0715 (ppp) REVERT: M 243 MET cc_start: 0.4344 (ptt) cc_final: 0.4118 (mtt) REVERT: N 158 MET cc_start: 0.4383 (ttm) cc_final: 0.4140 (mtt) REVERT: N 211 MET cc_start: 0.4389 (mmt) cc_final: 0.4158 (tpt) REVERT: O 243 MET cc_start: 0.8677 (mmt) cc_final: 0.7722 (tpt) REVERT: Q 161 ASP cc_start: 0.4533 (OUTLIER) cc_final: 0.3561 (t0) REVERT: Q 211 MET cc_start: -0.1026 (ttp) cc_final: -0.2361 (ttp) REVERT: Q 213 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7449 (pm20) REVERT: Q 248 PHE cc_start: 0.9273 (t80) cc_final: 0.8954 (t80) REVERT: R 125 MET cc_start: 0.8944 (ttp) cc_final: 0.8598 (ppp) REVERT: R 158 MET cc_start: 0.2368 (mmm) cc_final: 0.2039 (mmm) REVERT: R 211 MET cc_start: 0.2840 (mmm) cc_final: 0.2267 (mmm) REVERT: S 210 MET cc_start: 0.3765 (ppp) cc_final: 0.3531 (ppp) REVERT: S 211 MET cc_start: -0.0709 (ttm) cc_final: -0.1185 (ttp) REVERT: S 243 MET cc_start: 0.8313 (mmm) cc_final: 0.7630 (tpt) REVERT: S 252 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7847 (mm) outliers start: 43 outliers final: 27 residues processed: 169 average time/residue: 0.1463 time to fit residues: 42.8855 Evaluate side-chains 160 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 124 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 90 MET 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 37 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 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 D residue 102 LEU 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 37 LEU 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 41 VAL 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 223 SER Chi-restraints excluded: chain L residue 223 SER Chi-restraints excluded: chain O residue 34 ASN 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 201 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: 20.0000 chunk 178 optimal weight: 30.0000 chunk 90 optimal weight: 20.0000 chunk 83 optimal weight: 30.0000 chunk 325 optimal weight: 20.0000 chunk 228 optimal weight: 10.0000 chunk 327 optimal weight: 9.9990 chunk 195 optimal weight: 40.0000 chunk 80 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 2.9990 overall best weight: 10.5996 ------------------------------------------------------------------------------- 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 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.076085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.042898 restraints weight = 223193.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.044261 restraints weight = 81325.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.045011 restraints weight = 45477.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.045406 restraints weight = 31990.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.045580 restraints weight = 25924.657| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.139 31483 Z= 0.343 Angle : 0.799 18.610 43787 Z= 0.426 Chirality : 0.048 0.284 5011 Planarity : 0.005 0.082 4558 Dihedral : 25.866 104.308 6814 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.59 % Allowed : 9.32 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.15), residues: 3051 helix: 0.90 (0.13), residues: 1589 sheet: 1.22 (0.25), residues: 384 loop : -0.69 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 17 TYR 0.023 0.002 TYR H 40 PHE 0.022 0.002 PHE C 25 HIS 0.011 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00674 / 0.34 (31483) covalent geometry : angle 0.79920 / 0.43 (43787) hydrogen bonds : bond 0.08415 / 5.73 ( 1642) hydrogen bonds : angle 4.72274 / 3.38 ( 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: 65 poor density : 113 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8487 (tp30) REVERT: A 81 ASP cc_start: 0.8879 (OUTLIER) cc_final: 0.8003 (t70) REVERT: A 94 GLU cc_start: 0.9401 (OUTLIER) cc_final: 0.8803 (tp30) REVERT: A 120 MET cc_start: 0.8481 (mmm) cc_final: 0.8077 (mmm) REVERT: B 84 MET cc_start: 0.9308 (tpp) cc_final: 0.8839 (tpp) REVERT: B 92 ARG cc_start: 0.9230 (OUTLIER) cc_final: 0.8849 (ttp80) REVERT: D 64 SER cc_start: 0.9099 (m) cc_final: 0.8747 (t) REVERT: D 71 GLU cc_start: 0.9321 (mm-30) cc_final: 0.9099 (mm-30) REVERT: D 94 ILE cc_start: 0.9596 (OUTLIER) cc_final: 0.9361 (tt) REVERT: D 109 HIS cc_start: 0.9382 (OUTLIER) cc_final: 0.9157 (m-70) REVERT: E 39 HIS cc_start: 0.7858 (OUTLIER) cc_final: 0.7430 (t70) REVERT: E 120 MET cc_start: 0.8770 (mtm) cc_final: 0.8495 (mtm) REVERT: E 129 ARG cc_start: 0.9432 (OUTLIER) cc_final: 0.8995 (tmm-80) REVERT: F 63 GLU cc_start: 0.9391 (tt0) cc_final: 0.8954 (tm-30) REVERT: H 59 MET cc_start: 0.9548 (tpp) cc_final: 0.9321 (tpp) REVERT: H 62 MET cc_start: 0.9660 (mmm) cc_final: 0.9383 (mmm) REVERT: H 94 ILE cc_start: 0.9584 (OUTLIER) cc_final: 0.9360 (tt) REVERT: K 161 ASP cc_start: 0.3923 (OUTLIER) cc_final: 0.3542 (t70) REVERT: K 243 MET cc_start: 0.8824 (ptm) cc_final: 0.8248 (mmp) REVERT: M 125 MET cc_start: -0.2225 (pmm) cc_final: -0.2483 (ptp) REVERT: M 158 MET cc_start: 0.4306 (mmm) cc_final: 0.3834 (ttt) REVERT: M 210 MET cc_start: -0.0076 (ppp) cc_final: -0.0918 (ppp) REVERT: M 243 MET cc_start: 0.4257 (ptt) cc_final: 0.4007 (mtt) REVERT: N 211 MET cc_start: 0.4344 (mmt) cc_final: 0.3780 (mmm) REVERT: O 211 MET cc_start: -0.0382 (tpt) cc_final: -0.0878 (tpt) REVERT: Q 161 ASP cc_start: 0.3973 (OUTLIER) cc_final: 0.3068 (t0) REVERT: Q 211 MET cc_start: -0.0715 (ttp) cc_final: -0.2079 (ttp) REVERT: Q 213 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7704 (pm20) REVERT: Q 248 PHE cc_start: 0.9246 (t80) cc_final: 0.8961 (t80) REVERT: R 125 MET cc_start: 0.8927 (ttp) cc_final: 0.8587 (ppp) REVERT: S 210 MET cc_start: 0.3800 (ppp) cc_final: 0.3579 (ppp) REVERT: S 211 MET cc_start: -0.0944 (ttm) cc_final: -0.1399 (ttp) REVERT: S 243 MET cc_start: 0.8378 (mmm) cc_final: 0.7712 (tpt) REVERT: S 252 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7856 (mm) outliers start: 65 outliers final: 38 residues processed: 169 average time/residue: 0.1467 time to fit residues: 42.3795 Evaluate side-chains 160 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 110 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP 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 34 ILE 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 102 LEU 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 E residue 129 ARG Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 37 LEU 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 H residue 41 VAL 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 223 SER Chi-restraints excluded: chain K residue 248 PHE Chi-restraints excluded: chain K residue 266 THR Chi-restraints excluded: chain L residue 223 SER Chi-restraints excluded: chain O residue 34 ASN Chi-restraints excluded: chain O residue 37 ASP Chi-restraints excluded: chain O residue 201 THR Chi-restraints excluded: chain O residue 219 LEU Chi-restraints excluded: chain P residue 326 MET 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 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: 20.0000 chunk 289 optimal weight: 6.9990 chunk 226 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 170 optimal weight: 8.9990 chunk 214 optimal weight: 6.9990 chunk 175 optimal weight: 5.9990 chunk 326 optimal weight: 9.9990 chunk 325 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 129 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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** M 114 GLN ** N 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 206 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.077723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.044567 restraints weight = 221946.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.045995 restraints weight = 79910.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.046723 restraints weight = 43870.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.047109 restraints weight = 30903.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.047255 restraints weight = 25173.875| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31483 Z= 0.187 Angle : 0.628 15.107 43787 Z= 0.347 Chirality : 0.044 0.292 5011 Planarity : 0.003 0.044 4558 Dihedral : 25.898 104.850 6814 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.71 % Allowed : 10.27 % Favored : 88.02 % 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: 0.90 (0.15), residues: 3051 helix: 1.25 (0.13), residues: 1608 sheet: 1.00 (0.25), residues: 396 loop : -0.51 (0.18), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 42 TYR 0.022 0.001 TYR O 232 PHE 0.012 0.001 PHE C 25 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.19 (31483) covalent geometry : angle 0.62784 / 0.35 (43787) hydrogen bonds : bond 0.05334 / 3.62 ( 1642) hydrogen bonds : angle 4.17944 / 2.99 ( 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 165 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 122 time to evaluate : 0.839 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: 0.9173 (mm-30) cc_final: 0.8476 (tp30) REVERT: A 120 MET cc_start: 0.8462 (mmm) cc_final: 0.8038 (mmm) REVERT: B 84 MET cc_start: 0.9186 (tpp) cc_final: 0.8758 (tpp) REVERT: B 92 ARG cc_start: 0.9226 (OUTLIER) cc_final: 0.8887 (ttp80) REVERT: D 64 SER cc_start: 0.9079 (m) cc_final: 0.8761 (t) REVERT: D 71 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8926 (mm-30) REVERT: D 93 GLU cc_start: 0.9443 (mp0) cc_final: 0.8968 (mp0) REVERT: D 94 ILE cc_start: 0.9582 (mm) cc_final: 0.9335 (tt) REVERT: D 109 HIS cc_start: 0.9368 (OUTLIER) cc_final: 0.9099 (m-70) REVERT: E 39 HIS cc_start: 0.7903 (OUTLIER) cc_final: 0.7463 (t70) REVERT: E 120 MET cc_start: 0.8624 (mtm) cc_final: 0.8085 (mtm) REVERT: F 63 GLU cc_start: 0.9317 (tt0) cc_final: 0.8760 (tm-30) REVERT: H 62 MET cc_start: 0.9672 (mmm) cc_final: 0.9314 (mmm) REVERT: H 94 ILE cc_start: 0.9533 (OUTLIER) cc_final: 0.9290 (tt) REVERT: H 105 GLU cc_start: 0.8987 (mp0) cc_final: 0.8740 (pm20) REVERT: K 161 ASP cc_start: 0.3830 (OUTLIER) cc_final: 0.3473 (t70) REVERT: K 243 MET cc_start: 0.8809 (ptm) cc_final: 0.8231 (mmp) REVERT: M 125 MET cc_start: -0.2303 (pmm) cc_final: -0.2568 (ptp) REVERT: M 158 MET cc_start: 0.4454 (mmm) cc_final: 0.3967 (ttt) REVERT: M 210 MET cc_start: -0.0035 (ppp) cc_final: -0.0855 (ppp) REVERT: M 243 MET cc_start: 0.4434 (ptt) cc_final: 0.4212 (mtt) REVERT: O 211 MET cc_start: -0.0515 (tpt) cc_final: -0.1428 (tpt) REVERT: Q 125 MET cc_start: 0.8484 (ptt) cc_final: 0.8264 (ppp) REVERT: Q 161 ASP cc_start: 0.4023 (OUTLIER) cc_final: 0.3163 (t0) REVERT: Q 211 MET cc_start: -0.0333 (ttp) cc_final: -0.1671 (ttp) REVERT: Q 213 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7660 (pm20) REVERT: Q 248 PHE cc_start: 0.9263 (t80) cc_final: 0.8969 (t80) REVERT: R 125 MET cc_start: 0.8865 (ttp) cc_final: 0.8522 (ppp) REVERT: R 211 MET cc_start: 0.2715 (mmm) cc_final: 0.1356 (mmm) REVERT: S 158 MET cc_start: 0.3378 (mmm) cc_final: 0.2775 (mmm) REVERT: S 210 MET cc_start: 0.3787 (ppp) cc_final: 0.3532 (ppp) REVERT: S 211 MET cc_start: -0.0733 (ttm) cc_final: -0.1212 (ttp) REVERT: S 243 MET cc_start: 0.8377 (mmm) cc_final: 0.7715 (tpt) REVERT: S 252 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7861 (mm) REVERT: S 326 MET cc_start: 0.6820 (tpt) cc_final: 0.6278 (pmm) outliers start: 43 outliers final: 31 residues processed: 157 average time/residue: 0.1516 time to fit residues: 41.4256 Evaluate side-chains 155 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 116 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET 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 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 102 LEU 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 90 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain H residue 41 VAL 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 223 SER Chi-restraints excluded: chain K residue 266 THR Chi-restraints excluded: chain L residue 223 SER Chi-restraints excluded: chain O residue 34 ASN Chi-restraints excluded: chain O residue 37 ASP Chi-restraints excluded: chain O residue 201 THR 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 201 THR Chi-restraints excluded: chain S residue 252 LEU 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: 20.0000 chunk 120 optimal weight: 5.9990 chunk 320 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 chunk 126 optimal weight: 6.9990 chunk 258 optimal weight: 50.0000 chunk 7 optimal weight: 0.9980 chunk 154 optimal weight: 8.9990 chunk 283 optimal weight: 6.9990 chunk 284 optimal weight: 50.0000 overall best weight: 4.3786 ------------------------------------------------------------------------------- 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 244 HIS ** 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 = 0.4055 r_free = 0.4055 target = 0.078085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.046468 restraints weight = 214718.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.047866 restraints weight = 74880.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.048477 restraints weight = 40711.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.048849 restraints weight = 28385.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.049037 restraints weight = 23390.345| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31483 Z= 0.167 Angle : 0.614 13.820 43787 Z= 0.338 Chirality : 0.043 0.276 5011 Planarity : 0.003 0.049 4558 Dihedral : 25.810 105.081 6814 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 1.79 % Allowed : 10.11 % Favored : 88.10 % 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: 1.14 (0.15), residues: 3051 helix: 1.51 (0.13), residues: 1587 sheet: 1.26 (0.26), residues: 381 loop : -0.52 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 83 TYR 0.020 0.001 TYR O 159 PHE 0.016 0.001 PHE O 248 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.17 (31483) covalent geometry : angle 0.61387 / 0.34 (43787) hydrogen bonds : bond 0.05130 / 3.49 ( 1642) hydrogen bonds : angle 4.01152 / 2.88 ( 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 172 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 127 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8457 (tp30) REVERT: A 94 GLU cc_start: 0.9285 (OUTLIER) cc_final: 0.8728 (tp30) REVERT: A 120 MET cc_start: 0.8430 (mmm) cc_final: 0.8015 (mmm) REVERT: B 84 MET cc_start: 0.9114 (tpp) cc_final: 0.8668 (tpp) REVERT: B 92 ARG cc_start: 0.9207 (OUTLIER) cc_final: 0.8890 (ttp80) REVERT: D 64 SER cc_start: 0.9049 (m) cc_final: 0.8722 (t) REVERT: D 71 GLU cc_start: 0.9216 (mm-30) cc_final: 0.8941 (mm-30) REVERT: D 93 GLU cc_start: 0.9447 (mp0) cc_final: 0.9012 (mp0) REVERT: D 94 ILE cc_start: 0.9604 (mm) cc_final: 0.9350 (tt) REVERT: E 39 HIS cc_start: 0.7902 (OUTLIER) cc_final: 0.7507 (t70) REVERT: E 90 MET cc_start: 0.9121 (mmm) cc_final: 0.8838 (mmp) REVERT: E 120 MET cc_start: 0.8646 (mtm) cc_final: 0.8190 (mtm) REVERT: F 63 GLU cc_start: 0.9308 (tt0) cc_final: 0.8754 (tm-30) REVERT: H 62 MET cc_start: 0.9677 (mmm) cc_final: 0.9335 (mmm) REVERT: H 94 ILE cc_start: 0.9541 (OUTLIER) cc_final: 0.9308 (tt) REVERT: H 105 GLU cc_start: 0.9054 (mp0) cc_final: 0.8810 (pm20) REVERT: K 161 ASP cc_start: 0.3702 (OUTLIER) cc_final: 0.3341 (t70) REVERT: K 243 MET cc_start: 0.8798 (ptm) cc_final: 0.8189 (mmp) REVERT: M 125 MET cc_start: -0.2195 (pmm) cc_final: -0.2449 (ptp) REVERT: M 158 MET cc_start: 0.4318 (mmm) cc_final: 0.3844 (ttt) REVERT: M 210 MET cc_start: -0.0177 (ppp) cc_final: -0.0967 (ppp) REVERT: M 243 MET cc_start: 0.4417 (ptt) cc_final: 0.4185 (mtt) REVERT: O 211 MET cc_start: -0.1118 (tpt) cc_final: -0.1486 (tpt) REVERT: Q 125 MET cc_start: 0.8469 (ptt) cc_final: 0.8242 (ppp) REVERT: Q 161 ASP cc_start: 0.4241 (OUTLIER) cc_final: 0.3377 (t70) REVERT: Q 211 MET cc_start: -0.0667 (ttp) cc_final: -0.1921 (ttp) REVERT: Q 213 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7618 (pm20) REVERT: Q 248 PHE cc_start: 0.9296 (t80) cc_final: 0.9012 (t80) REVERT: R 125 MET cc_start: 0.8856 (ttp) cc_final: 0.8490 (ppp) REVERT: R 158 MET cc_start: 0.3992 (tpp) cc_final: 0.2914 (tpp) REVERT: S 158 MET cc_start: 0.3315 (mmm) cc_final: 0.2751 (mmm) REVERT: S 210 MET cc_start: 0.3827 (ppp) cc_final: 0.3579 (ppp) REVERT: S 211 MET cc_start: -0.1029 (ttm) cc_final: -0.1450 (ttp) REVERT: S 243 MET cc_start: 0.8447 (mmm) cc_final: 0.7807 (tpt) REVERT: S 252 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7889 (mm) outliers start: 45 outliers final: 35 residues processed: 166 average time/residue: 0.1753 time to fit residues: 50.2873 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 : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 102 LEU Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain H residue 41 VAL 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 223 SER Chi-restraints excluded: chain K residue 266 THR Chi-restraints excluded: chain L residue 223 SER Chi-restraints excluded: chain O residue 34 ASN Chi-restraints excluded: chain O residue 37 ASP Chi-restraints excluded: chain O residue 201 THR Chi-restraints excluded: chain P residue 326 MET 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 311 ILE 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 201 THR Chi-restraints excluded: chain S residue 252 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 153 optimal weight: 10.0000 chunk 262 optimal weight: 50.0000 chunk 309 optimal weight: 6.9990 chunk 167 optimal weight: 8.9990 chunk 70 optimal weight: 7.9990 chunk 273 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 166 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 93 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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** O 244 HIS ** P 244 HIS ** 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 = 0.4034 r_free = 0.4034 target = 0.077584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.045817 restraints weight = 213287.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.047065 restraints weight = 74585.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.047778 restraints weight = 40761.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.048161 restraints weight = 28510.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.048336 restraints weight = 23431.783| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 31483 Z= 0.197 Angle : 0.637 14.566 43787 Z= 0.349 Chirality : 0.043 0.276 5011 Planarity : 0.004 0.052 4558 Dihedral : 25.780 106.030 6814 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.75 % Allowed : 10.59 % Favored : 87.66 % 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: 1.35 (0.13), residues: 1605 sheet: 1.05 (0.26), residues: 393 loop : -0.46 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 19 TYR 0.031 0.001 TYR F 88 PHE 0.023 0.002 PHE O 248 HIS 0.008 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.20 (31483) covalent geometry : angle 0.63741 / 0.35 (43787) hydrogen bonds : bond 0.05373 / 3.66 ( 1642) hydrogen bonds : angle 4.12305 / 2.96 ( 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: 44 poor density : 123 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8505 (tp30) REVERT: A 94 GLU cc_start: 0.9283 (OUTLIER) cc_final: 0.8708 (tp30) REVERT: A 120 MET cc_start: 0.8465 (mmm) cc_final: 0.8043 (mmm) REVERT: B 84 MET cc_start: 0.9136 (tpp) cc_final: 0.8702 (tpp) REVERT: B 92 ARG cc_start: 0.9212 (OUTLIER) cc_final: 0.8893 (ttp80) REVERT: D 64 SER cc_start: 0.9055 (m) cc_final: 0.8725 (t) REVERT: D 71 GLU cc_start: 0.9234 (mm-30) cc_final: 0.8992 (mm-30) REVERT: D 93 GLU cc_start: 0.9437 (mp0) cc_final: 0.8974 (mp0) REVERT: D 94 ILE cc_start: 0.9611 (mm) cc_final: 0.9364 (tt) REVERT: E 39 HIS cc_start: 0.7926 (OUTLIER) cc_final: 0.7535 (t70) REVERT: E 90 MET cc_start: 0.9108 (mmm) cc_final: 0.8807 (mmp) REVERT: E 120 MET cc_start: 0.8660 (mtm) cc_final: 0.8190 (mtm) REVERT: F 63 GLU cc_start: 0.9351 (tt0) cc_final: 0.8798 (tm-30) REVERT: H 59 MET cc_start: 0.9548 (tpp) cc_final: 0.9319 (tpp) REVERT: H 62 MET cc_start: 0.9689 (mmm) cc_final: 0.9448 (mmm) REVERT: H 94 ILE cc_start: 0.9521 (OUTLIER) cc_final: 0.9268 (tt) REVERT: H 105 GLU cc_start: 0.8987 (mp0) cc_final: 0.8708 (pm20) REVERT: K 161 ASP cc_start: 0.3830 (OUTLIER) cc_final: 0.3475 (t70) REVERT: K 243 MET cc_start: 0.8801 (ptm) cc_final: 0.8187 (mmp) REVERT: M 125 MET cc_start: -0.2158 (pmm) cc_final: -0.2413 (ptp) REVERT: M 158 MET cc_start: 0.4388 (mmm) cc_final: 0.3913 (ttp) REVERT: M 210 MET cc_start: -0.0229 (ppp) cc_final: -0.0892 (ppp) REVERT: M 243 MET cc_start: 0.4343 (ptt) cc_final: 0.4121 (mtt) REVERT: N 211 MET cc_start: 0.5391 (tpt) cc_final: 0.3976 (mmm) REVERT: O 211 MET cc_start: -0.1381 (tpt) cc_final: -0.1725 (tpt) REVERT: O 243 MET cc_start: 0.8689 (mmt) cc_final: 0.7593 (tpt) REVERT: Q 125 MET cc_start: 0.8533 (ptt) cc_final: 0.8298 (ppp) REVERT: Q 161 ASP cc_start: 0.4359 (OUTLIER) cc_final: 0.3419 (t70) REVERT: Q 211 MET cc_start: -0.0732 (ttp) cc_final: -0.1951 (ttp) REVERT: Q 213 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7597 (pm20) REVERT: Q 248 PHE cc_start: 0.9302 (t80) cc_final: 0.9024 (t80) REVERT: R 125 MET cc_start: 0.8841 (ttp) cc_final: 0.8467 (ppp) REVERT: R 158 MET cc_start: 0.3990 (tpp) cc_final: 0.3266 (tpp) REVERT: S 158 MET cc_start: 0.3497 (mmm) cc_final: 0.2964 (mmm) REVERT: S 210 MET cc_start: 0.3890 (ppp) cc_final: 0.3640 (ppp) REVERT: S 211 MET cc_start: -0.1068 (ttm) cc_final: -0.1467 (ttp) REVERT: S 243 MET cc_start: 0.8467 (mmm) cc_final: 0.7833 (tpt) REVERT: S 252 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7904 (mm) REVERT: S 326 MET cc_start: 0.7006 (tpt) cc_final: 0.6680 (pmm) outliers start: 44 outliers final: 33 residues processed: 162 average time/residue: 0.1608 time to fit residues: 45.3751 Evaluate side-chains 159 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 118 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 102 LEU Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 30 THR 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 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 223 SER Chi-restraints excluded: chain K residue 266 THR Chi-restraints excluded: chain L residue 223 SER Chi-restraints excluded: chain O residue 34 ASN Chi-restraints excluded: chain O residue 37 ASP Chi-restraints excluded: chain O residue 201 THR Chi-restraints excluded: chain P residue 326 MET 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 311 ILE 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 201 THR Chi-restraints excluded: chain S residue 252 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 257 optimal weight: 0.9980 chunk 87 optimal weight: 30.0000 chunk 163 optimal weight: 30.0000 chunk 39 optimal weight: 0.9980 chunk 186 optimal weight: 9.9990 chunk 135 optimal weight: 30.0000 chunk 95 optimal weight: 20.0000 chunk 224 optimal weight: 8.9990 chunk 75 optimal weight: 20.0000 chunk 59 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 overall best weight: 3.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 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** ** O 244 HIS ** 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 = 0.4049 r_free = 0.4049 target = 0.077987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.045302 restraints weight = 220043.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.046694 restraints weight = 79117.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.047415 restraints weight = 43883.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.047850 restraints weight = 30987.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.047925 restraints weight = 25249.081| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 31483 Z= 0.153 Angle : 0.604 13.667 43787 Z= 0.334 Chirality : 0.043 0.274 5011 Planarity : 0.003 0.050 4558 Dihedral : 25.722 106.476 6814 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.63 % Allowed : 10.87 % 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: 1.12 (0.15), residues: 3051 helix: 1.45 (0.13), residues: 1605 sheet: 1.04 (0.26), residues: 393 loop : -0.42 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 250 TYR 0.061 0.001 TYR H 83 PHE 0.031 0.001 PHE O 248 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.15 (31483) covalent geometry : angle 0.60370 / 0.33 (43787) hydrogen bonds : bond 0.04766 / 3.24 ( 1642) hydrogen bonds : angle 3.95409 / 2.84 ( 4440) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10280.22 seconds wall clock time: 175 minutes 46.79 seconds (10546.79 seconds total)