Starting phenix.real_space_refine on Wed May 28 01:03:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jnd_36442/05_2025/8jnd_36442.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jnd_36442/05_2025/8jnd_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_36442/05_2025/8jnd_36442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jnd_36442/05_2025/8jnd_36442.map" model { file = "/net/cci-nas-00/data/ceres_data/8jnd_36442/05_2025/8jnd_36442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jnd_36442/05_2025/8jnd_36442.cif" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 309 5.49 5 S 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 16.71, per 1000 atoms: 0.55 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: 7.20 Conformation dependent library (CDL) restraints added in 3.3 seconds 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5702 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 19 sheets defined 57.7% alpha, 14.1% beta 156 base pairs and 269 stacking pairs defined. Time for finding SS restraints: 11.88 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: 11.78 Time building geometry restraints manager: 8.57 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=" CZ ARG P 150 " pdb=" NH2 ARG P 150 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.48e+00 bond pdb=" C GLY P 151 " pdb=" O GLY P 151 " ideal model delta sigma weight residual 1.238 1.207 0.030 1.42e-02 4.96e+03 4.60e+00 bond pdb=" P DC I 151 " pdb=" OP2 DC I 151 " ideal model delta sigma weight residual 1.480 1.519 -0.039 2.00e-02 2.50e+03 3.88e+00 bond pdb=" P DT J 14 " pdb=" OP1 DT J 14 " ideal model delta sigma weight residual 1.480 1.519 -0.039 2.00e-02 2.50e+03 3.81e+00 bond pdb=" P DA I 146 " pdb=" OP2 DA I 146 " ideal model delta sigma weight residual 1.480 1.519 -0.039 2.00e-02 2.50e+03 3.80e+00 ... (remaining 31478 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 43096 2.53 - 5.07: 600 5.07 - 7.60: 71 7.60 - 10.13: 18 10.13 - 12.67: 2 Bond angle restraints: 43787 Sorted by residual: angle pdb=" C4' DA I 153 " pdb=" C3' DA I 153 " pdb=" O3' DA I 153 " ideal model delta sigma weight residual 110.00 117.49 -7.49 1.50e+00 4.44e-01 2.49e+01 angle pdb=" C ILE P 102 " pdb=" N THR P 103 " pdb=" CA THR P 103 " ideal model delta sigma weight residual 121.05 127.30 -6.25 1.43e+00 4.89e-01 1.91e+01 angle pdb=" O3' DA I 147 " pdb=" P DC I 148 " pdb=" O5' DC I 148 " ideal model delta sigma weight residual 104.00 98.14 5.86 1.50e+00 4.44e-01 1.52e+01 angle pdb=" C3' DA I 153 " pdb=" O3' DA I 153 " pdb=" P DC I 154 " ideal model delta sigma weight residual 120.20 114.37 5.83 1.50e+00 4.44e-01 1.51e+01 angle pdb=" CA GLY P 151 " pdb=" C GLY P 151 " pdb=" N GLY P 152 " ideal model delta sigma weight residual 118.48 122.99 -4.51 1.17e+00 7.31e-01 1.49e+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 - 0.113: 4865 0.113 - 0.225: 136 0.225 - 0.338: 4 0.338 - 0.451: 0 0.451 - 0.564: 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 2.35 -2.91 -0.56 2.00e-01 2.50e+01 7.94e+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 2.35 -2.91 -0.56 2.00e-01 2.50e+01 7.84e+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 2.35 -2.90 -0.56 2.00e-01 2.50e+01 7.76e+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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.240 Check model and map are aligned: 0.230 Set scattering table: 0.300 Process input model: 72.080 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 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 0.040 31483 Z= 0.277 Angle : 0.803 12.666 43787 Z= 0.460 Chirality : 0.051 0.564 5011 Planarity : 0.006 0.064 4558 Dihedral : 21.262 102.065 12549 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 12.97 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (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 HIS 0.011 0.001 HIS A 39 PHE 0.027 0.002 PHE E 78 TYR 0.025 0.002 TYR S 54 ARG 0.017 0.002 ARG R 299 Details of bonding type rmsd hydrogen bonds : bond 0.14945 ( 1642) hydrogen bonds : angle 5.89333 ( 4440) covalent geometry : bond 0.00581 (31483) covalent geometry : angle 0.80265 (43787) *********************** 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 : 3.134 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: 0.7840 (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: -0.0678 (mmm) REVERT: L 326 MET cc_start: 0.2790 (tpt) cc_final: 0.2469 (tpt) REVERT: M 125 MET cc_start: -0.1932 (pmm) cc_final: -0.2551 (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: 0.6450 (ptt) REVERT: Q 248 PHE cc_start: 0.9258 (t80) cc_final: 0.8919 (t80) outliers start: 1 outliers final: 0 residues processed: 299 average time/residue: 0.4451 time to fit residues: 206.9494 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 : 3.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 282 optimal weight: 30.0000 chunk 253 optimal weight: 9.9990 chunk 140 optimal weight: 20.0000 chunk 86 optimal weight: 10.0000 chunk 171 optimal weight: 7.9990 chunk 135 optimal weight: 40.0000 chunk 262 optimal weight: 7.9990 chunk 101 optimal weight: 0.0670 chunk 159 optimal weight: 5.9990 chunk 195 optimal weight: 50.0000 chunk 304 optimal weight: 20.0000 overall best weight: 6.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS G 73 ASN H 84 ASN K 23 GLN K 47 HIS ** K 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 GLN N 47 HIS O 23 GLN O 47 HIS P 23 GLN P 47 HIS P 244 HIS Q 23 GLN Q 47 HIS Q 62 ASN R 206 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.096135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.063539 restraints weight = 239380.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.063909 restraints weight = 96746.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.064039 restraints weight = 49149.405| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 31483 Z= 0.274 Angle : 0.661 14.914 43787 Z= 0.372 Chirality : 0.042 0.158 5011 Planarity : 0.004 0.056 4558 Dihedral : 25.610 92.710 6814 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 1.00 % Allowed : 5.61 % Favored : 93.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.15), residues: 3051 helix: 1.17 (0.13), residues: 1584 sheet: 0.92 (0.22), residues: 444 loop : -0.60 (0.18), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.002 HIS B 75 PHE 0.015 0.002 PHE L 248 TYR 0.025 0.002 TYR S 232 ARG 0.008 0.001 ARG M 150 Details of bonding type rmsd hydrogen bonds : bond 0.05968 ( 1642) hydrogen bonds : angle 4.59739 ( 4440) covalent geometry : bond 0.00593 (31483) covalent geometry : angle 0.66086 (43787) *********************** 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 184 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 2.874 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: 0.9451 (mt-10) cc_final: 0.9213 (mm-30) REVERT: A 81 ASP cc_start: 0.8717 (t0) cc_final: 0.7928 (t70) REVERT: A 120 MET cc_start: 0.8231 (mmm) cc_final: 0.7931 (mmm) REVERT: B 63 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8635 (mt-10) REVERT: B 84 MET cc_start: 0.9070 (mmm) cc_final: 0.8707 (tpp) REVERT: C 56 GLU cc_start: 0.9044 (tt0) cc_final: 0.8383 (tt0) REVERT: D 62 MET cc_start: 0.9581 (mmm) cc_final: 0.9303 (mmp) REVERT: D 64 SER cc_start: 0.9056 (m) cc_final: 0.8714 (t) REVERT: D 71 GLU cc_start: 0.9234 (mm-30) cc_final: 0.8856 (mm-30) REVERT: D 106 LEU cc_start: 0.9627 (mt) cc_final: 0.9398 (mt) REVERT: E 120 MET cc_start: 0.8528 (mtm) cc_final: 0.8273 (mtm) REVERT: F 63 GLU cc_start: 0.9326 (tt0) cc_final: 0.8643 (tp30) REVERT: G 64 GLU cc_start: 0.9200 (tp30) cc_final: 0.8953 (tm-30) REVERT: H 62 MET cc_start: 0.9673 (mmm) cc_final: 0.9345 (mmm) REVERT: H 94 ILE cc_start: 0.9627 (mm) cc_final: 0.9395 (tt) REVERT: K 294 HIS cc_start: 0.3807 (t70) cc_final: 0.3592 (t70) REVERT: L 211 MET cc_start: 0.1277 (mtt) cc_final: 0.0930 (mtt) REVERT: M 125 MET cc_start: -0.2563 (pmm) cc_final: -0.3021 (ptp) REVERT: M 158 MET cc_start: 0.4990 (mmm) cc_final: 0.4350 (ttt) REVERT: M 210 MET cc_start: 0.1795 (ppp) cc_final: 0.1045 (ppp) REVERT: O 158 MET cc_start: 0.5879 (tpp) cc_final: 0.5599 (ptm) REVERT: O 210 MET cc_start: 0.3135 (ptt) cc_final: 0.2242 (ptt) REVERT: P 211 MET cc_start: 0.2029 (mmm) cc_final: 0.1448 (tpt) REVERT: Q 248 PHE cc_start: 0.8943 (t80) cc_final: 0.8500 (t80) REVERT: S 210 MET cc_start: 0.4540 (ptt) cc_final: 0.4066 (ppp) REVERT: S 211 MET cc_start: 0.3724 (ttm) cc_final: 0.3030 (ttp) outliers start: 25 outliers final: 15 residues processed: 177 average time/residue: 0.3891 time to fit residues: 113.9965 Evaluate side-chains 142 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 2.841 ------------------------------------------------------------------------------- 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 46 ILE Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 81 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 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 P residue 326 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 126 optimal weight: 40.0000 chunk 125 optimal weight: 20.0000 chunk 315 optimal weight: 30.0000 chunk 301 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 295 optimal weight: 8.9990 chunk 255 optimal weight: 6.9990 chunk 214 optimal weight: 40.0000 chunk 179 optimal weight: 10.0000 chunk 160 optimal weight: 10.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 31 HIS ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 GLN K 294 HIS L 101 GLN L 206 GLN M 114 GLN M 206 GLN N 23 GLN ** N 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 206 GLN Q 114 GLN S 206 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.076704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.043629 restraints weight = 222250.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.044790 restraints weight = 84511.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.045468 restraints weight = 45536.641| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 31483 Z= 0.322 Angle : 0.704 16.802 43787 Z= 0.390 Chirality : 0.043 0.156 5011 Planarity : 0.005 0.064 4558 Dihedral : 25.555 100.153 6814 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.83 % Allowed : 7.17 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.15), residues: 3051 helix: 1.00 (0.13), residues: 1577 sheet: 1.23 (0.23), residues: 441 loop : -0.43 (0.18), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS F 75 PHE 0.019 0.002 PHE C 25 TYR 0.025 0.002 TYR D 83 ARG 0.007 0.001 ARG F 35 Details of bonding type rmsd hydrogen bonds : bond 0.06653 ( 1642) hydrogen bonds : angle 4.66442 ( 4440) covalent geometry : bond 0.00696 (31483) covalent geometry : angle 0.70363 (43787) *********************** 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 181 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 135 time to evaluate : 2.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8873 (OUTLIER) cc_final: 0.7923 (t70) REVERT: A 120 MET cc_start: 0.8380 (mmm) cc_final: 0.8118 (mmm) REVERT: B 88 TYR cc_start: 0.9155 (m-10) cc_final: 0.8812 (m-10) REVERT: B 92 ARG cc_start: 0.9288 (OUTLIER) cc_final: 0.8688 (ttp80) REVERT: D 64 SER cc_start: 0.9079 (m) cc_final: 0.8709 (t) REVERT: D 71 GLU cc_start: 0.9277 (mm-30) cc_final: 0.9008 (mm-30) REVERT: E 120 MET cc_start: 0.8806 (mtm) cc_final: 0.8490 (mtm) REVERT: F 63 GLU cc_start: 0.9387 (tt0) cc_final: 0.8970 (tm-30) REVERT: G 64 GLU cc_start: 0.9130 (tp30) cc_final: 0.8715 (tp30) REVERT: H 61 ILE cc_start: 0.9427 (OUTLIER) cc_final: 0.9204 (tp) REVERT: H 62 MET cc_start: 0.9644 (mmm) cc_final: 0.9302 (mmm) REVERT: H 71 GLU cc_start: 0.9329 (tp30) cc_final: 0.9122 (tm-30) REVERT: H 93 GLU cc_start: 0.9112 (mp0) cc_final: 0.8798 (mp0) REVERT: H 94 ILE cc_start: 0.9583 (OUTLIER) cc_final: 0.9312 (tt) REVERT: M 125 MET cc_start: -0.2277 (pmm) cc_final: -0.2513 (ptp) REVERT: M 158 MET cc_start: 0.4750 (mmm) cc_final: 0.4297 (ttt) REVERT: M 210 MET cc_start: 0.0195 (ppp) cc_final: -0.0469 (ppp) REVERT: N 211 MET cc_start: 0.3521 (OUTLIER) cc_final: 0.1763 (mmm) REVERT: O 210 MET cc_start: 0.2035 (ptt) cc_final: 0.0957 (ppp) REVERT: O 243 MET cc_start: 0.8758 (mmt) cc_final: 0.7840 (tpt) REVERT: P 205 TYR cc_start: 0.8989 (t80) cc_final: 0.8550 (t80) REVERT: P 211 MET cc_start: -0.2096 (mmm) cc_final: -0.2332 (tpt) REVERT: Q 211 MET cc_start: 0.0851 (ttm) cc_final: 0.0483 (ttp) REVERT: Q 248 PHE cc_start: 0.9300 (t80) cc_final: 0.9007 (t80) REVERT: R 211 MET cc_start: 0.2742 (mmm) cc_final: 0.2541 (mmm) REVERT: R 235 ARG cc_start: 0.4939 (mmt180) cc_final: 0.3791 (mmp80) REVERT: S 37 ASP cc_start: 0.3158 (OUTLIER) cc_final: 0.2596 (m-30) REVERT: S 211 MET cc_start: -0.0922 (ttm) cc_final: -0.2037 (tpt) REVERT: S 243 MET cc_start: 0.8311 (mmm) cc_final: 0.7627 (tpt) outliers start: 46 outliers final: 23 residues processed: 172 average time/residue: 0.3674 time to fit residues: 106.5046 Evaluate side-chains 152 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 2.882 ------------------------------------------------------------------------------- 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 107 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 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 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 F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain N residue 211 MET Chi-restraints excluded: chain Q residue 46 PHE Chi-restraints excluded: chain R residue 309 THR Chi-restraints excluded: chain S residue 37 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 276 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 246 optimal weight: 8.9990 chunk 139 optimal weight: 30.0000 chunk 156 optimal weight: 50.0000 chunk 188 optimal weight: 6.9990 chunk 212 optimal weight: 30.0000 chunk 287 optimal weight: 0.7980 chunk 317 optimal weight: 9.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.078908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.047244 restraints weight = 214966.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.048716 restraints weight = 74876.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.049411 restraints weight = 40235.266| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31483 Z= 0.154 Angle : 0.550 11.351 43787 Z= 0.313 Chirality : 0.038 0.133 5011 Planarity : 0.003 0.040 4558 Dihedral : 25.465 100.541 6814 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 0.96 % Allowed : 8.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.15), residues: 3051 helix: 1.52 (0.13), residues: 1584 sheet: 1.41 (0.23), residues: 438 loop : -0.35 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 75 PHE 0.011 0.001 PHE S 248 TYR 0.013 0.001 TYR D 83 ARG 0.005 0.000 ARG E 131 Details of bonding type rmsd hydrogen bonds : bond 0.04255 ( 1642) hydrogen bonds : angle 3.86152 ( 4440) covalent geometry : bond 0.00330 (31483) covalent geometry : angle 0.55007 (43787) *********************** 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 170 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 2.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8816 (t0) cc_final: 0.7856 (t70) REVERT: D 64 SER cc_start: 0.9035 (m) cc_final: 0.8659 (t) REVERT: D 71 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8956 (mm-30) REVERT: D 93 GLU cc_start: 0.9497 (mp0) cc_final: 0.8997 (mp0) REVERT: E 90 MET cc_start: 0.8983 (tpp) cc_final: 0.8648 (mmp) REVERT: E 120 MET cc_start: 0.8563 (mtm) cc_final: 0.8350 (mtm) REVERT: F 63 GLU cc_start: 0.9311 (tt0) cc_final: 0.8815 (tm-30) REVERT: H 62 MET cc_start: 0.9677 (mmm) cc_final: 0.9451 (mmm) REVERT: H 71 GLU cc_start: 0.9303 (tp30) cc_final: 0.8920 (tm-30) REVERT: H 93 GLU cc_start: 0.9037 (mp0) cc_final: 0.8455 (mp0) REVERT: H 94 ILE cc_start: 0.9585 (mm) cc_final: 0.9340 (tt) REVERT: K 161 ASP cc_start: 0.3831 (OUTLIER) cc_final: 0.3494 (t70) REVERT: K 243 MET cc_start: 0.8855 (ptm) cc_final: 0.8298 (mmp) REVERT: K 326 MET cc_start: 0.7539 (mmp) cc_final: 0.6513 (tpt) REVERT: M 125 MET cc_start: -0.2145 (pmm) cc_final: -0.2454 (ptp) REVERT: M 158 MET cc_start: 0.4421 (mmm) cc_final: 0.4073 (ttt) REVERT: M 210 MET cc_start: 0.0160 (ppp) cc_final: -0.0629 (ppp) REVERT: O 210 MET cc_start: 0.1406 (ptt) cc_final: 0.0841 (ppp) REVERT: O 211 MET cc_start: 0.1473 (mmm) cc_final: 0.1030 (tpt) REVERT: P 211 MET cc_start: -0.1948 (mmm) cc_final: -0.2180 (tpt) REVERT: Q 248 PHE cc_start: 0.9299 (t80) cc_final: 0.9008 (t80) REVERT: R 211 MET cc_start: 0.2731 (mmm) cc_final: 0.2341 (mmm) REVERT: S 211 MET cc_start: -0.0809 (ttm) cc_final: -0.1289 (ttp) REVERT: S 243 MET cc_start: 0.8454 (mmm) cc_final: 0.7818 (tpt) outliers start: 24 outliers final: 17 residues processed: 163 average time/residue: 0.3739 time to fit residues: 105.0821 Evaluate side-chains 140 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 2.935 ------------------------------------------------------------------------------- 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 43 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 161 ASP Chi-restraints excluded: chain L residue 309 THR Chi-restraints excluded: chain O residue 34 ASN Chi-restraints excluded: chain R residue 309 THR Chi-restraints excluded: chain S residue 34 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 20 optimal weight: 0.7980 chunk 283 optimal weight: 10.0000 chunk 332 optimal weight: 30.0000 chunk 92 optimal weight: 7.9990 chunk 181 optimal weight: 50.0000 chunk 21 optimal weight: 0.9980 chunk 325 optimal weight: 40.0000 chunk 187 optimal weight: 20.0000 chunk 85 optimal weight: 10.0000 chunk 123 optimal weight: 20.0000 chunk 17 optimal weight: 2.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 244 HIS ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.077688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.045098 restraints weight = 220626.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.046482 restraints weight = 79095.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.047220 restraints weight = 43756.862| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 31483 Z= 0.207 Angle : 0.579 12.939 43787 Z= 0.325 Chirality : 0.039 0.163 5011 Planarity : 0.003 0.047 4558 Dihedral : 25.352 102.158 6814 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.35 % Allowed : 9.39 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.15), residues: 3051 helix: 1.50 (0.13), residues: 1584 sheet: 1.51 (0.24), residues: 438 loop : -0.30 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 75 PHE 0.010 0.001 PHE L 248 TYR 0.027 0.001 TYR F 88 ARG 0.005 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.04836 ( 1642) hydrogen bonds : angle 3.95251 ( 4440) covalent geometry : bond 0.00448 (31483) covalent geometry : angle 0.57925 (43787) *********************** 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 164 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 2.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8836 (t0) cc_final: 0.8014 (t70) REVERT: B 84 MET cc_start: 0.9255 (tpp) cc_final: 0.9025 (tpp) REVERT: B 88 TYR cc_start: 0.9105 (m-10) cc_final: 0.8888 (m-80) REVERT: B 92 ARG cc_start: 0.9234 (OUTLIER) cc_final: 0.8913 (ttp80) REVERT: D 64 SER cc_start: 0.9057 (m) cc_final: 0.8698 (t) REVERT: D 71 GLU cc_start: 0.9214 (mm-30) cc_final: 0.8957 (mm-30) REVERT: D 93 GLU cc_start: 0.9429 (mp0) cc_final: 0.8884 (mp0) REVERT: E 39 HIS cc_start: 0.7885 (OUTLIER) cc_final: 0.7555 (t70) REVERT: E 120 MET cc_start: 0.8710 (mtm) cc_final: 0.8452 (mtm) REVERT: F 63 GLU cc_start: 0.9323 (tt0) cc_final: 0.8826 (tm-30) REVERT: H 62 MET cc_start: 0.9642 (mmm) cc_final: 0.9337 (mmm) REVERT: H 71 GLU cc_start: 0.9301 (tp30) cc_final: 0.8957 (tm-30) REVERT: H 93 GLU cc_start: 0.9032 (mp0) cc_final: 0.8657 (mp0) REVERT: H 94 ILE cc_start: 0.9598 (mm) cc_final: 0.9353 (tt) REVERT: K 161 ASP cc_start: 0.3899 (OUTLIER) cc_final: 0.3545 (t70) REVERT: K 243 MET cc_start: 0.8827 (ptm) cc_final: 0.8234 (mmp) REVERT: K 326 MET cc_start: 0.7593 (mmp) cc_final: 0.6555 (tpt) REVERT: M 125 MET cc_start: -0.2152 (pmm) cc_final: -0.2394 (ptp) REVERT: M 158 MET cc_start: 0.4111 (mmm) cc_final: 0.3752 (ttp) REVERT: M 210 MET cc_start: -0.0559 (ppp) cc_final: -0.1168 (ppp) REVERT: N 211 MET cc_start: 0.3330 (tpt) cc_final: 0.2620 (tpt) REVERT: O 210 MET cc_start: 0.0995 (ptt) cc_final: 0.0705 (ppp) REVERT: O 211 MET cc_start: 0.1634 (mmm) cc_final: 0.0921 (tpt) REVERT: Q 248 PHE cc_start: 0.9318 (t80) cc_final: 0.9030 (t80) REVERT: S 158 MET cc_start: 0.3888 (mmm) cc_final: 0.3581 (mmm) REVERT: S 211 MET cc_start: -0.0932 (ttm) cc_final: -0.1225 (ttp) REVERT: S 243 MET cc_start: 0.8545 (mmm) cc_final: 0.7916 (tpt) outliers start: 34 outliers final: 22 residues processed: 159 average time/residue: 0.3548 time to fit residues: 97.0419 Evaluate side-chains 148 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 3.059 ------------------------------------------------------------------------------- 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 43 VAL Chi-restraints excluded: chain B residue 81 VAL 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 63 LEU Chi-restraints excluded: chain C residue 79 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 90 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 161 ASP Chi-restraints excluded: chain L residue 309 THR Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain O residue 34 ASN Chi-restraints excluded: chain R residue 309 THR Chi-restraints excluded: chain S residue 34 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 56 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 227 optimal weight: 40.0000 chunk 273 optimal weight: 7.9990 chunk 242 optimal weight: 5.9990 chunk 131 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 284 optimal weight: 50.0000 chunk 281 optimal weight: 8.9990 chunk 147 optimal weight: 9.9990 chunk 332 optimal weight: 3.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN ** K 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.078775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.046277 restraints weight = 221210.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.047734 restraints weight = 78902.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.048430 restraints weight = 42885.570| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4161 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 : 0.528 10.053 43787 Z= 0.299 Chirality : 0.037 0.166 5011 Planarity : 0.003 0.050 4558 Dihedral : 25.197 101.717 6814 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 1.31 % Allowed : 9.79 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.15), residues: 3051 helix: 1.77 (0.13), residues: 1580 sheet: 1.74 (0.26), residues: 372 loop : -0.39 (0.18), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS E 113 PHE 0.010 0.001 PHE E 104 TYR 0.016 0.001 TYR Q 216 ARG 0.004 0.000 ARG B 67 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 1642) hydrogen bonds : angle 3.61738 ( 4440) covalent geometry : bond 0.00303 (31483) covalent geometry : angle 0.52834 (43787) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 2.860 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 81 ASP cc_start: 0.8887 (OUTLIER) cc_final: 0.7951 (t70) REVERT: B 84 MET cc_start: 0.9123 (tpp) cc_final: 0.8874 (tpp) REVERT: B 92 ARG cc_start: 0.9212 (OUTLIER) cc_final: 0.8914 (ttp80) REVERT: D 64 SER cc_start: 0.8989 (m) cc_final: 0.8630 (t) REVERT: D 71 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8966 (mm-30) REVERT: D 93 GLU cc_start: 0.9354 (mp0) cc_final: 0.8831 (mp0) REVERT: E 39 HIS cc_start: 0.7724 (OUTLIER) cc_final: 0.7513 (t70) REVERT: E 90 MET cc_start: 0.8934 (tpp) cc_final: 0.8601 (mmp) REVERT: E 120 MET cc_start: 0.8542 (mtm) cc_final: 0.8310 (mtm) REVERT: F 63 GLU cc_start: 0.9277 (tt0) cc_final: 0.8726 (tm-30) REVERT: H 71 GLU cc_start: 0.9258 (tp30) cc_final: 0.8933 (tm-30) REVERT: H 93 GLU cc_start: 0.9008 (mp0) cc_final: 0.8392 (mp0) REVERT: H 94 ILE cc_start: 0.9585 (mm) cc_final: 0.9342 (tt) REVERT: K 161 ASP cc_start: 0.3839 (OUTLIER) cc_final: 0.3480 (t70) REVERT: K 243 MET cc_start: 0.8757 (ptm) cc_final: 0.8170 (mmp) REVERT: M 125 MET cc_start: -0.2179 (pmm) cc_final: -0.2432 (ptp) REVERT: M 158 MET cc_start: 0.3645 (mmm) cc_final: 0.3320 (ttp) REVERT: M 210 MET cc_start: -0.0594 (ppp) cc_final: -0.1078 (ppp) REVERT: N 211 MET cc_start: 0.3132 (tpt) cc_final: 0.2650 (tpt) REVERT: O 211 MET cc_start: 0.1868 (mmm) cc_final: 0.1493 (tpt) REVERT: O 243 MET cc_start: 0.8795 (mmt) cc_final: 0.7855 (tpt) REVERT: Q 211 MET cc_start: -0.1085 (ttp) cc_final: -0.2080 (ptm) REVERT: Q 248 PHE cc_start: 0.9340 (t80) cc_final: 0.9049 (t80) REVERT: S 158 MET cc_start: 0.3810 (mmm) cc_final: 0.3342 (mmm) REVERT: S 210 MET cc_start: 0.5098 (ppp) cc_final: 0.4471 (ppp) REVERT: S 211 MET cc_start: -0.0848 (ttm) cc_final: -0.1135 (ttp) REVERT: S 243 MET cc_start: 0.8657 (mmm) cc_final: 0.8136 (tpt) REVERT: S 252 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7898 (mm) outliers start: 33 outliers final: 23 residues processed: 167 average time/residue: 0.3674 time to fit residues: 103.5246 Evaluate side-chains 156 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 3.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 92 LEU 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 H residue 90 THR Chi-restraints excluded: chain K residue 161 ASP Chi-restraints excluded: chain L residue 309 THR Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain O residue 34 ASN Chi-restraints excluded: chain P residue 37 ASP Chi-restraints excluded: chain R residue 309 THR Chi-restraints excluded: chain S residue 34 ASN 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 25 optimal weight: 10.0000 chunk 124 optimal weight: 30.0000 chunk 112 optimal weight: 30.0000 chunk 291 optimal weight: 8.9990 chunk 193 optimal weight: 20.0000 chunk 167 optimal weight: 30.0000 chunk 264 optimal weight: 5.9990 chunk 156 optimal weight: 50.0000 chunk 91 optimal weight: 8.9990 chunk 79 optimal weight: 8.9990 chunk 132 optimal weight: 50.0000 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN E 68 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 62 ASN ** Q 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 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 = 0.3996 r_free = 0.3996 target = 0.075975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.042938 restraints weight = 224662.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.044249 restraints weight = 80302.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.044845 restraints weight = 44065.754| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 31483 Z= 0.337 Angle : 0.688 15.566 43787 Z= 0.381 Chirality : 0.042 0.157 5011 Planarity : 0.004 0.050 4558 Dihedral : 25.370 105.543 6814 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.31 % Allowed : 9.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.15), residues: 3051 helix: 1.17 (0.13), residues: 1593 sheet: 1.81 (0.26), residues: 369 loop : -0.54 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS E 113 PHE 0.016 0.002 PHE E 84 TYR 0.017 0.002 TYR H 40 ARG 0.007 0.001 ARG F 35 Details of bonding type rmsd hydrogen bonds : bond 0.06494 ( 1642) hydrogen bonds : angle 4.41302 ( 4440) covalent geometry : bond 0.00732 (31483) covalent geometry : angle 0.68783 (43787) *********************** 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 177 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 119 time to evaluate : 3.045 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: 0.9139 (mm-30) cc_final: 0.8491 (tp30) REVERT: A 81 ASP cc_start: 0.9065 (OUTLIER) cc_final: 0.8270 (t70) REVERT: B 88 TYR cc_start: 0.9092 (m-10) cc_final: 0.8690 (m-80) REVERT: B 92 ARG cc_start: 0.9261 (OUTLIER) cc_final: 0.8892 (ttp80) REVERT: D 64 SER cc_start: 0.9122 (m) cc_final: 0.8807 (t) REVERT: D 71 GLU cc_start: 0.9310 (mm-30) cc_final: 0.9099 (mm-30) REVERT: D 93 GLU cc_start: 0.9409 (mp0) cc_final: 0.8886 (mp0) REVERT: E 39 HIS cc_start: 0.7961 (OUTLIER) cc_final: 0.7673 (t70) REVERT: E 120 MET cc_start: 0.8858 (mtm) cc_final: 0.8581 (mtm) REVERT: F 63 GLU cc_start: 0.9408 (tt0) cc_final: 0.8957 (tm-30) REVERT: H 93 GLU cc_start: 0.9040 (mp0) cc_final: 0.8694 (mp0) REVERT: H 94 ILE cc_start: 0.9594 (OUTLIER) cc_final: 0.9341 (tt) REVERT: K 161 ASP cc_start: 0.4025 (OUTLIER) cc_final: 0.3705 (t0) REVERT: K 243 MET cc_start: 0.8806 (ptm) cc_final: 0.8241 (mmp) REVERT: M 125 MET cc_start: -0.1750 (pmm) cc_final: -0.2010 (ptp) REVERT: M 158 MET cc_start: 0.3910 (mmm) cc_final: 0.3575 (ttp) REVERT: M 210 MET cc_start: -0.0624 (ppp) cc_final: -0.1078 (ppp) REVERT: N 211 MET cc_start: 0.3425 (tpt) cc_final: 0.2903 (tpt) REVERT: O 211 MET cc_start: 0.2681 (mmm) cc_final: 0.2179 (tpt) REVERT: P 211 MET cc_start: -0.2372 (tpt) cc_final: -0.2692 (tpp) REVERT: Q 211 MET cc_start: 0.0424 (ttp) cc_final: 0.0162 (ttp) REVERT: Q 248 PHE cc_start: 0.9308 (t80) cc_final: 0.9031 (t80) REVERT: R 235 ARG cc_start: 0.4843 (mmt180) cc_final: 0.3671 (mmp80) REVERT: S 158 MET cc_start: 0.4309 (mmm) cc_final: 0.4071 (mmm) REVERT: S 210 MET cc_start: 0.5198 (ppp) cc_final: 0.4593 (ppp) REVERT: S 211 MET cc_start: -0.0704 (ttm) cc_final: -0.1132 (ttp) REVERT: S 243 MET cc_start: 0.8638 (mmm) cc_final: 0.8128 (tpt) REVERT: S 252 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7956 (mm) outliers start: 58 outliers final: 36 residues processed: 169 average time/residue: 0.3743 time to fit residues: 108.1783 Evaluate side-chains 157 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 115 time to evaluate : 2.779 ------------------------------------------------------------------------------- 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 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 82 THR 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 63 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 63 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 248 PHE Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain O residue 34 ASN Chi-restraints excluded: chain Q residue 223 SER Chi-restraints excluded: chain R residue 251 MET Chi-restraints excluded: chain R residue 309 THR Chi-restraints excluded: chain S residue 34 ASN Chi-restraints excluded: chain S residue 37 ASP Chi-restraints excluded: chain S residue 252 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 172 optimal weight: 0.0670 chunk 212 optimal weight: 50.0000 chunk 175 optimal weight: 20.0000 chunk 265 optimal weight: 50.0000 chunk 228 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 325 optimal weight: 50.0000 chunk 315 optimal weight: 50.0000 chunk 104 optimal weight: 30.0000 chunk 105 optimal weight: 0.0370 chunk 36 optimal weight: 4.9990 overall best weight: 4.2204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.077347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.044793 restraints weight = 222448.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.046095 restraints weight = 79472.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.046737 restraints weight = 43804.560| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 31483 Z= 0.196 Angle : 0.584 12.361 43787 Z= 0.326 Chirality : 0.039 0.256 5011 Planarity : 0.003 0.050 4558 Dihedral : 25.366 105.226 6814 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.43 % Allowed : 10.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.15), residues: 3051 helix: 1.46 (0.13), residues: 1588 sheet: 1.86 (0.26), residues: 363 loop : -0.42 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS E 113 PHE 0.018 0.001 PHE O 248 TYR 0.014 0.001 TYR R 216 ARG 0.004 0.000 ARG F 19 Details of bonding type rmsd hydrogen bonds : bond 0.04736 ( 1642) hydrogen bonds : angle 3.90563 ( 4440) covalent geometry : bond 0.00423 (31483) covalent geometry : angle 0.58355 (43787) *********************** 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: 36 poor density : 129 time to evaluate : 2.715 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 81 ASP cc_start: 0.9009 (OUTLIER) cc_final: 0.8189 (t70) REVERT: B 85 ASP cc_start: 0.8822 (OUTLIER) cc_final: 0.8483 (m-30) REVERT: B 88 TYR cc_start: 0.9077 (m-10) cc_final: 0.8766 (m-80) REVERT: B 92 ARG cc_start: 0.9238 (OUTLIER) cc_final: 0.8907 (ttp80) REVERT: D 64 SER cc_start: 0.9098 (m) cc_final: 0.8753 (t) REVERT: D 71 GLU cc_start: 0.9271 (mm-30) cc_final: 0.9041 (mm-30) REVERT: D 93 GLU cc_start: 0.9341 (mp0) cc_final: 0.8965 (mp0) REVERT: E 39 HIS cc_start: 0.7955 (OUTLIER) cc_final: 0.7683 (t70) REVERT: E 120 MET cc_start: 0.8735 (mtm) cc_final: 0.8448 (mtm) REVERT: F 63 GLU cc_start: 0.9325 (tt0) cc_final: 0.8835 (tm-30) REVERT: H 93 GLU cc_start: 0.9023 (mp0) cc_final: 0.8414 (mp0) REVERT: H 94 ILE cc_start: 0.9613 (mm) cc_final: 0.9376 (tt) REVERT: K 161 ASP cc_start: 0.3867 (OUTLIER) cc_final: 0.3552 (t70) REVERT: K 243 MET cc_start: 0.8797 (ptm) cc_final: 0.8223 (mmp) REVERT: M 125 MET cc_start: -0.1765 (pmm) cc_final: -0.2010 (ptp) REVERT: M 158 MET cc_start: 0.3875 (mmm) cc_final: 0.3515 (ttt) REVERT: M 210 MET cc_start: -0.0935 (ppp) cc_final: -0.1474 (ppp) REVERT: N 211 MET cc_start: 0.3141 (tpt) cc_final: 0.2759 (tpt) REVERT: O 211 MET cc_start: 0.2152 (mmm) cc_final: 0.1665 (tpt) REVERT: P 211 MET cc_start: -0.2162 (tpt) cc_final: -0.2471 (tpp) REVERT: Q 125 MET cc_start: 0.8518 (ptt) cc_final: 0.8283 (tmm) REVERT: Q 211 MET cc_start: 0.0566 (ttp) cc_final: -0.0495 (ptm) REVERT: Q 248 PHE cc_start: 0.9318 (t80) cc_final: 0.9042 (t80) REVERT: R 235 ARG cc_start: 0.4875 (mmt180) cc_final: 0.3692 (mmp80) REVERT: S 158 MET cc_start: 0.4106 (mmm) cc_final: 0.3901 (mmm) REVERT: S 210 MET cc_start: 0.5107 (ppp) cc_final: 0.4531 (ppp) REVERT: S 211 MET cc_start: -0.0841 (ttm) cc_final: -0.1267 (ttp) REVERT: S 243 MET cc_start: 0.8702 (mmm) cc_final: 0.8210 (tpt) outliers start: 36 outliers final: 28 residues processed: 160 average time/residue: 0.3489 time to fit residues: 95.6757 Evaluate side-chains 158 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 2.702 ------------------------------------------------------------------------------- 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 107 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 30 THR 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 55 LEU Chi-restraints excluded: chain H residue 90 THR 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 L residue 309 THR Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain O residue 34 ASN Chi-restraints excluded: chain Q residue 223 SER Chi-restraints excluded: chain S residue 34 ASN Chi-restraints excluded: chain S residue 37 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 297 optimal weight: 50.0000 chunk 185 optimal weight: 20.0000 chunk 39 optimal weight: 0.9980 chunk 104 optimal weight: 30.0000 chunk 152 optimal weight: 1.9990 chunk 236 optimal weight: 7.9990 chunk 167 optimal weight: 7.9990 chunk 234 optimal weight: 7.9990 chunk 302 optimal weight: 0.9990 chunk 145 optimal weight: 20.0000 chunk 111 optimal weight: 0.5980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 206 GLN ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.078296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.045921 restraints weight = 220229.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.047338 restraints weight = 79117.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.048013 restraints weight = 43710.950| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31483 Z= 0.146 Angle : 0.553 9.758 43787 Z= 0.307 Chirality : 0.038 0.172 5011 Planarity : 0.003 0.052 4558 Dihedral : 25.152 103.882 6814 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 1.23 % Allowed : 10.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.15), residues: 3051 helix: 1.71 (0.13), residues: 1586 sheet: 1.91 (0.26), residues: 363 loop : -0.28 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 113 PHE 0.010 0.001 PHE O 248 TYR 0.012 0.001 TYR N 159 ARG 0.008 0.000 ARG S 250 Details of bonding type rmsd hydrogen bonds : bond 0.03947 ( 1642) hydrogen bonds : angle 3.60794 ( 4440) covalent geometry : bond 0.00313 (31483) covalent geometry : angle 0.55305 (43787) *********************** 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 166 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 3.027 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 81 ASP cc_start: 0.8985 (OUTLIER) cc_final: 0.8176 (t70) REVERT: B 88 TYR cc_start: 0.8881 (m-10) cc_final: 0.8653 (m-80) REVERT: B 92 ARG cc_start: 0.9203 (OUTLIER) cc_final: 0.8620 (ttp80) REVERT: D 64 SER cc_start: 0.9014 (m) cc_final: 0.8667 (t) REVERT: D 71 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8961 (mm-30) REVERT: D 93 GLU cc_start: 0.9298 (mp0) cc_final: 0.8844 (mp0) REVERT: E 39 HIS cc_start: 0.7835 (OUTLIER) cc_final: 0.7572 (t70) REVERT: E 90 MET cc_start: 0.8909 (tpp) cc_final: 0.8579 (mmp) REVERT: E 120 MET cc_start: 0.8722 (mtm) cc_final: 0.8443 (mtm) REVERT: F 63 GLU cc_start: 0.9286 (tt0) cc_final: 0.8721 (tm-30) REVERT: H 59 MET cc_start: 0.9495 (tpp) cc_final: 0.9280 (tpp) REVERT: H 93 GLU cc_start: 0.9020 (mp0) cc_final: 0.8382 (mp0) REVERT: H 94 ILE cc_start: 0.9597 (mm) cc_final: 0.9363 (tt) REVERT: K 243 MET cc_start: 0.8757 (ptm) cc_final: 0.8166 (mmp) REVERT: M 125 MET cc_start: -0.1914 (pmm) cc_final: -0.2156 (ptp) REVERT: M 158 MET cc_start: 0.3571 (mmm) cc_final: 0.3208 (ttt) REVERT: M 210 MET cc_start: -0.0873 (ppp) cc_final: -0.1432 (ppp) REVERT: N 211 MET cc_start: 0.3291 (tpt) cc_final: 0.3032 (tpt) REVERT: O 211 MET cc_start: 0.1773 (mmm) cc_final: 0.1373 (tpt) REVERT: P 211 MET cc_start: -0.2211 (tpt) cc_final: -0.2531 (tpp) REVERT: Q 211 MET cc_start: 0.0135 (ttp) cc_final: -0.0883 (ptm) REVERT: Q 248 PHE cc_start: 0.9343 (t80) cc_final: 0.9083 (t80) REVERT: S 210 MET cc_start: 0.5042 (ppp) cc_final: 0.4430 (ppp) REVERT: S 211 MET cc_start: -0.1016 (ttm) cc_final: -0.1429 (ttp) REVERT: S 243 MET cc_start: 0.8756 (mmm) cc_final: 0.8238 (tpt) outliers start: 31 outliers final: 26 residues processed: 158 average time/residue: 0.3843 time to fit residues: 102.8991 Evaluate side-chains 156 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 2.943 ------------------------------------------------------------------------------- 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 107 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 30 THR 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 H residue 90 THR Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 223 SER Chi-restraints excluded: chain L residue 326 MET Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain N residue 187 ASP Chi-restraints excluded: chain O residue 34 ASN Chi-restraints excluded: chain Q residue 223 SER Chi-restraints excluded: chain S residue 34 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 34 optimal weight: 3.9990 chunk 309 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 222 optimal weight: 50.0000 chunk 117 optimal weight: 7.9990 chunk 187 optimal weight: 6.9990 chunk 333 optimal weight: 10.0000 chunk 318 optimal weight: 40.0000 chunk 56 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 285 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 HIS ** 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 244 HIS N 206 GLN ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 294 HIS ** Q 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.076487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.043980 restraints weight = 221423.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.045135 restraints weight = 79045.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.045758 restraints weight = 43931.635| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 31483 Z= 0.253 Angle : 0.636 14.224 43787 Z= 0.350 Chirality : 0.040 0.225 5011 Planarity : 0.004 0.071 4558 Dihedral : 25.291 105.788 6814 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.55 % Allowed : 10.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.15), residues: 3051 helix: 1.45 (0.13), residues: 1579 sheet: 1.93 (0.26), residues: 357 loop : -0.30 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS A 113 PHE 0.012 0.001 PHE C 25 TYR 0.016 0.001 TYR R 216 ARG 0.006 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.05490 ( 1642) hydrogen bonds : angle 4.07039 ( 4440) covalent geometry : bond 0.00550 (31483) covalent geometry : angle 0.63618 (43787) ********************** 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 162 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 123 time to evaluate : 2.808 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 81 ASP cc_start: 0.9121 (OUTLIER) cc_final: 0.8373 (t70) REVERT: B 85 ASP cc_start: 0.8826 (OUTLIER) cc_final: 0.8509 (m-30) REVERT: B 88 TYR cc_start: 0.9033 (m-10) cc_final: 0.8620 (m-80) REVERT: B 92 ARG cc_start: 0.9230 (OUTLIER) cc_final: 0.8873 (ttp80) REVERT: D 64 SER cc_start: 0.9090 (m) cc_final: 0.8782 (t) REVERT: D 71 GLU cc_start: 0.9276 (mm-30) cc_final: 0.9054 (mm-30) REVERT: D 93 GLU cc_start: 0.9346 (mp0) cc_final: 0.8989 (mp0) REVERT: E 120 MET cc_start: 0.8797 (mtm) cc_final: 0.8494 (mtm) REVERT: F 63 GLU cc_start: 0.9337 (tt0) cc_final: 0.8857 (tm-30) REVERT: H 93 GLU cc_start: 0.9025 (mp0) cc_final: 0.8443 (mp0) REVERT: K 161 ASP cc_start: 0.3757 (OUTLIER) cc_final: 0.3464 (t0) REVERT: K 243 MET cc_start: 0.8798 (ptm) cc_final: 0.8206 (mmp) REVERT: M 125 MET cc_start: -0.1732 (pmm) cc_final: -0.1992 (ptp) REVERT: M 158 MET cc_start: 0.3834 (mmm) cc_final: 0.3455 (ttt) REVERT: M 210 MET cc_start: -0.0749 (ppp) cc_final: -0.1304 (ppp) REVERT: N 210 MET cc_start: 0.1092 (ppp) cc_final: 0.0240 (mmm) REVERT: N 211 MET cc_start: 0.3172 (tpt) cc_final: 0.1955 (mmm) REVERT: N 338 LYS cc_start: 0.4210 (mmtt) cc_final: 0.3893 (mttt) REVERT: O 211 MET cc_start: 0.2203 (mmm) cc_final: 0.1716 (tpt) REVERT: O 243 MET cc_start: 0.8799 (mmt) cc_final: 0.7909 (tpt) REVERT: P 211 MET cc_start: -0.2068 (tpt) cc_final: -0.2343 (tpp) REVERT: Q 211 MET cc_start: 0.0348 (ttp) cc_final: 0.0119 (ttp) REVERT: Q 248 PHE cc_start: 0.9333 (t80) cc_final: 0.9070 (t80) REVERT: R 195 PHE cc_start: 0.6436 (OUTLIER) cc_final: 0.6094 (m-10) REVERT: R 235 ARG cc_start: 0.5052 (mmt180) cc_final: 0.3863 (mmp80) REVERT: S 158 MET cc_start: 0.4158 (mmt) cc_final: 0.3346 (mmm) REVERT: S 210 MET cc_start: 0.4814 (ppp) cc_final: 0.4280 (ppp) REVERT: S 211 MET cc_start: -0.0807 (ttm) cc_final: -0.1239 (ttp) REVERT: S 243 MET cc_start: 0.8899 (mmm) cc_final: 0.8439 (tpt) outliers start: 39 outliers final: 30 residues processed: 155 average time/residue: 0.3699 time to fit residues: 97.0518 Evaluate side-chains 157 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 3.119 ------------------------------------------------------------------------------- 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 107 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 97 LEU 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 73 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 30 THR 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 H residue 90 THR 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 L residue 326 MET Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain N residue 187 ASP Chi-restraints excluded: chain P residue 294 HIS Chi-restraints excluded: chain Q residue 223 SER Chi-restraints excluded: chain R residue 195 PHE Chi-restraints excluded: chain S residue 34 ASN Chi-restraints excluded: chain S residue 37 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 261 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 309 optimal weight: 30.0000 chunk 43 optimal weight: 0.9990 chunk 242 optimal weight: 8.9990 chunk 326 optimal weight: 30.0000 chunk 166 optimal weight: 40.0000 chunk 213 optimal weight: 8.9990 chunk 212 optimal weight: 50.0000 chunk 59 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 294 HIS ** Q 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.078343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.045940 restraints weight = 219697.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.047341 restraints weight = 78254.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.048038 restraints weight = 42912.133| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.5196 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= 0.137 Angle : 0.558 10.098 43787 Z= 0.309 Chirality : 0.038 0.165 5011 Planarity : 0.003 0.054 4558 Dihedral : 25.219 104.165 6814 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 1.23 % Allowed : 10.99 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.15), residues: 3051 helix: 1.71 (0.13), residues: 1586 sheet: 1.94 (0.27), residues: 357 loop : -0.23 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.020 0.001 HIS P 294 PHE 0.011 0.001 PHE S 248 TYR 0.018 0.001 TYR S 205 ARG 0.013 0.000 ARG F 35 Details of bonding type rmsd hydrogen bonds : bond 0.03899 ( 1642) hydrogen bonds : angle 3.60643 ( 4440) covalent geometry : bond 0.00291 (31483) covalent geometry : angle 0.55751 (43787) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17492.48 seconds wall clock time: 302 minutes 19.57 seconds (18139.57 seconds total)