Starting phenix.real_space_refine on Wed Aug 5 11:39:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/30of_57890/08_2026/30of_57890.cif Found real_map, /net/cci-nas-00/data/ceres_data/30of_57890/08_2026/30of_57890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/30of_57890/08_2026/30of_57890.map" default_real_map = "/net/cci-nas-00/data/ceres_data/30of_57890/08_2026/30of_57890.map" model { file = "/net/cci-nas-00/data/ceres_data/30of_57890/08_2026/30of_57890.cif" } default_model = "/net/cci-nas-00/data/ceres_data/30of_57890/08_2026/30of_57890.cif" } resolution = 4.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.031 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: 4 Type Number sf(0) Gaussians S 67 5.16 5 C 5933 2.51 5 N 1639 2.21 5 O 1762 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9401 Number of models: 1 Model: "" Number of chains: 7 Chain: "S" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 79 Classifications: {'peptide': 8} Link IDs: {'PTRANS': 1, 'TRANS': 6} Chain: "D" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1635 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 194} Chain breaks: 2 Chain: "E" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1578 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 187} Chain breaks: 1 Chain: "G" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1375 Classifications: {'peptide': 175} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 164} Chain breaks: 1 Chain: "L" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1578 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 187} Chain breaks: 1 Chain: "N" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1578 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 187} Chain breaks: 1 Chain: "O" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1578 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 187} Chain breaks: 1 Time building chain proxies: 2.19, per 1000 atoms: 0.23 Number of scatterers: 9401 At special positions: 0 Unit cell: (134.2, 130.9, 84.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 67 16.00 O 1762 8.00 N 1639 7.00 C 5933 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: 0.86 Conformation dependent library (CDL) restraints added in 357.3 milliseconds 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2228 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 1 sheets defined 74.9% alpha, 0.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'D' and resid 17 through 32 removed outlier: 4.046A pdb=" N ALA D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS D 26 " --> pdb=" O ASN D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 44 removed outlier: 3.975A pdb=" N MET D 40 " --> pdb=" O GLU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 59 Processing helix chain 'D' and resid 65 through 75 removed outlier: 5.426A pdb=" N LYS D 71 " --> pdb=" O MET D 67 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU D 72 " --> pdb=" O GLN D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 81 Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 111 through 121 Processing helix chain 'D' and resid 126 through 146 removed outlier: 3.626A pdb=" N ILE D 142 " --> pdb=" O GLY D 138 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ARG D 144 " --> pdb=" O ASN D 140 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET D 145 " --> pdb=" O LYS D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 176 removed outlier: 3.684A pdb=" N ASP D 167 " --> pdb=" O ARG D 163 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR D 172 " --> pdb=" O ARG D 168 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU D 173 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA D 175 " --> pdb=" O LYS D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 194 removed outlier: 4.168A pdb=" N LEU D 191 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N VAL D 192 " --> pdb=" O GLU D 188 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN D 193 " --> pdb=" O THR D 189 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 204 removed outlier: 4.232A pdb=" N LYS D 204 " --> pdb=" O LYS D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 219 Processing helix chain 'D' and resid 224 through 232 Processing helix chain 'E' and resid 18 through 31 removed outlier: 4.404A pdb=" N LYS E 26 " --> pdb=" O ASN E 22 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL E 28 " --> pdb=" O TRP E 24 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLU E 29 " --> pdb=" O VAL E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 44 removed outlier: 3.514A pdb=" N MET E 40 " --> pdb=" O GLU E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 59 Processing helix chain 'E' and resid 63 through 85 removed outlier: 3.685A pdb=" N MET E 69 " --> pdb=" O ALA E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 106 Processing helix chain 'E' and resid 111 through 121 Processing helix chain 'E' and resid 126 through 146 removed outlier: 4.364A pdb=" N ARG E 144 " --> pdb=" O ASN E 140 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N MET E 145 " --> pdb=" O LYS E 141 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR E 146 " --> pdb=" O ILE E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 154 removed outlier: 3.945A pdb=" N ILE E 154 " --> pdb=" O ILE E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 176 removed outlier: 3.562A pdb=" N ASP E 167 " --> pdb=" O ARG E 163 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TYR E 170 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N LYS E 171 " --> pdb=" O ASP E 167 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N THR E 172 " --> pdb=" O ARG E 168 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU E 173 " --> pdb=" O PHE E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 194 removed outlier: 3.877A pdb=" N GLU E 188 " --> pdb=" O ASN E 184 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR E 189 " --> pdb=" O TRP E 185 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU E 190 " --> pdb=" O MET E 186 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU E 191 " --> pdb=" O THR E 187 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL E 192 " --> pdb=" O GLU E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 204 Processing helix chain 'E' and resid 205 through 207 No H-bonds generated for 'chain 'E' and resid 205 through 207' Processing helix chain 'E' and resid 211 through 219 removed outlier: 3.785A pdb=" N THR E 217 " --> pdb=" O GLU E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 230 Processing helix chain 'G' and resid 18 through 31 removed outlier: 4.337A pdb=" N LYS G 26 " --> pdb=" O ASN G 22 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLU G 29 " --> pdb=" O VAL G 25 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LYS G 31 " --> pdb=" O VAL G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 45 Processing helix chain 'G' and resid 49 through 58 Processing helix chain 'G' and resid 63 through 85 removed outlier: 4.267A pdb=" N MET G 67 " --> pdb=" O HIS G 63 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN G 68 " --> pdb=" O GLN G 64 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N MET G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU G 72 " --> pdb=" O GLN G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 144 removed outlier: 3.628A pdb=" N LEU G 137 " --> pdb=" O ARG G 133 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG G 144 " --> pdb=" O ASN G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 147 No H-bonds generated for 'chain 'G' and resid 145 through 147' Processing helix chain 'G' and resid 150 through 154 Processing helix chain 'G' and resid 161 through 176 Processing helix chain 'G' and resid 179 through 188 Processing helix chain 'G' and resid 196 through 204 Processing helix chain 'G' and resid 205 through 207 No H-bonds generated for 'chain 'G' and resid 205 through 207' Processing helix chain 'G' and resid 211 through 219 Processing helix chain 'G' and resid 224 through 229 removed outlier: 3.787A pdb=" N LYS G 228 " --> pdb=" O GLY G 224 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 26 Processing helix chain 'L' and resid 26 through 31 Processing helix chain 'L' and resid 36 through 44 removed outlier: 3.707A pdb=" N MET L 40 " --> pdb=" O GLU L 36 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 58 removed outlier: 3.642A pdb=" N ASN L 54 " --> pdb=" O PRO L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 85 removed outlier: 4.128A pdb=" N GLU L 76 " --> pdb=" O GLU L 72 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU L 77 " --> pdb=" O THR L 73 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASP L 82 " --> pdb=" O ALA L 78 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ARG L 83 " --> pdb=" O ALA L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 101 through 106 Processing helix chain 'L' and resid 111 through 121 removed outlier: 3.635A pdb=" N MET L 119 " --> pdb=" O GLN L 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 146 removed outlier: 4.464A pdb=" N LYS L 141 " --> pdb=" O LEU L 137 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE L 142 " --> pdb=" O GLY L 138 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL L 143 " --> pdb=" O LEU L 139 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG L 144 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 154 Processing helix chain 'L' and resid 162 through 174 removed outlier: 3.638A pdb=" N ASP L 167 " --> pdb=" O ARG L 163 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG L 168 " --> pdb=" O ASP L 164 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS L 171 " --> pdb=" O ASP L 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 179 through 188 Processing helix chain 'L' and resid 189 through 194 removed outlier: 3.900A pdb=" N ASN L 194 " --> pdb=" O LEU L 190 " (cutoff:3.500A) Processing helix chain 'L' and resid 196 through 204 Processing helix chain 'L' and resid 205 through 207 No H-bonds generated for 'chain 'L' and resid 205 through 207' Processing helix chain 'L' and resid 211 through 219 Processing helix chain 'L' and resid 226 through 231 Processing helix chain 'N' and resid 18 through 31 removed outlier: 4.502A pdb=" N ALA N 23 " --> pdb=" O ARG N 19 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TRP N 24 " --> pdb=" O THR N 20 " (cutoff:3.500A) Processing helix chain 'N' and resid 36 through 44 removed outlier: 4.369A pdb=" N ALA N 43 " --> pdb=" O PRO N 39 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU N 44 " --> pdb=" O MET N 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 59 removed outlier: 3.809A pdb=" N ASN N 54 " --> pdb=" O PRO N 50 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR N 55 " --> pdb=" O GLN N 51 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN N 58 " --> pdb=" O ASN N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 66 through 85 removed outlier: 4.200A pdb=" N LEU N 70 " --> pdb=" O ALA N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 101 through 106 Processing helix chain 'N' and resid 111 through 121 Processing helix chain 'N' and resid 126 through 146 removed outlier: 4.134A pdb=" N LEU N 137 " --> pdb=" O ARG N 133 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY N 138 " --> pdb=" O TRP N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 150 through 154 Processing helix chain 'N' and resid 164 through 173 removed outlier: 4.060A pdb=" N THR N 172 " --> pdb=" O ARG N 168 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU N 173 " --> pdb=" O PHE N 169 " (cutoff:3.500A) Processing helix chain 'N' and resid 179 through 195 removed outlier: 3.635A pdb=" N GLU N 188 " --> pdb=" O ASN N 184 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR N 189 " --> pdb=" O TRP N 185 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU N 191 " --> pdb=" O THR N 187 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N VAL N 192 " --> pdb=" O GLU N 188 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA N 195 " --> pdb=" O LEU N 191 " (cutoff:3.500A) Processing helix chain 'N' and resid 196 through 204 removed outlier: 5.194A pdb=" N ILE N 202 " --> pdb=" O ASP N 198 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS N 204 " --> pdb=" O LYS N 200 " (cutoff:3.500A) Processing helix chain 'N' and resid 205 through 207 No H-bonds generated for 'chain 'N' and resid 205 through 207' Processing helix chain 'N' and resid 211 through 219 removed outlier: 3.854A pdb=" N MET N 215 " --> pdb=" O THR N 211 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR N 217 " --> pdb=" O GLU N 213 " (cutoff:3.500A) Processing helix chain 'N' and resid 224 through 232 removed outlier: 4.616A pdb=" N ARG N 230 " --> pdb=" O GLY N 226 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL N 231 " --> pdb=" O HIS N 227 " (cutoff:3.500A) Processing helix chain 'O' and resid 18 through 30 removed outlier: 4.512A pdb=" N LYS O 26 " --> pdb=" O ASN O 22 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL O 27 " --> pdb=" O ALA O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 36 through 43 removed outlier: 4.053A pdb=" N MET O 40 " --> pdb=" O GLU O 36 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 59 Processing helix chain 'O' and resid 64 through 85 removed outlier: 3.809A pdb=" N GLN O 68 " --> pdb=" O GLN O 64 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N MET O 69 " --> pdb=" O ALA O 65 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU O 77 " --> pdb=" O THR O 73 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU O 80 " --> pdb=" O GLU O 76 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TRP O 81 " --> pdb=" O GLU O 77 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP O 82 " --> pdb=" O ALA O 78 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 106 Processing helix chain 'O' and resid 111 through 121 removed outlier: 3.861A pdb=" N MET O 119 " --> pdb=" O GLN O 115 " (cutoff:3.500A) Processing helix chain 'O' and resid 126 through 146 removed outlier: 3.508A pdb=" N LEU O 137 " --> pdb=" O ARG O 133 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG O 144 " --> pdb=" O ASN O 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 150 through 154 Processing helix chain 'O' and resid 161 through 174 removed outlier: 4.456A pdb=" N ASP O 167 " --> pdb=" O ARG O 163 " (cutoff:3.500A) Processing helix chain 'O' and resid 181 through 195 removed outlier: 3.630A pdb=" N TRP O 185 " --> pdb=" O GLU O 181 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N LEU O 191 " --> pdb=" O THR O 187 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL O 192 " --> pdb=" O GLU O 188 " (cutoff:3.500A) Processing helix chain 'O' and resid 196 through 207 removed outlier: 4.297A pdb=" N ILE O 202 " --> pdb=" O ASP O 198 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA O 205 " --> pdb=" O THR O 201 " (cutoff:3.500A) Processing helix chain 'O' and resid 211 through 219 Processing helix chain 'O' and resid 226 through 231 removed outlier: 3.797A pdb=" N ARG O 230 " --> pdb=" O HIS O 227 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 3 through 4 477 hydrogen bonds defined for protein. 1386 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.41 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2809 1.34 - 1.46: 1412 1.46 - 1.58: 5259 1.58 - 1.71: 0 1.71 - 1.83: 122 Bond restraints: 9602 Sorted by residual: bond pdb=" N VAL G 231 " pdb=" CA VAL G 231 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.25e-02 6.40e+03 1.16e+01 bond pdb=" N LYS O 228 " pdb=" CA LYS O 228 " ideal model delta sigma weight residual 1.459 1.500 -0.042 1.28e-02 6.10e+03 1.06e+01 bond pdb=" N LYS N 159 " pdb=" CA LYS N 159 " ideal model delta sigma weight residual 1.459 1.489 -0.030 9.10e-03 1.21e+04 1.05e+01 bond pdb=" N LYS E 159 " pdb=" CA LYS E 159 " ideal model delta sigma weight residual 1.458 1.487 -0.029 9.00e-03 1.23e+04 1.04e+01 bond pdb=" CZ ARG N 168 " pdb=" NH2 ARG N 168 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 1.02e+01 ... (remaining 9597 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.44: 12801 4.44 - 8.89: 215 8.89 - 13.33: 2 13.33 - 17.78: 2 17.78 - 22.22: 1 Bond angle restraints: 13021 Sorted by residual: angle pdb=" CA VAL L 182 " pdb=" CB VAL L 182 " pdb=" CG1 VAL L 182 " ideal model delta sigma weight residual 110.40 132.62 -22.22 1.70e+00 3.46e-01 1.71e+02 angle pdb=" C LYS E 228 " pdb=" CA LYS E 228 " pdb=" CB LYS E 228 " ideal model delta sigma weight residual 110.63 127.72 -17.09 1.85e+00 2.92e-01 8.54e+01 angle pdb=" C LYS O 228 " pdb=" CA LYS O 228 " pdb=" CB LYS O 228 " ideal model delta sigma weight residual 110.67 126.63 -15.96 1.92e+00 2.71e-01 6.91e+01 angle pdb=" CA ASP O 198 " pdb=" CB ASP O 198 " pdb=" CG ASP O 198 " ideal model delta sigma weight residual 112.60 120.04 -7.44 1.00e+00 1.00e+00 5.53e+01 angle pdb=" CA PRO S1321 " pdb=" N PRO S1321 " pdb=" CD PRO S1321 " ideal model delta sigma weight residual 112.00 102.41 9.59 1.40e+00 5.10e-01 4.69e+01 ... (remaining 13016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 5293 17.89 - 35.78: 451 35.78 - 53.66: 70 53.66 - 71.55: 31 71.55 - 89.44: 14 Dihedral angle restraints: 5859 sinusoidal: 2419 harmonic: 3440 Sorted by residual: dihedral pdb=" C LYS E 228 " pdb=" N LYS E 228 " pdb=" CA LYS E 228 " pdb=" CB LYS E 228 " ideal model delta harmonic sigma weight residual -122.60 -154.13 31.53 0 2.50e+00 1.60e-01 1.59e+02 dihedral pdb=" C LYS O 228 " pdb=" N LYS O 228 " pdb=" CA LYS O 228 " pdb=" CB LYS O 228 " ideal model delta harmonic sigma weight residual -122.60 -154.05 31.45 0 2.50e+00 1.60e-01 1.58e+02 dihedral pdb=" N LYS O 228 " pdb=" C LYS O 228 " pdb=" CA LYS O 228 " pdb=" CB LYS O 228 " ideal model delta harmonic sigma weight residual 122.80 150.40 -27.60 0 2.50e+00 1.60e-01 1.22e+02 ... (remaining 5856 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.239: 1424 0.239 - 0.479: 24 0.479 - 0.718: 0 0.718 - 0.958: 0 0.958 - 1.197: 3 Chirality restraints: 1451 Sorted by residual: chirality pdb=" CA LYS E 228 " pdb=" N LYS E 228 " pdb=" C LYS E 228 " pdb=" CB LYS E 228 " both_signs ideal model delta sigma weight residual False 2.51 1.31 1.20 2.00e-01 2.50e+01 3.58e+01 chirality pdb=" CA LYS O 228 " pdb=" N LYS O 228 " pdb=" C LYS O 228 " pdb=" CB LYS O 228 " both_signs ideal model delta sigma weight residual False 2.51 1.32 1.19 2.00e-01 2.50e+01 3.56e+01 chirality pdb=" CB VAL L 182 " pdb=" CA VAL L 182 " pdb=" CG1 VAL L 182 " pdb=" CG2 VAL L 182 " both_signs ideal model delta sigma weight residual False -2.63 -1.58 -1.05 2.00e-01 2.50e+01 2.75e+01 ... (remaining 1448 not shown) Planarity restraints: 1682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 185 " -0.192 2.00e-02 2.50e+03 9.62e-02 2.31e+02 pdb=" CG TRP G 185 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP G 185 " 0.088 2.00e-02 2.50e+03 pdb=" CD2 TRP G 185 " 0.065 2.00e-02 2.50e+03 pdb=" NE1 TRP G 185 " 0.053 2.00e-02 2.50e+03 pdb=" CE2 TRP G 185 " -0.017 2.00e-02 2.50e+03 pdb=" CE3 TRP G 185 " 0.114 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 185 " -0.127 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 185 " 0.058 2.00e-02 2.50e+03 pdb=" CH2 TRP G 185 " -0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP S1322 " -0.168 2.00e-02 2.50e+03 9.24e-02 2.13e+02 pdb=" CG TRP S1322 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP S1322 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP S1322 " 0.095 2.00e-02 2.50e+03 pdb=" NE1 TRP S1322 " 0.067 2.00e-02 2.50e+03 pdb=" CE2 TRP S1322 " 0.027 2.00e-02 2.50e+03 pdb=" CE3 TRP S1322 " 0.135 2.00e-02 2.50e+03 pdb=" CZ2 TRP S1322 " -0.098 2.00e-02 2.50e+03 pdb=" CZ3 TRP S1322 " 0.027 2.00e-02 2.50e+03 pdb=" CH2 TRP S1322 " -0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 146 " 0.190 2.00e-02 2.50e+03 1.02e-01 2.09e+02 pdb=" CG TYR G 146 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR G 146 " -0.085 2.00e-02 2.50e+03 pdb=" CD2 TYR G 146 " -0.085 2.00e-02 2.50e+03 pdb=" CE1 TYR G 146 " -0.056 2.00e-02 2.50e+03 pdb=" CE2 TYR G 146 " -0.052 2.00e-02 2.50e+03 pdb=" CZ TYR G 146 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR G 146 " 0.152 2.00e-02 2.50e+03 ... (remaining 1679 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 4881 3.02 - 3.49: 10431 3.49 - 3.96: 14440 3.96 - 4.43: 15438 4.43 - 4.90: 24166 Nonbonded interactions: 69356 Sorted by model distance: nonbonded pdb=" OD1 ASP E 104 " pdb=" OG1 THR E 109 " model vdw 2.546 3.040 nonbonded pdb=" OD1 ASP D 104 " pdb=" OG1 THR D 109 " model vdw 2.549 3.040 nonbonded pdb=" OG SER N 34 " pdb=" OE1 GLU N 36 " model vdw 2.552 3.040 nonbonded pdb=" O LYS O 228 " pdb=" C ALA O 229 " model vdw 2.554 3.270 nonbonded pdb=" OD1 ASP O 104 " pdb=" OG1 THR O 109 " model vdw 2.555 3.040 ... (remaining 69351 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 'D' and resid 17 through 232) selection = (chain 'E' and (resid 17 through 82 or resid 100 through 232)) selection = (chain 'L' and (resid 17 through 82 or resid 100 through 232)) selection = (chain 'N' and (resid 17 through 82 or resid 100 through 232)) selection = (chain 'O' and (resid 17 through 82 or resid 100 through 232)) } 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: 1.050 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: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.750 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 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 : 0.013 0.048 9602 Z= 0.773 Angle : 1.841 22.224 13021 Z= 1.236 Chirality : 0.112 1.197 1451 Planarity : 0.025 0.505 1682 Dihedral : 14.855 89.437 3631 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.60 % Allowed : 5.12 % Favored : 94.29 % Rotamer: Outliers : 2.46 % Allowed : 4.52 % Favored : 93.03 % Cbeta Deviations : 0.54 % Peptide Plane: Cis-proline : 6.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.22), residues: 1173 helix: -2.20 (0.15), residues: 749 sheet: None (None), residues: 0 loop : -0.37 (0.33), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 168 TYR 0.190 0.030 TYR G 146 PHE 0.050 0.012 PHE L 169 TRP 0.192 0.025 TRP G 185 HIS 0.011 0.003 HIS D 63 Details of bonding type rmsd/Z covalent geometry : bond 0.01272 / 0.77 ( 9602) covalent geometry : angle 1.84050 / 1.24 (13021) hydrogen bonds : bond 0.19767 / 12.62 ( 477) hydrogen bonds : angle 8.12879 / 5.83 ( 1386) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 235 time to evaluate : 0.381 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: D 13 HIS cc_start: 0.7282 (t-170) cc_final: 0.7031 (t-170) REVERT: D 30 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7529 (tp30) REVERT: D 40 MET cc_start: 0.9227 (tpp) cc_final: 0.8450 (mtm) REVERT: D 133 ARG cc_start: 0.8836 (mtm-85) cc_final: 0.8603 (ttp-110) REVERT: D 183 LYS cc_start: 0.8157 (mttt) cc_final: 0.7730 (mttt) REVERT: D 214 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8482 (tp30) REVERT: D 219 CYS cc_start: 0.8705 (m) cc_final: 0.8420 (t) REVERT: E 56 MET cc_start: 0.8708 (tpp) cc_final: 0.8374 (tpp) REVERT: E 103 SER cc_start: 0.8344 (p) cc_final: 0.8074 (t) REVERT: E 104 ASP cc_start: 0.8437 (m-30) cc_final: 0.8215 (m-30) REVERT: E 115 GLN cc_start: 0.7592 (mt0) cc_final: 0.7341 (mt0) REVERT: E 177 GLN cc_start: 0.7886 (tp-100) cc_final: 0.7641 (tp-100) REVERT: E 230 ARG cc_start: 0.5818 (OUTLIER) cc_final: 0.5427 (tmt170) REVERT: G 75 ASN cc_start: 0.8627 (m110) cc_final: 0.8405 (m110) REVERT: L 51 GLN cc_start: 0.8519 (tm-30) cc_final: 0.8179 (tm-30) REVERT: L 54 ASN cc_start: 0.8541 (m-40) cc_final: 0.7596 (m-40) REVERT: L 58 ASN cc_start: 0.8494 (m-40) cc_final: 0.8244 (t0) REVERT: L 188 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8241 (tp30) REVERT: N 67 MET cc_start: 0.8731 (mmt) cc_final: 0.8469 (mmt) REVERT: N 101 ARG cc_start: 0.7196 (mmm160) cc_final: 0.6513 (mmp-170) REVERT: N 118 TRP cc_start: 0.8649 (m100) cc_final: 0.8387 (m-90) REVERT: N 170 TYR cc_start: 0.6187 (OUTLIER) cc_final: 0.4191 (t80) REVERT: N 190 LEU cc_start: 0.7962 (mt) cc_final: 0.7641 (mt) REVERT: O 30 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7642 (mm-30) REVERT: O 31 LYS cc_start: 0.8782 (tptt) cc_final: 0.8272 (mttt) REVERT: O 52 ASP cc_start: 0.8965 (m-30) cc_final: 0.8659 (m-30) REVERT: O 75 ASN cc_start: 0.9189 (m110) cc_final: 0.8946 (m110) REVERT: O 119 MET cc_start: 0.7676 (mtp) cc_final: 0.6861 (mmm) REVERT: O 141 LYS cc_start: 0.8876 (mttt) cc_final: 0.8195 (ttpt) REVERT: O 150 SER cc_start: 0.9171 (p) cc_final: 0.8897 (m) REVERT: O 183 LYS cc_start: 0.9028 (pttp) cc_final: 0.8545 (mttp) REVERT: O 232 LEU cc_start: 0.6374 (OUTLIER) cc_final: 0.6027 (tt) outliers start: 25 outliers final: 7 residues processed: 257 average time/residue: 0.1136 time to fit residues: 38.4479 Evaluate side-chains 184 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 174 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 140 ASN N 180 GLN O 75 ASN O 85 HIS O 122 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.119016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.097103 restraints weight = 33472.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.097896 restraints weight = 24926.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.098651 restraints weight = 20375.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.098943 restraints weight = 17960.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.099136 restraints weight = 17285.638| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9602 Z= 0.168 Angle : 0.707 8.011 13021 Z= 0.378 Chirality : 0.044 0.247 1451 Planarity : 0.006 0.061 1682 Dihedral : 6.516 33.562 1279 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.84 % Favored : 96.08 % Rotamer: Outliers : 0.10 % Allowed : 3.34 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.24), residues: 1173 helix: -0.75 (0.18), residues: 762 sheet: -2.01 (0.64), residues: 7 loop : -0.17 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O 133 TYR 0.018 0.002 TYR D 165 PHE 0.011 0.002 PHE G 41 TRP 0.023 0.002 TRP L 81 HIS 0.005 0.001 HIS O 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 ( 9602) covalent geometry : angle 0.70699 / 0.38 (13021) hydrogen bonds : bond 0.05123 / 3.33 ( 477) hydrogen bonds : angle 5.25861 / 3.78 ( 1386) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 0.365 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: D 40 MET cc_start: 0.8818 (tpp) cc_final: 0.8563 (mtm) REVERT: D 82 ASP cc_start: 0.6219 (m-30) cc_final: 0.5554 (m-30) REVERT: E 56 MET cc_start: 0.8284 (tpp) cc_final: 0.8048 (tmm) REVERT: E 103 SER cc_start: 0.8565 (p) cc_final: 0.8326 (p) REVERT: E 104 ASP cc_start: 0.8524 (m-30) cc_final: 0.8217 (m-30) REVERT: E 140 ASN cc_start: 0.8571 (m-40) cc_final: 0.8341 (m-40) REVERT: G 19 ARG cc_start: 0.8719 (ttt-90) cc_final: 0.8489 (ttt180) REVERT: G 30 GLU cc_start: 0.7114 (pt0) cc_final: 0.6866 (pt0) REVERT: G 75 ASN cc_start: 0.8380 (m110) cc_final: 0.8158 (m110) REVERT: L 54 ASN cc_start: 0.7798 (m-40) cc_final: 0.6915 (m110) REVERT: L 133 ARG cc_start: 0.8817 (ttm170) cc_final: 0.8442 (ttm110) REVERT: N 82 ASP cc_start: 0.7376 (m-30) cc_final: 0.7062 (m-30) REVERT: O 31 LYS cc_start: 0.8443 (tptt) cc_final: 0.8129 (mttt) REVERT: O 52 ASP cc_start: 0.8802 (m-30) cc_final: 0.8302 (m-30) REVERT: O 101 ARG cc_start: 0.9135 (mmt180) cc_final: 0.8500 (mmp80) REVERT: O 119 MET cc_start: 0.7497 (mtp) cc_final: 0.6932 (mmm) outliers start: 1 outliers final: 0 residues processed: 224 average time/residue: 0.1052 time to fit residues: 31.3708 Evaluate side-chains 166 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 76 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 51 optimal weight: 0.0270 chunk 16 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 106 optimal weight: 20.0000 chunk 110 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 overall best weight: 3.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 220 GLN G 184 ASN L 140 ASN N 180 GLN O 122 ASN ** O 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.117195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.093983 restraints weight = 34128.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.095441 restraints weight = 25810.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.096313 restraints weight = 21394.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.096605 restraints weight = 19056.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.097520 restraints weight = 18035.548| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9602 Z= 0.192 Angle : 0.689 11.385 13021 Z= 0.362 Chirality : 0.044 0.163 1451 Planarity : 0.006 0.063 1682 Dihedral : 6.142 34.821 1279 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.77 % Favored : 95.14 % Rotamer: Outliers : 0.20 % Allowed : 3.93 % Favored : 95.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.25), residues: 1173 helix: -0.33 (0.19), residues: 767 sheet: -3.39 (0.61), residues: 7 loop : -0.30 (0.34), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 163 TYR 0.020 0.003 TYR N 170 PHE 0.014 0.002 PHE N 41 TRP 0.048 0.002 TRP L 118 HIS 0.004 0.001 HIS D 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 ( 9602) covalent geometry : angle 0.68939 / 0.36 (13021) hydrogen bonds : bond 0.04562 / 2.99 ( 477) hydrogen bonds : angle 5.13249 / 3.69 ( 1386) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 208 time to evaluate : 0.376 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: D 40 MET cc_start: 0.8840 (tpp) cc_final: 0.8516 (mtm) REVERT: D 82 ASP cc_start: 0.5453 (m-30) cc_final: 0.5183 (m-30) REVERT: E 51 GLN cc_start: 0.8953 (tt0) cc_final: 0.8425 (pp30) REVERT: E 56 MET cc_start: 0.8397 (tpp) cc_final: 0.8074 (tpp) REVERT: E 104 ASP cc_start: 0.8495 (m-30) cc_final: 0.8280 (m-30) REVERT: G 75 ASN cc_start: 0.8350 (m110) cc_final: 0.8124 (m110) REVERT: G 165 TYR cc_start: 0.7846 (t80) cc_final: 0.7399 (t80) REVERT: L 54 ASN cc_start: 0.7632 (m-40) cc_final: 0.7094 (m-40) REVERT: L 179 SER cc_start: 0.8075 (t) cc_final: 0.7852 (t) REVERT: N 82 ASP cc_start: 0.7482 (m-30) cc_final: 0.7116 (m-30) REVERT: O 31 LYS cc_start: 0.8450 (tptt) cc_final: 0.8126 (mttt) REVERT: O 51 GLN cc_start: 0.8251 (pp30) cc_final: 0.7921 (pp30) REVERT: O 52 ASP cc_start: 0.8848 (m-30) cc_final: 0.8335 (m-30) REVERT: O 83 ARG cc_start: 0.8402 (tmt170) cc_final: 0.8023 (ttt-90) REVERT: O 101 ARG cc_start: 0.9148 (mmt180) cc_final: 0.8709 (mmt-90) REVERT: O 119 MET cc_start: 0.7579 (mtp) cc_final: 0.7003 (mmm) REVERT: O 141 LYS cc_start: 0.8782 (mttt) cc_final: 0.7941 (tttp) REVERT: O 231 VAL cc_start: -0.0110 (OUTLIER) cc_final: -0.0482 (t) outliers start: 2 outliers final: 1 residues processed: 209 average time/residue: 0.1024 time to fit residues: 28.8970 Evaluate side-chains 160 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 158 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 49 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 4 optimal weight: 0.0980 chunk 108 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 118 optimal weight: 0.0030 chunk 103 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 26 optimal weight: 0.0030 chunk 7 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 overall best weight: 1.6204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 54 ASN G 177 GLN L 140 ASN ** N 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 184 ASN O 121 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.119362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.096774 restraints weight = 34578.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.097513 restraints weight = 28142.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.098435 restraints weight = 23206.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.098964 restraints weight = 20376.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.099132 restraints weight = 19012.810| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9602 Z= 0.130 Angle : 0.619 7.519 13021 Z= 0.322 Chirality : 0.042 0.193 1451 Planarity : 0.005 0.061 1682 Dihedral : 5.607 31.512 1279 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.58 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.25), residues: 1173 helix: -0.12 (0.19), residues: 768 sheet: -3.68 (0.76), residues: 7 loop : -0.21 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 133 TYR 0.030 0.002 TYR N 170 PHE 0.008 0.001 PHE G 33 TRP 0.023 0.002 TRP L 118 HIS 0.004 0.001 HIS D 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 9602) covalent geometry : angle 0.61904 / 0.32 (13021) hydrogen bonds : bond 0.03920 / 2.52 ( 477) hydrogen bonds : angle 4.81223 / 3.44 ( 1386) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.234 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: D 40 MET cc_start: 0.8680 (tpp) cc_final: 0.8431 (mtm) REVERT: E 51 GLN cc_start: 0.8778 (tt0) cc_final: 0.8317 (pp30) REVERT: E 56 MET cc_start: 0.8355 (tpp) cc_final: 0.8111 (tpp) REVERT: E 67 MET cc_start: 0.7808 (mmt) cc_final: 0.7531 (mmt) REVERT: E 104 ASP cc_start: 0.8335 (m-30) cc_final: 0.8088 (m-30) REVERT: G 75 ASN cc_start: 0.8246 (m110) cc_final: 0.7936 (m110) REVERT: G 129 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8700 (tp30) REVERT: G 165 TYR cc_start: 0.7810 (t80) cc_final: 0.7414 (t80) REVERT: L 52 ASP cc_start: 0.8485 (m-30) cc_final: 0.7750 (m-30) REVERT: L 54 ASN cc_start: 0.7339 (m-40) cc_final: 0.6733 (m-40) REVERT: L 56 MET cc_start: 0.8412 (tpp) cc_final: 0.8180 (tpp) REVERT: N 82 ASP cc_start: 0.7569 (m-30) cc_final: 0.7200 (m-30) REVERT: O 31 LYS cc_start: 0.8417 (tptt) cc_final: 0.8059 (mttt) REVERT: O 52 ASP cc_start: 0.8834 (m-30) cc_final: 0.8603 (m-30) REVERT: O 101 ARG cc_start: 0.9129 (mmt180) cc_final: 0.8708 (mmt-90) REVERT: O 119 MET cc_start: 0.7535 (mtp) cc_final: 0.7277 (mmt) REVERT: O 141 LYS cc_start: 0.8779 (mttt) cc_final: 0.7908 (tttp) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.1001 time to fit residues: 28.1473 Evaluate side-chains 165 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 81 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 51 optimal weight: 0.0770 overall best weight: 1.7344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 115 GLN L 140 ASN N 180 GLN N 184 ASN O 121 HIS O 122 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.119267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.096216 restraints weight = 34287.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.097861 restraints weight = 25651.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.099017 restraints weight = 21037.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.099615 restraints weight = 18390.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.100298 restraints weight = 16929.344| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9602 Z= 0.129 Angle : 0.599 7.470 13021 Z= 0.311 Chirality : 0.041 0.152 1451 Planarity : 0.005 0.058 1682 Dihedral : 5.283 29.646 1279 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.01 % Favored : 95.91 % Rotamer: Outliers : 0.10 % Allowed : 2.95 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.25), residues: 1173 helix: -0.03 (0.19), residues: 762 sheet: -3.19 (0.98), residues: 7 loop : -0.18 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 101 TYR 0.022 0.002 TYR O 131 PHE 0.010 0.001 PHE G 33 TRP 0.052 0.002 TRP L 118 HIS 0.003 0.001 HIS G 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 9602) covalent geometry : angle 0.59924 / 0.31 (13021) hydrogen bonds : bond 0.03640 / 2.34 ( 477) hydrogen bonds : angle 4.68738 / 3.35 ( 1386) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 0.369 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: D 82 ASP cc_start: 0.5204 (m-30) cc_final: 0.4984 (m-30) REVERT: E 51 GLN cc_start: 0.8793 (tt0) cc_final: 0.8310 (pp30) REVERT: E 56 MET cc_start: 0.8274 (tpp) cc_final: 0.8048 (tpp) REVERT: E 69 MET cc_start: 0.6760 (mtt) cc_final: 0.6480 (mtm) REVERT: E 115 GLN cc_start: 0.7510 (mt0) cc_final: 0.7090 (mt0) REVERT: E 119 MET cc_start: 0.7327 (mmt) cc_final: 0.7044 (mmm) REVERT: E 144 ARG cc_start: 0.8265 (tpt90) cc_final: 0.7877 (tpt90) REVERT: G 75 ASN cc_start: 0.8265 (m110) cc_final: 0.7990 (m110) REVERT: G 129 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8555 (tp30) REVERT: G 165 TYR cc_start: 0.7760 (t80) cc_final: 0.7408 (t80) REVERT: G 186 MET cc_start: 0.7371 (mtm) cc_final: 0.7168 (mtm) REVERT: L 52 ASP cc_start: 0.8413 (m-30) cc_final: 0.7688 (m-30) REVERT: L 54 ASN cc_start: 0.7080 (m-40) cc_final: 0.6588 (m-40) REVERT: L 115 GLN cc_start: 0.9261 (mp10) cc_final: 0.8990 (mp10) REVERT: L 145 MET cc_start: 0.7110 (ttm) cc_final: 0.6857 (ttm) REVERT: N 82 ASP cc_start: 0.7500 (m-30) cc_final: 0.7161 (m-30) REVERT: O 30 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6701 (mp0) REVERT: O 31 LYS cc_start: 0.8381 (tptt) cc_final: 0.8061 (mttt) REVERT: O 52 ASP cc_start: 0.8838 (m-30) cc_final: 0.8631 (m-30) REVERT: O 75 ASN cc_start: 0.9016 (m110) cc_final: 0.8814 (m110) REVERT: O 118 TRP cc_start: 0.6195 (m-10) cc_final: 0.5839 (m-90) REVERT: O 119 MET cc_start: 0.7364 (mtt) cc_final: 0.7120 (mmt) REVERT: O 141 LYS cc_start: 0.8778 (mttt) cc_final: 0.7863 (tttp) outliers start: 1 outliers final: 0 residues processed: 201 average time/residue: 0.0969 time to fit residues: 26.1682 Evaluate side-chains 169 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 91 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 21 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 64 GLN L 63 HIS L 140 ASN O 121 HIS O 122 ASN O 156 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.117956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.095000 restraints weight = 35067.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.096521 restraints weight = 26756.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.097566 restraints weight = 22307.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.098326 restraints weight = 19720.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.098522 restraints weight = 18072.883| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9602 Z= 0.164 Angle : 0.627 7.984 13021 Z= 0.326 Chirality : 0.042 0.172 1451 Planarity : 0.005 0.062 1682 Dihedral : 5.354 29.014 1279 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.18 % Favored : 95.74 % Rotamer: Outliers : 0.10 % Allowed : 2.06 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.25), residues: 1173 helix: -0.04 (0.19), residues: 768 sheet: -2.71 (1.27), residues: 7 loop : -0.28 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 101 TYR 0.016 0.002 TYR O 131 PHE 0.016 0.002 PHE G 33 TRP 0.034 0.002 TRP L 118 HIS 0.004 0.001 HIS O 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 ( 9602) covalent geometry : angle 0.62673 / 0.33 (13021) hydrogen bonds : bond 0.03672 / 2.36 ( 477) hydrogen bonds : angle 4.77047 / 3.38 ( 1386) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 0.437 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: D 179 SER cc_start: 0.7542 (t) cc_final: 0.7070 (t) REVERT: E 51 GLN cc_start: 0.8793 (tt0) cc_final: 0.8311 (pp30) REVERT: E 56 MET cc_start: 0.8318 (tpp) cc_final: 0.8082 (tpp) REVERT: E 67 MET cc_start: 0.7907 (mmt) cc_final: 0.7672 (mmt) REVERT: E 69 MET cc_start: 0.6319 (mtt) cc_final: 0.6023 (mtm) REVERT: E 115 GLN cc_start: 0.7509 (mt0) cc_final: 0.7034 (mt0) REVERT: E 119 MET cc_start: 0.7508 (mmt) cc_final: 0.7215 (mmm) REVERT: G 75 ASN cc_start: 0.8247 (m110) cc_final: 0.7918 (m110) REVERT: G 129 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8915 (tp30) REVERT: G 165 TYR cc_start: 0.7868 (t80) cc_final: 0.7439 (t80) REVERT: L 52 ASP cc_start: 0.8523 (m-30) cc_final: 0.7827 (m-30) REVERT: L 54 ASN cc_start: 0.7217 (m-40) cc_final: 0.6673 (m-40) REVERT: N 82 ASP cc_start: 0.7619 (m-30) cc_final: 0.7310 (m-30) REVERT: O 30 GLU cc_start: 0.7236 (mm-30) cc_final: 0.6663 (mp0) REVERT: O 31 LYS cc_start: 0.8482 (tptt) cc_final: 0.8142 (mttt) REVERT: O 52 ASP cc_start: 0.8898 (m-30) cc_final: 0.8696 (m-30) REVERT: O 75 ASN cc_start: 0.9043 (m110) cc_final: 0.8820 (m110) REVERT: O 119 MET cc_start: 0.7314 (mtt) cc_final: 0.6953 (mmt) REVERT: O 141 LYS cc_start: 0.8878 (mttt) cc_final: 0.7937 (tttp) outliers start: 1 outliers final: 1 residues processed: 194 average time/residue: 0.0972 time to fit residues: 25.5434 Evaluate side-chains 158 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 32 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 30 optimal weight: 40.0000 chunk 76 optimal weight: 0.4980 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 122 ASN E 156 GLN G 177 GLN L 140 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.117923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.096681 restraints weight = 34544.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.096340 restraints weight = 27891.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.097031 restraints weight = 24719.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.097440 restraints weight = 22841.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.097556 restraints weight = 21479.536| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9602 Z= 0.158 Angle : 0.631 8.354 13021 Z= 0.327 Chirality : 0.042 0.177 1451 Planarity : 0.005 0.064 1682 Dihedral : 5.346 29.635 1279 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.43 % Favored : 95.48 % Rotamer: Outliers : 0.10 % Allowed : 1.87 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.25), residues: 1173 helix: -0.07 (0.19), residues: 768 sheet: -2.74 (1.31), residues: 7 loop : -0.27 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG N 83 TYR 0.020 0.002 TYR O 131 PHE 0.015 0.002 PHE G 33 TRP 0.031 0.002 TRP L 118 HIS 0.003 0.001 HIS G 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 9602) covalent geometry : angle 0.63089 / 0.33 (13021) hydrogen bonds : bond 0.03603 / 2.34 ( 477) hydrogen bonds : angle 4.79970 / 3.41 ( 1386) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 199 time to evaluate : 0.277 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: symmetry clash revert: symmetry clash REVERT: E 51 GLN cc_start: 0.8771 (tt0) cc_final: 0.8309 (pp30) REVERT: E 52 ASP cc_start: 0.8396 (t70) cc_final: 0.8143 (t70) REVERT: E 56 MET cc_start: 0.8274 (tpp) cc_final: 0.8055 (tpp) REVERT: E 67 MET cc_start: 0.7972 (mmt) cc_final: 0.7641 (mmt) REVERT: E 69 MET cc_start: 0.6343 (mtt) cc_final: 0.6068 (mtm) REVERT: E 115 GLN cc_start: 0.7505 (mt0) cc_final: 0.7050 (mt0) REVERT: E 119 MET cc_start: 0.7655 (mmt) cc_final: 0.7333 (mmm) REVERT: E 144 ARG cc_start: 0.8334 (tpt90) cc_final: 0.7830 (tpt90) REVERT: G 36 GLU cc_start: 0.6256 (mm-30) cc_final: 0.6029 (mm-30) REVERT: G 75 ASN cc_start: 0.8364 (m110) cc_final: 0.7934 (m110) REVERT: G 142 ILE cc_start: 0.9042 (pt) cc_final: 0.8727 (pt) REVERT: G 165 TYR cc_start: 0.7748 (t80) cc_final: 0.7347 (t80) REVERT: L 52 ASP cc_start: 0.8478 (m-30) cc_final: 0.7892 (m-30) REVERT: L 54 ASN cc_start: 0.7133 (m-40) cc_final: 0.6619 (m-40) REVERT: L 115 GLN cc_start: 0.9240 (mp10) cc_final: 0.8806 (mp10) REVERT: L 119 MET cc_start: 0.6782 (mtp) cc_final: 0.6502 (mmm) REVERT: N 82 ASP cc_start: 0.7521 (m-30) cc_final: 0.7090 (m-30) REVERT: O 31 LYS cc_start: 0.8377 (tptt) cc_final: 0.8037 (mttt) REVERT: O 75 ASN cc_start: 0.9063 (m110) cc_final: 0.8855 (m110) REVERT: O 119 MET cc_start: 0.7298 (mtt) cc_final: 0.6906 (mmt) REVERT: O 141 LYS cc_start: 0.8843 (mttt) cc_final: 0.7939 (tttp) REVERT: O 186 MET cc_start: 0.7428 (mmp) cc_final: 0.7195 (mmm) outliers start: 1 outliers final: 1 residues processed: 199 average time/residue: 0.1013 time to fit residues: 27.1300 Evaluate side-chains 168 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 74 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 chunk 82 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 54 ASN L 140 ASN O 121 HIS O 122 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.118538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.096306 restraints weight = 34821.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.097789 restraints weight = 26886.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.098825 restraints weight = 22511.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.099366 restraints weight = 19918.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.099986 restraints weight = 18477.906| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9602 Z= 0.141 Angle : 0.608 8.070 13021 Z= 0.315 Chirality : 0.041 0.167 1451 Planarity : 0.005 0.063 1682 Dihedral : 5.241 30.641 1279 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.18 % Favored : 95.74 % Rotamer: Outliers : 0.10 % Allowed : 1.38 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.25), residues: 1173 helix: -0.03 (0.19), residues: 767 sheet: -2.74 (1.33), residues: 7 loop : -0.24 (0.33), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 101 TYR 0.020 0.002 TYR O 131 PHE 0.011 0.001 PHE G 33 TRP 0.028 0.002 TRP L 118 HIS 0.003 0.001 HIS G 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 9602) covalent geometry : angle 0.60820 / 0.32 (13021) hydrogen bonds : bond 0.03513 / 2.29 ( 477) hydrogen bonds : angle 4.72601 / 3.37 ( 1386) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 202 time to evaluate : 0.395 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: D 14 GLN cc_start: 0.8137 (pm20) cc_final: 0.7850 (pp30) REVERT: E 51 GLN cc_start: 0.8741 (tt0) cc_final: 0.8252 (pp30) REVERT: E 52 ASP cc_start: 0.8336 (t70) cc_final: 0.8105 (t70) REVERT: E 56 MET cc_start: 0.8239 (tpp) cc_final: 0.8022 (tpp) REVERT: E 67 MET cc_start: 0.7968 (mmt) cc_final: 0.7623 (mmt) REVERT: E 115 GLN cc_start: 0.7550 (mt0) cc_final: 0.7128 (mt0) REVERT: E 119 MET cc_start: 0.7494 (mmt) cc_final: 0.7190 (mmp) REVERT: E 140 ASN cc_start: 0.8822 (m-40) cc_final: 0.8534 (t0) REVERT: E 144 ARG cc_start: 0.8397 (tpt90) cc_final: 0.7913 (tpt90) REVERT: G 75 ASN cc_start: 0.8136 (m110) cc_final: 0.7783 (m110) REVERT: G 165 TYR cc_start: 0.7774 (t80) cc_final: 0.7403 (t80) REVERT: L 54 ASN cc_start: 0.7169 (m-40) cc_final: 0.6725 (m-40) REVERT: L 119 MET cc_start: 0.6822 (mtp) cc_final: 0.6500 (mmm) REVERT: L 132 LYS cc_start: 0.8622 (ttmt) cc_final: 0.8403 (ttmt) REVERT: L 133 ARG cc_start: 0.8861 (ttm170) cc_final: 0.8352 (ttm110) REVERT: L 217 THR cc_start: 0.8424 (m) cc_final: 0.8216 (p) REVERT: N 52 ASP cc_start: 0.7573 (m-30) cc_final: 0.7269 (m-30) REVERT: O 31 LYS cc_start: 0.8418 (tptt) cc_final: 0.8028 (mttt) REVERT: O 52 ASP cc_start: 0.8937 (m-30) cc_final: 0.8673 (m-30) REVERT: O 75 ASN cc_start: 0.9107 (m110) cc_final: 0.8845 (m110) REVERT: O 119 MET cc_start: 0.7282 (mtt) cc_final: 0.6865 (mmt) REVERT: O 141 LYS cc_start: 0.8782 (mttt) cc_final: 0.7827 (tttp) REVERT: O 216 MET cc_start: 0.6600 (ptp) cc_final: 0.5849 (ptp) outliers start: 1 outliers final: 0 residues processed: 202 average time/residue: 0.1054 time to fit residues: 28.5394 Evaluate side-chains 168 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 55 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 122 ASN G 177 GLN L 140 ASN O 121 HIS O 122 ASN ** O 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.117054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.095003 restraints weight = 35141.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.096268 restraints weight = 28430.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.096980 restraints weight = 24476.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.097375 restraints weight = 22242.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.097961 restraints weight = 20981.895| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9602 Z= 0.200 Angle : 0.704 12.022 13021 Z= 0.366 Chirality : 0.044 0.172 1451 Planarity : 0.006 0.085 1682 Dihedral : 5.577 33.116 1279 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.54 % Favored : 94.37 % Rotamer: Outliers : 0.20 % Allowed : 1.08 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.25), residues: 1173 helix: -0.21 (0.19), residues: 758 sheet: -2.80 (1.27), residues: 7 loop : -0.21 (0.34), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG O 133 TYR 0.022 0.002 TYR O 131 PHE 0.021 0.002 PHE G 33 TRP 0.073 0.003 TRP L 118 HIS 0.004 0.001 HIS G 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.20 ( 9602) covalent geometry : angle 0.70410 / 0.37 (13021) hydrogen bonds : bond 0.03863 / 2.55 ( 477) hydrogen bonds : angle 4.98756 / 3.54 ( 1386) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 192 time to evaluate : 0.349 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: D 14 GLN cc_start: 0.8187 (pm20) cc_final: 0.7916 (pp30) REVERT: D 40 MET cc_start: 0.6984 (mtm) cc_final: 0.6470 (mtm) REVERT: D 144 ARG cc_start: 0.7731 (tpt170) cc_final: 0.7190 (tpt170) REVERT: E 51 GLN cc_start: 0.8721 (tt0) cc_final: 0.8278 (pp30) REVERT: E 52 ASP cc_start: 0.8415 (t70) cc_final: 0.8172 (t70) REVERT: E 115 GLN cc_start: 0.7465 (mt0) cc_final: 0.7246 (mt0) REVERT: E 119 MET cc_start: 0.7483 (mmt) cc_final: 0.7245 (mmm) REVERT: E 140 ASN cc_start: 0.8840 (m-40) cc_final: 0.8471 (t0) REVERT: E 144 ARG cc_start: 0.8355 (tpt90) cc_final: 0.7778 (tpt90) REVERT: G 37 VAL cc_start: 0.8272 (m) cc_final: 0.7928 (p) REVERT: G 75 ASN cc_start: 0.8189 (m110) cc_final: 0.7848 (m110) REVERT: G 165 TYR cc_start: 0.7703 (t80) cc_final: 0.7309 (t80) REVERT: L 54 ASN cc_start: 0.7207 (m-40) cc_final: 0.6935 (m-40) REVERT: L 119 MET cc_start: 0.6988 (mtp) cc_final: 0.6637 (mmm) REVERT: L 132 LYS cc_start: 0.8586 (ttmt) cc_final: 0.8295 (ttmt) REVERT: N 52 ASP cc_start: 0.7535 (m-30) cc_final: 0.7274 (m-30) REVERT: O 31 LYS cc_start: 0.8406 (tptt) cc_final: 0.8076 (mttt) REVERT: O 52 ASP cc_start: 0.8912 (m-30) cc_final: 0.8689 (m-30) REVERT: O 75 ASN cc_start: 0.9116 (m110) cc_final: 0.8855 (m110) REVERT: O 83 ARG cc_start: 0.8161 (tmt170) cc_final: 0.7830 (tmt170) REVERT: O 119 MET cc_start: 0.7271 (mtt) cc_final: 0.6784 (mmm) REVERT: O 141 LYS cc_start: 0.8838 (mttt) cc_final: 0.7987 (ttpp) outliers start: 2 outliers final: 1 residues processed: 192 average time/residue: 0.1115 time to fit residues: 28.6612 Evaluate side-chains 162 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 86 optimal weight: 10.0000 chunk 115 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 59 optimal weight: 0.0070 chunk 35 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 45 optimal weight: 0.0570 overall best weight: 1.1920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 177 GLN L 140 ASN O 121 HIS O 122 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.119609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.098386 restraints weight = 34249.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.098254 restraints weight = 28263.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.099036 restraints weight = 23908.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.099347 restraints weight = 21635.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.099499 restraints weight = 20411.130| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9602 Z= 0.128 Angle : 0.637 8.009 13021 Z= 0.331 Chirality : 0.042 0.158 1451 Planarity : 0.005 0.066 1682 Dihedral : 5.173 33.055 1279 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.67 % Favored : 96.25 % Rotamer: Outliers : 0.10 % Allowed : 0.20 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.25), residues: 1173 helix: -0.05 (0.19), residues: 756 sheet: -2.77 (1.41), residues: 7 loop : -0.16 (0.33), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG L 83 TYR 0.018 0.002 TYR N 170 PHE 0.016 0.001 PHE G 41 TRP 0.068 0.003 TRP L 118 HIS 0.004 0.001 HIS G 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 9602) covalent geometry : angle 0.63674 / 0.33 (13021) hydrogen bonds : bond 0.03657 / 2.40 ( 477) hydrogen bonds : angle 4.76045 / 3.40 ( 1386) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 204 time to evaluate : 0.352 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: symmetry clash REVERT: D 144 ARG cc_start: 0.7887 (tpt170) cc_final: 0.7328 (tpt170) REVERT: E 51 GLN cc_start: 0.8778 (tt0) cc_final: 0.8341 (pp30) REVERT: E 52 ASP cc_start: 0.8393 (t70) cc_final: 0.8154 (t70) REVERT: E 67 MET cc_start: 0.8201 (mmt) cc_final: 0.7748 (mmt) REVERT: E 119 MET cc_start: 0.7593 (mmt) cc_final: 0.7311 (mmp) REVERT: E 140 ASN cc_start: 0.8723 (m-40) cc_final: 0.8406 (t0) REVERT: E 144 ARG cc_start: 0.8271 (tpt90) cc_final: 0.7746 (tpt90) REVERT: G 37 VAL cc_start: 0.8128 (m) cc_final: 0.7830 (p) REVERT: G 75 ASN cc_start: 0.8246 (m110) cc_final: 0.7893 (m110) REVERT: G 165 TYR cc_start: 0.7734 (t80) cc_final: 0.7408 (t80) REVERT: G 216 MET cc_start: 0.6038 (ttt) cc_final: 0.5726 (ttt) REVERT: L 54 ASN cc_start: 0.7141 (m-40) cc_final: 0.6740 (m-40) REVERT: L 115 GLN cc_start: 0.9358 (mp10) cc_final: 0.9150 (mp-120) REVERT: L 133 ARG cc_start: 0.8886 (ttm170) cc_final: 0.8504 (ttm110) REVERT: L 217 THR cc_start: 0.8340 (m) cc_final: 0.8100 (p) REVERT: N 52 ASP cc_start: 0.7559 (m-30) cc_final: 0.7271 (m-30) REVERT: N 215 MET cc_start: 0.6821 (tmm) cc_final: 0.6473 (mpp) REVERT: O 31 LYS cc_start: 0.8369 (tptt) cc_final: 0.8027 (mttt) REVERT: O 52 ASP cc_start: 0.8936 (m-30) cc_final: 0.8695 (m-30) REVERT: O 83 ARG cc_start: 0.8133 (tmt170) cc_final: 0.7743 (tmt170) REVERT: O 119 MET cc_start: 0.7219 (mtt) cc_final: 0.6762 (mmm) REVERT: O 141 LYS cc_start: 0.8782 (mttt) cc_final: 0.7913 (tttp) outliers start: 1 outliers final: 0 residues processed: 204 average time/residue: 0.1173 time to fit residues: 31.7607 Evaluate side-chains 171 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 102 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 108 optimal weight: 0.5980 chunk 116 optimal weight: 7.9990 chunk 113 optimal weight: 0.0970 chunk 71 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 118 optimal weight: 8.9990 chunk 10 optimal weight: 20.0000 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 122 ASN G 180 GLN G 184 ASN L 122 ASN L 140 ASN O 122 ASN O 180 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.119515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.097026 restraints weight = 33959.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.098256 restraints weight = 28407.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.098375 restraints weight = 22182.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.098740 restraints weight = 21570.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.098875 restraints weight = 21204.263| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9602 Z= 0.127 Angle : 0.625 7.674 13021 Z= 0.323 Chirality : 0.041 0.168 1451 Planarity : 0.005 0.063 1682 Dihedral : 5.087 32.598 1279 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.09 % Favored : 95.82 % Rotamer: Outliers : 0.20 % Allowed : 0.59 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.25), residues: 1173 helix: -0.02 (0.19), residues: 757 sheet: -2.20 (1.69), residues: 7 loop : -0.16 (0.33), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 101 TYR 0.011 0.001 TYR N 131 PHE 0.008 0.001 PHE G 33 TRP 0.066 0.003 TRP L 118 HIS 0.007 0.001 HIS L 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 9602) covalent geometry : angle 0.62472 / 0.32 (13021) hydrogen bonds : bond 0.03437 / 2.26 ( 477) hydrogen bonds : angle 4.72808 / 3.40 ( 1386) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1435.60 seconds wall clock time: 25 minutes 39.37 seconds (1539.37 seconds total)