Starting phenix.real_space_refine on Sat Sep 12 17:25:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d3l_27159/09_2026/8d3l_27159.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d3l_27159/09_2026/8d3l_27159.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8d3l_27159/09_2026/8d3l_27159.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d3l_27159/09_2026/8d3l_27159.cif" model { file = "/net/cci-nas-00/data/ceres_data/8d3l_27159/09_2026/8d3l_27159.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d3l_27159/09_2026/8d3l_27159.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d3l_27159/09_2026/8d3l_27159.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d3l_27159/09_2026/8d3l_27159.map" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.028 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: 7 Type Number sf(0) Gaussians Mn 2 7.51 5 Fe 8 7.16 5 P 63 5.49 5 S 106 5.16 5 C 10874 2.51 5 N 3066 2.21 5 O 3366 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17485 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2768 Classifications: {'peptide': 343} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 331} Chain: "B" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2758 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 11, 'TRANS': 330} Chain: "C" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2768 Classifications: {'peptide': 343} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 331} Chain: "D" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2758 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 11, 'TRANS': 330} Chain: "E" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 771 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "F" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 771 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "G" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 671 Classifications: {'DNA': 33} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 32} Chain: "H" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 653 Classifications: {'DNA': 32} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 31} Chain: "I" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1775 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 8, 'TRANS': 209} Chain: "J" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1770 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 8, 'TRANS': 208} Chain: "I" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {' MN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {' MN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14084 SG CYS I 21 44.947 62.454 123.034 1.00 8.72 S ATOM 15460 SG CYS I 190 44.559 60.728 119.782 1.00 10.07 S ATOM 15460 SG CYS I 190 44.559 60.728 119.782 1.00 10.07 S ATOM 15482 SG CYS I 193 48.647 61.031 119.637 1.00 10.89 S ATOM 15525 SG CYS I 199 47.994 58.265 120.908 1.00 7.81 S ATOM 15525 SG CYS I 199 47.994 58.265 120.908 1.00 7.81 S ATOM 14084 SG CYS I 21 44.947 62.454 123.034 1.00 8.72 S ATOM 15460 SG CYS I 190 44.559 60.728 119.782 1.00 10.07 S ATOM 15482 SG CYS I 193 48.647 61.031 119.637 1.00 10.89 S ATOM 15854 SG CYS J 21 43.498 43.198 61.747 1.00 3.29 S ATOM 17295 SG CYS J 199 42.009 47.355 61.495 1.00 4.28 S ATOM 17252 SG CYS J 193 45.117 45.989 64.802 1.00 3.36 S ATOM 17295 SG CYS J 199 42.009 47.355 61.495 1.00 4.28 S ATOM 15854 SG CYS J 21 43.498 43.198 61.747 1.00 3.29 S ATOM 17230 SG CYS J 190 42.383 43.388 65.022 1.00 5.47 S ATOM 17252 SG CYS J 193 45.117 45.989 64.802 1.00 3.36 S ATOM 17230 SG CYS J 190 42.383 43.388 65.022 1.00 5.47 S Time building chain proxies: 3.74, per 1000 atoms: 0.21 Number of scatterers: 17485 At special positions: 0 Unit cell: (112.381, 116.006, 175.822, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 8 26.01 Mn 2 24.99 S 106 16.00 P 63 15.00 O 3366 8.00 N 3066 7.00 C 10874 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: 1.37 Conformation dependent library (CDL) restraints added in 726.9 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 I 301 " pdb="FE1 SF4 I 301 " - pdb=" SG CYS I 190 " pdb="FE2 SF4 I 301 " - pdb=" SG CYS I 199 " pdb="FE4 SF4 I 301 " - pdb=" SG CYS I 21 " pdb="FE4 SF4 I 301 " - pdb=" SG CYS I 193 " pdb=" SF4 J 301 " pdb="FE2 SF4 J 301 " - pdb=" SG CYS J 199 " pdb="FE1 SF4 J 301 " - pdb=" SG CYS J 21 " pdb="FE3 SF4 J 301 " - pdb=" SG CYS J 193 " pdb="FE4 SF4 J 301 " - pdb=" SG CYS J 190 " Number of angles added : 24 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3754 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 19 sheets defined 49.6% alpha, 16.3% beta 20 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 53 through 63 Processing helix chain 'A' and resid 88 through 99 removed outlier: 3.546A pdb=" N GLU A 99 " --> pdb=" O TYR A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 130 removed outlier: 3.544A pdb=" N SER A 104 " --> pdb=" O ASN A 100 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 154 removed outlier: 3.574A pdb=" N PHE A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 178 removed outlier: 4.273A pdb=" N ASP A 178 " --> pdb=" O ASN A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 201 through 225 removed outlier: 3.635A pdb=" N MET A 205 " --> pdb=" O ASN A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 266 removed outlier: 4.851A pdb=" N GLU A 250 " --> pdb=" O ASP A 246 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLY A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LEU A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ARG A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE A 259 " --> pdb=" O TYR A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 285 through 301 removed outlier: 3.590A pdb=" N GLN A 301 " --> pdb=" O GLN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 331 Processing helix chain 'B' and resid 53 through 63 removed outlier: 3.526A pdb=" N GLU B 62 " --> pdb=" O GLY B 58 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG B 63 " --> pdb=" O TYR B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 99 removed outlier: 3.734A pdb=" N ARG B 91 " --> pdb=" O ASN B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 130 removed outlier: 3.522A pdb=" N SER B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU B 129 " --> pdb=" O ARG B 125 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS B 130 " --> pdb=" O MET B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 155 removed outlier: 3.954A pdb=" N GLN B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU B 152 " --> pdb=" O VAL B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 178 removed outlier: 3.760A pdb=" N VAL B 176 " --> pdb=" O ASN B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 189 Processing helix chain 'B' and resid 202 through 225 removed outlier: 3.822A pdb=" N PHE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA B 219 " --> pdb=" O ASN B 215 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 249 Processing helix chain 'B' and resid 251 through 256 removed outlier: 3.840A pdb=" N ALA B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 266 Processing helix chain 'B' and resid 270 through 274 Processing helix chain 'B' and resid 285 through 300 Processing helix chain 'B' and resid 317 through 331 removed outlier: 3.877A pdb=" N ALA B 323 " --> pdb=" O PRO B 319 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE B 329 " --> pdb=" O LEU B 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 63 removed outlier: 3.655A pdb=" N GLU C 62 " --> pdb=" O GLY C 58 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG C 63 " --> pdb=" O TYR C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 100 Processing helix chain 'C' and resid 101 through 130 Processing helix chain 'C' and resid 135 through 155 removed outlier: 3.584A pdb=" N PHE C 139 " --> pdb=" O ASN C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 181 removed outlier: 3.563A pdb=" N GLN C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA C 169 " --> pdb=" O TRP C 165 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA C 170 " --> pdb=" O GLU C 166 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE C 171 " --> pdb=" O GLY C 167 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASN C 172 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 203 removed outlier: 3.952A pdb=" N ASN C 203 " --> pdb=" O ASP C 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 200 through 203' Processing helix chain 'C' and resid 204 through 223 Processing helix chain 'C' and resid 241 through 252 Processing helix chain 'C' and resid 256 through 265 Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 285 through 301 Processing helix chain 'C' and resid 316 through 331 removed outlier: 4.486A pdb=" N TYR C 320 " --> pdb=" O GLY C 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 63 Processing helix chain 'D' and resid 87 through 98 removed outlier: 3.580A pdb=" N SER D 98 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 130 removed outlier: 3.573A pdb=" N SER D 104 " --> pdb=" O ASN D 100 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS D 130 " --> pdb=" O MET D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 155 removed outlier: 3.897A pdb=" N PHE D 139 " --> pdb=" O ASN D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 172 removed outlier: 3.914A pdb=" N LEU D 162 " --> pdb=" O SER D 158 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 179 removed outlier: 4.183A pdb=" N GLN D 179 " --> pdb=" O LYS D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 225 removed outlier: 3.587A pdb=" N VAL D 224 " --> pdb=" O ALA D 220 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY D 225 " --> pdb=" O LEU D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 247 Processing helix chain 'D' and resid 248 through 256 removed outlier: 4.122A pdb=" N GLY D 253 " --> pdb=" O GLU D 249 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N LEU D 254 " --> pdb=" O GLU D 250 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA D 256 " --> pdb=" O ARG D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 266 Processing helix chain 'D' and resid 270 through 272 No H-bonds generated for 'chain 'D' and resid 270 through 272' Processing helix chain 'D' and resid 285 through 302 removed outlier: 3.670A pdb=" N GLU D 302 " --> pdb=" O THR D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 331 removed outlier: 4.474A pdb=" N TYR D 320 " --> pdb=" O GLY D 316 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU D 326 " --> pdb=" O GLN D 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 29 Processing helix chain 'E' and resid 44 through 59 Processing helix chain 'E' and resid 74 through 77 Processing helix chain 'F' and resid 15 through 30 removed outlier: 3.549A pdb=" N ASN F 29 " --> pdb=" O LYS F 25 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TYR F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 56 Processing helix chain 'I' and resid 12 through 21 removed outlier: 4.226A pdb=" N GLN I 16 " --> pdb=" O LEU I 12 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N HIS I 17 " --> pdb=" O SER I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 30 removed outlier: 3.775A pdb=" N ALA I 26 " --> pdb=" O LYS I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 50 Processing helix chain 'I' and resid 119 through 135 Processing helix chain 'I' and resid 158 through 179 Processing helix chain 'I' and resid 188 through 192 removed outlier: 3.828A pdb=" N ASN I 191 " --> pdb=" O PRO I 188 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN I 192 " --> pdb=" O PHE I 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 188 through 192' Processing helix chain 'I' and resid 195 through 200 Processing helix chain 'I' and resid 201 through 205 removed outlier: 3.597A pdb=" N MET I 204 " --> pdb=" O PRO I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 218 removed outlier: 3.542A pdb=" N TYR I 212 " --> pdb=" O SER I 208 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 20 removed outlier: 3.641A pdb=" N GLN J 16 " --> pdb=" O SER J 13 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N HIS J 17 " --> pdb=" O GLY J 14 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHE J 18 " --> pdb=" O LEU J 15 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 30 removed outlier: 4.014A pdb=" N ALA J 26 " --> pdb=" O LYS J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 51 removed outlier: 4.191A pdb=" N GLU J 42 " --> pdb=" O VAL J 38 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLY J 43 " --> pdb=" O ARG J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 120 through 134 removed outlier: 3.648A pdb=" N LEU J 124 " --> pdb=" O ASP J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 178 removed outlier: 3.996A pdb=" N LYS J 164 " --> pdb=" O ALA J 160 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN J 178 " --> pdb=" O HIS J 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 188 through 192 Processing helix chain 'J' and resid 195 through 200 Processing helix chain 'J' and resid 207 through 219 removed outlier: 3.940A pdb=" N ARG J 211 " --> pdb=" O ARG J 207 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR J 212 " --> pdb=" O SER J 208 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 10 removed outlier: 6.360A pdb=" N LEU A 8 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE A 44 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU A 70 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N GLY A 46 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 81 " --> pdb=" O ARG B 79 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA B 78 " --> pdb=" O PHE B 69 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ILE B 67 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ASN B 6 " --> pdb=" O ALA B 43 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N VAL B 45 " --> pdb=" O ASN B 6 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU B 8 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N PHE B 47 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL B 10 " --> pdb=" O PHE B 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 20 removed outlier: 3.796A pdb=" N GLY A 34 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 274 through 276 removed outlier: 4.113A pdb=" N LEU A 283 " --> pdb=" O TYR A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 303 through 305 Processing sheet with id=AA5, first strand: chain 'B' and resid 31 through 37 removed outlier: 6.596A pdb=" N LEU B 26 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ARG B 35 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL B 24 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY B 51 " --> pdb=" O THR B 15 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 303 through 305 Processing sheet with id=AA7, first strand: chain 'C' and resid 7 through 10 removed outlier: 5.613A pdb=" N LEU C 8 " --> pdb=" O VAL C 45 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE C 44 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N LEU C 70 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLY C 46 " --> pdb=" O LEU C 70 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG C 79 " --> pdb=" O VAL D 81 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 31 through 37 removed outlier: 5.909A pdb=" N LYS C 32 " --> pdb=" O LYS C 28 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LYS C 28 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 17 " --> pdb=" O GLY C 51 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 303 through 305 Processing sheet with id=AB1, first strand: chain 'D' and resid 6 through 10 removed outlier: 7.535A pdb=" N ASN D 6 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE D 44 " --> pdb=" O ASN D 6 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU D 8 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N GLY D 46 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL D 10 " --> pdb=" O GLY D 46 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N GLU D 42 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 9.067A pdb=" N THR D 68 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE D 44 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N LEU D 70 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY D 46 " --> pdb=" O LEU D 70 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG D 75 " --> pdb=" O THR D 71 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 32 through 37 removed outlier: 3.915A pdb=" N GLY D 34 " --> pdb=" O LEU D 26 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 274 through 276 Processing sheet with id=AB4, first strand: chain 'D' and resid 303 through 305 Processing sheet with id=AB5, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.675A pdb=" N VAL E 34 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VAL E 38 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU E 2 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 79 through 81 removed outlier: 7.008A pdb=" N LEU F 2 " --> pdb=" O LEU F 71 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU F 40 " --> pdb=" O ARG F 33 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ARG F 33 " --> pdb=" O GLU F 40 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 10 through 11 removed outlier: 5.585A pdb=" N LEU I 10 " --> pdb=" O SER I 78 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N ILE I 80 " --> pdb=" O LEU I 10 " (cutoff:3.500A) removed outlier: 10.612A pdb=" N CYS I 81 " --> pdb=" O TYR I 109 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N TYR I 109 " --> pdb=" O CYS I 81 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR I 102 " --> pdb=" O ILE I 93 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE I 93 " --> pdb=" O TYR I 102 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 57 through 58 removed outlier: 4.027A pdb=" N GLU I 57 " --> pdb=" O THR I 64 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR I 64 " --> pdb=" O GLU I 85 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLU I 85 " --> pdb=" O THR I 64 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ARG I 66 " --> pdb=" O VAL I 83 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL I 83 " --> pdb=" O ARG I 66 " (cutoff:3.500A) removed outlier: 10.612A pdb=" N CYS I 81 " --> pdb=" O TYR I 109 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N TYR I 109 " --> pdb=" O CYS I 81 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LYS I 141 " --> pdb=" O ALA I 104 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR I 143 " --> pdb=" O PRO I 106 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU I 108 " --> pdb=" O TYR I 143 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE I 145 " --> pdb=" O GLU I 108 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 10 through 11 removed outlier: 5.608A pdb=" N LEU J 10 " --> pdb=" O SER J 78 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE J 80 " --> pdb=" O LEU J 10 " (cutoff:3.500A) removed outlier: 10.790A pdb=" N CYS J 81 " --> pdb=" O TYR J 109 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N TYR J 109 " --> pdb=" O CYS J 81 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLY J 100 " --> pdb=" O LEU J 95 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LEU J 95 " --> pdb=" O GLY J 100 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR J 102 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE J 93 " --> pdb=" O TYR J 102 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 63 through 72 removed outlier: 6.805A pdb=" N THR J 64 " --> pdb=" O GLU J 85 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLU J 85 " --> pdb=" O THR J 64 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ARG J 66 " --> pdb=" O VAL J 83 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL J 83 " --> pdb=" O ARG J 66 " (cutoff:3.500A) removed outlier: 10.790A pdb=" N CYS J 81 " --> pdb=" O TYR J 109 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N TYR J 109 " --> pdb=" O CYS J 81 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N TYR J 143 " --> pdb=" O ALA J 104 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N PHE J 145 " --> pdb=" O PRO J 106 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLU J 108 " --> pdb=" O PHE J 145 " (cutoff:3.500A) 802 hydrogen bonds defined for protein. 2313 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 2.92 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 7519 1.42 - 1.64: 10230 1.64 - 1.85: 169 1.85 - 2.07: 1 2.07 - 2.29: 24 Bond restraints: 17943 Sorted by residual: bond pdb=" CA TYR E 7 " pdb=" C TYR E 7 " ideal model delta sigma weight residual 1.523 1.469 0.054 1.21e-02 6.83e+03 1.98e+01 bond pdb=" C3' DC G 13 " pdb=" O3' DC G 13 " ideal model delta sigma weight residual 1.435 1.393 0.042 1.30e-02 5.92e+03 1.04e+01 bond pdb=" C3' DC H 13 " pdb=" C2' DC H 13 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C1' DT H 7 " pdb=" N1 DT H 7 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.40e+00 bond pdb=" C3' DC G 4 " pdb=" C2' DC G 4 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.99e+00 ... (remaining 17938 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 24348 3.21 - 6.41: 108 6.41 - 9.62: 7 9.62 - 12.83: 1 12.83 - 16.04: 1 Bond angle restraints: 24465 Sorted by residual: angle pdb=" N ASN C 203 " pdb=" CA ASN C 203 " pdb=" C ASN C 203 " ideal model delta sigma weight residual 113.89 97.85 16.04 1.58e+00 4.01e-01 1.03e+02 angle pdb=" N PRO C 197 " pdb=" CA PRO C 197 " pdb=" C PRO C 197 " ideal model delta sigma weight residual 110.70 99.98 10.72 1.22e+00 6.72e-01 7.72e+01 angle pdb=" C ARG C 196 " pdb=" N PRO C 197 " pdb=" CA PRO C 197 " ideal model delta sigma weight residual 120.38 115.00 5.38 1.03e+00 9.43e-01 2.73e+01 angle pdb=" N ALA C 204 " pdb=" CA ALA C 204 " pdb=" C ALA C 204 " ideal model delta sigma weight residual 113.12 106.98 6.14 1.25e+00 6.40e-01 2.41e+01 angle pdb=" N3 DT G 14 " pdb=" C4 DT G 14 " pdb=" O4 DT G 14 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 ... (remaining 24460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.55: 10068 30.55 - 61.11: 634 61.11 - 91.66: 31 91.66 - 122.22: 0 122.22 - 152.77: 4 Dihedral angle restraints: 10737 sinusoidal: 4910 harmonic: 5827 Sorted by residual: dihedral pdb=" C ARG C 196 " pdb=" N ARG C 196 " pdb=" CA ARG C 196 " pdb=" CB ARG C 196 " ideal model delta harmonic sigma weight residual -122.60 -135.44 12.84 0 2.50e+00 1.60e-01 2.64e+01 dihedral pdb=" N ARG C 196 " pdb=" C ARG C 196 " pdb=" CA ARG C 196 " pdb=" CB ARG C 196 " ideal model delta harmonic sigma weight residual 122.80 135.24 -12.44 0 2.50e+00 1.60e-01 2.48e+01 dihedral pdb=" CA ARG A 196 " pdb=" C ARG A 196 " pdb=" N PRO A 197 " pdb=" CA PRO A 197 " ideal model delta harmonic sigma weight residual 180.00 -157.35 -22.65 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 10734 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 2624 0.108 - 0.216: 60 0.216 - 0.323: 2 0.323 - 0.431: 0 0.431 - 0.539: 1 Chirality restraints: 2687 Sorted by residual: chirality pdb=" CA ARG C 196 " pdb=" N ARG C 196 " pdb=" C ARG C 196 " pdb=" CB ARG C 196 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.27e+00 chirality pdb=" CA ASP C 200 " pdb=" N ASP C 200 " pdb=" C ASP C 200 " pdb=" CB ASP C 200 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA ARG C 195 " pdb=" N ARG C 195 " pdb=" C ARG C 195 " pdb=" CB ARG C 195 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 2684 not shown) Planarity restraints: 2912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 196 " -0.077 5.00e-02 4.00e+02 1.16e-01 2.16e+01 pdb=" N PRO A 197 " 0.201 5.00e-02 4.00e+02 pdb=" CA PRO A 197 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO A 197 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 92 " -0.041 5.00e-02 4.00e+02 6.29e-02 6.32e+00 pdb=" N PRO F 93 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO F 93 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO F 93 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 306 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO C 307 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 307 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 307 " 0.029 5.00e-02 4.00e+02 ... (remaining 2909 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 34 2.38 - 3.01: 9346 3.01 - 3.64: 25220 3.64 - 4.27: 36507 4.27 - 4.90: 61931 Nonbonded interactions: 133038 Sorted by model distance: nonbonded pdb=" OP1 DG H 29 " pdb="MN MN I 302 " model vdw 1.752 2.320 nonbonded pdb=" OD2 ASP I 82 " pdb="MN MN I 302 " model vdw 2.032 2.320 nonbonded pdb=" OG SER C 84 " pdb=" OH TYR D 229 " model vdw 2.137 3.040 nonbonded pdb=" OP1 DG G 29 " pdb="MN MN J 302 " model vdw 2.141 2.320 nonbonded pdb=" OG SER I 218 " pdb=" OE1 GLU I 219 " model vdw 2.191 3.040 ... (remaining 133033 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 342) selection = chain 'B' selection = (chain 'C' and resid 1 through 342) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'I' and resid 3 through 302) selection = chain 'J' } 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 individual isotropic 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: 3.100 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: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.830 Find NCS groups from input model: 0.310 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 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 : 0.010 1.218 17951 Z= 0.388 Angle : 1.670 84.418 24489 Z= 0.447 Chirality : 0.043 0.539 2687 Planarity : 0.005 0.116 2912 Dihedral : 17.744 152.772 6983 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.99 % Favored : 93.75 % Rotamer: Outliers : 0.23 % Allowed : 0.74 % Favored : 99.03 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.19), residues: 1985 helix: 1.15 (0.18), residues: 911 sheet: -0.20 (0.32), residues: 258 loop : -1.97 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 128 TYR 0.027 0.001 TYR E 7 PHE 0.026 0.001 PHE D 232 TRP 0.015 0.001 TRP B 296 HIS 0.010 0.001 HIS D 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.26 (17943) covalent geometry : angle 0.64716 / 0.43 (24465) hydrogen bonds : bond 0.14998 / 10.30 ( 840) hydrogen bonds : angle 6.08121 / 4.31 ( 2413) metal coordination : bond 0.46753 / 22.52 ( 8) metal coordination : angle 49.16666 / 27.92 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 260 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 180 MET cc_start: 0.5562 (mpp) cc_final: 0.4210 (mmt) REVERT: C 196 ARG cc_start: 0.5992 (OUTLIER) cc_final: 0.5759 (tpp-160) REVERT: D 178 ASP cc_start: 0.7391 (t0) cc_final: 0.7067 (t0) REVERT: D 197 PRO cc_start: 0.3979 (Cg_exo) cc_final: 0.3656 (Cg_endo) REVERT: D 200 ASP cc_start: 0.6884 (m-30) cc_final: 0.6485 (p0) outliers start: 4 outliers final: 0 residues processed: 262 average time/residue: 0.1478 time to fit residues: 58.3294 Evaluate side-chains 201 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 200 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 196 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.0270 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.0470 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 39 HIS ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 24 GLN ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.173497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.137118 restraints weight = 23146.405| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.45 r_work: 0.3496 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 17951 Z= 0.135 Angle : 1.578 83.110 24489 Z= 0.339 Chirality : 0.040 0.207 2687 Planarity : 0.005 0.116 2912 Dihedral : 16.954 156.600 2905 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.15 % Favored : 93.70 % Rotamer: Outliers : 0.80 % Allowed : 7.31 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.12 (0.19), residues: 1985 helix: 1.84 (0.18), residues: 903 sheet: 0.04 (0.33), residues: 250 loop : -2.01 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 8 TYR 0.022 0.001 TYR C 95 PHE 0.017 0.001 PHE J 20 TRP 0.016 0.001 TRP B 296 HIS 0.004 0.001 HIS C 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (17943) covalent geometry : angle 0.57493 / 0.31 (24465) hydrogen bonds : bond 0.04639 / 3.11 ( 840) hydrogen bonds : angle 4.52196 / 3.20 ( 2413) metal coordination : bond 0.02604 / 1.32 ( 8) metal coordination : angle 46.95199 / 27.55 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 210 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 12 GLN cc_start: 0.7758 (mp10) cc_final: 0.7453 (mp10) REVERT: B 150 MET cc_start: 0.5329 (tpp) cc_final: 0.5009 (tpp) REVERT: B 180 MET cc_start: 0.5345 (mpp) cc_final: 0.4937 (mmt) REVERT: B 313 MET cc_start: 0.8338 (ptt) cc_final: 0.8044 (ptt) REVERT: C 30 GLN cc_start: 0.7802 (tp-100) cc_final: 0.7397 (tt0) REVERT: C 248 MET cc_start: 0.7164 (tpt) cc_final: 0.6622 (ttt) REVERT: D 125 ARG cc_start: 0.6326 (tpp-160) cc_final: 0.5453 (tmt170) REVERT: D 126 MET cc_start: 0.8028 (tmm) cc_final: 0.7711 (tpp) REVERT: D 178 ASP cc_start: 0.7421 (t0) cc_final: 0.7066 (t0) REVERT: D 197 PRO cc_start: 0.3974 (Cg_exo) cc_final: 0.3689 (Cg_endo) REVERT: D 200 ASP cc_start: 0.7617 (m-30) cc_final: 0.6169 (p0) REVERT: D 336 GLU cc_start: 0.8384 (pm20) cc_final: 0.8149 (pm20) REVERT: E 62 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7962 (pm20) REVERT: I 48 LYS cc_start: 0.7451 (tptt) cc_final: 0.6653 (mttt) REVERT: J 154 GLU cc_start: 0.7774 (pp20) cc_final: 0.7558 (pp20) REVERT: J 175 TYR cc_start: 0.7933 (m-10) cc_final: 0.7520 (m-10) outliers start: 14 outliers final: 10 residues processed: 217 average time/residue: 0.1384 time to fit residues: 45.8200 Evaluate side-chains 204 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 193 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 275 TYR Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 198 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 128 optimal weight: 0.0020 chunk 36 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 183 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN J 71 GLN ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.168408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.131603 restraints weight = 23540.085| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.47 r_work: 0.3429 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 17951 Z= 0.167 Angle : 1.502 84.761 24489 Z= 0.340 Chirality : 0.041 0.254 2687 Planarity : 0.005 0.115 2912 Dihedral : 17.111 157.468 2901 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.75 % Favored : 93.10 % Rotamer: Outliers : 0.97 % Allowed : 12.00 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.19), residues: 1985 helix: 1.93 (0.18), residues: 910 sheet: -0.03 (0.33), residues: 250 loop : -2.09 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 91 TYR 0.012 0.001 TYR E 7 PHE 0.015 0.001 PHE D 111 TRP 0.016 0.002 TRP B 296 HIS 0.004 0.001 HIS J 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (17943) covalent geometry : angle 0.59749 / 0.32 (24465) hydrogen bonds : bond 0.04851 / 3.23 ( 840) hydrogen bonds : angle 4.23640 / 3.00 ( 2413) metal coordination : bond 0.02558 / 1.32 ( 8) metal coordination : angle 44.01394 / 26.29 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 200 time to evaluate : 0.545 Fit side-chains REVERT: A 150 MET cc_start: 0.5527 (tmm) cc_final: 0.5034 (tmm) REVERT: B 12 GLN cc_start: 0.7776 (mp10) cc_final: 0.7399 (mp10) REVERT: B 150 MET cc_start: 0.5353 (tpp) cc_final: 0.5064 (tpp) REVERT: B 180 MET cc_start: 0.5227 (mpp) cc_final: 0.3967 (mmt) REVERT: B 313 MET cc_start: 0.8250 (ptt) cc_final: 0.8020 (ptt) REVERT: C 126 MET cc_start: 0.8334 (tpp) cc_final: 0.8102 (tpp) REVERT: D 125 ARG cc_start: 0.6386 (tpp-160) cc_final: 0.5507 (tmt170) REVERT: D 126 MET cc_start: 0.8128 (tmm) cc_final: 0.7843 (tpp) REVERT: D 178 ASP cc_start: 0.7323 (t0) cc_final: 0.7105 (t0) REVERT: D 197 PRO cc_start: 0.3835 (Cg_exo) cc_final: 0.3553 (Cg_endo) REVERT: D 200 ASP cc_start: 0.7633 (m-30) cc_final: 0.6074 (p0) REVERT: D 201 ASN cc_start: 0.8031 (t0) cc_final: 0.7568 (t0) REVERT: E 62 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7973 (pm20) REVERT: I 48 LYS cc_start: 0.7530 (tptt) cc_final: 0.6680 (mttt) REVERT: J 44 GLN cc_start: 0.7827 (tp-100) cc_final: 0.7539 (tt0) REVERT: J 129 MET cc_start: 0.7715 (mtp) cc_final: 0.7488 (ttm) REVERT: J 154 GLU cc_start: 0.7972 (pp20) cc_final: 0.7680 (pp20) outliers start: 17 outliers final: 10 residues processed: 208 average time/residue: 0.1408 time to fit residues: 44.6248 Evaluate side-chains 206 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 195 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain J residue 71 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 156 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 185 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 139 optimal weight: 0.2980 chunk 137 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 39 HIS ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 ASN D 322 GLN J 32 GLN ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.163995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.127084 restraints weight = 23667.059| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.46 r_work: 0.3372 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 17951 Z= 0.209 Angle : 1.418 88.185 24489 Z= 0.356 Chirality : 0.043 0.248 2687 Planarity : 0.005 0.114 2912 Dihedral : 17.352 160.256 2901 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.05 % Favored : 92.75 % Rotamer: Outliers : 1.71 % Allowed : 14.51 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.19), residues: 1985 helix: 1.78 (0.18), residues: 911 sheet: 0.02 (0.33), residues: 240 loop : -2.15 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 91 TYR 0.017 0.002 TYR D 255 PHE 0.020 0.002 PHE C 340 TRP 0.023 0.002 TRP D 165 HIS 0.005 0.001 HIS J 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.21 (17943) covalent geometry : angle 0.63209 / 0.34 (24465) hydrogen bonds : bond 0.05274 / 3.52 ( 840) hydrogen bonds : angle 4.29211 / 3.05 ( 2413) metal coordination : bond 0.02598 / 1.45 ( 8) metal coordination : angle 40.53486 / 24.71 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 197 time to evaluate : 0.678 Fit side-chains REVERT: A 150 MET cc_start: 0.5518 (tmm) cc_final: 0.4988 (tmm) REVERT: A 200 ASP cc_start: 0.5937 (t70) cc_final: 0.5610 (t70) REVERT: B 125 ARG cc_start: 0.6784 (tmm-80) cc_final: 0.6393 (ttt90) REVERT: B 150 MET cc_start: 0.5394 (tpp) cc_final: 0.5074 (tpp) REVERT: B 180 MET cc_start: 0.5325 (mpp) cc_final: 0.4015 (mmt) REVERT: C 30 GLN cc_start: 0.7881 (tp40) cc_final: 0.7593 (mp10) REVERT: C 131 PRO cc_start: 0.8312 (Cg_endo) cc_final: 0.8010 (Cg_exo) REVERT: D 125 ARG cc_start: 0.6489 (tpp-160) cc_final: 0.5588 (tmt170) REVERT: D 126 MET cc_start: 0.8282 (tmm) cc_final: 0.7996 (tpp) REVERT: D 178 ASP cc_start: 0.7322 (t0) cc_final: 0.7075 (t0) REVERT: D 197 PRO cc_start: 0.3871 (Cg_exo) cc_final: 0.3573 (Cg_endo) REVERT: D 200 ASP cc_start: 0.7709 (m-30) cc_final: 0.6182 (p0) REVERT: D 201 ASN cc_start: 0.8091 (t0) cc_final: 0.7578 (t0) REVERT: D 313 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7902 (ttp) REVERT: D 330 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6853 (mp) REVERT: D 342 TRP cc_start: 0.8430 (OUTLIER) cc_final: 0.7881 (m-10) REVERT: I 48 LYS cc_start: 0.7572 (tptt) cc_final: 0.6689 (mttt) REVERT: I 147 ASN cc_start: 0.7956 (t0) cc_final: 0.7558 (t0) REVERT: J 44 GLN cc_start: 0.7855 (tp-100) cc_final: 0.7603 (tt0) REVERT: J 78 SER cc_start: 0.9142 (t) cc_final: 0.8849 (p) REVERT: J 129 MET cc_start: 0.7789 (mtp) cc_final: 0.7447 (ttm) REVERT: J 154 GLU cc_start: 0.7973 (pp20) cc_final: 0.7642 (pp20) outliers start: 30 outliers final: 19 residues processed: 215 average time/residue: 0.1269 time to fit residues: 42.1844 Evaluate side-chains 212 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain F residue 0 SER Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain I residue 130 CYS Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain J residue 38 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 44 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 39 HIS ** C 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 ASN ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 ASN ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.163942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.127190 restraints weight = 23360.647| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.44 r_work: 0.3375 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 17951 Z= 0.176 Angle : 1.326 88.364 24489 Z= 0.339 Chirality : 0.042 0.258 2687 Planarity : 0.004 0.112 2912 Dihedral : 17.413 161.775 2901 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.60 % Favored : 93.20 % Rotamer: Outliers : 2.06 % Allowed : 15.71 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.19), residues: 1985 helix: 1.82 (0.18), residues: 912 sheet: 0.10 (0.33), residues: 242 loop : -2.20 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 91 TYR 0.016 0.001 TYR D 255 PHE 0.017 0.001 PHE C 340 TRP 0.018 0.002 TRP D 165 HIS 0.004 0.001 HIS D 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (17943) covalent geometry : angle 0.60385 / 0.32 (24465) hydrogen bonds : bond 0.05030 / 3.34 ( 840) hydrogen bonds : angle 4.21561 / 2.99 ( 2413) metal coordination : bond 0.02481 / 1.36 ( 8) metal coordination : angle 37.71376 / 23.31 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 200 time to evaluate : 0.593 Fit side-chains REVERT: A 150 MET cc_start: 0.5683 (tmm) cc_final: 0.5129 (tmm) REVERT: A 200 ASP cc_start: 0.5922 (t70) cc_final: 0.5593 (t70) REVERT: A 268 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7626 (mm-30) REVERT: B 12 GLN cc_start: 0.7703 (mp10) cc_final: 0.7322 (mp10) REVERT: B 125 ARG cc_start: 0.6828 (tmm-80) cc_final: 0.6465 (ttt90) REVERT: B 150 MET cc_start: 0.5384 (tpp) cc_final: 0.5172 (tpp) REVERT: B 180 MET cc_start: 0.5330 (mpp) cc_final: 0.3967 (mmt) REVERT: B 183 GLN cc_start: 0.6243 (OUTLIER) cc_final: 0.5842 (tm-30) REVERT: C 131 PRO cc_start: 0.8299 (Cg_endo) cc_final: 0.7990 (Cg_exo) REVERT: D 125 ARG cc_start: 0.6484 (tpp-160) cc_final: 0.5617 (tmt170) REVERT: D 126 MET cc_start: 0.8293 (tmm) cc_final: 0.8011 (tpp) REVERT: D 178 ASP cc_start: 0.7339 (t0) cc_final: 0.6957 (t0) REVERT: D 197 PRO cc_start: 0.3882 (Cg_exo) cc_final: 0.3564 (Cg_endo) REVERT: D 200 ASP cc_start: 0.7757 (m-30) cc_final: 0.6237 (p0) REVERT: D 330 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.6915 (mp) REVERT: D 342 TRP cc_start: 0.8419 (OUTLIER) cc_final: 0.7842 (m-10) REVERT: I 48 LYS cc_start: 0.7575 (tptt) cc_final: 0.6718 (mttt) REVERT: J 78 SER cc_start: 0.9131 (t) cc_final: 0.8806 (p) REVERT: J 129 MET cc_start: 0.7797 (mtp) cc_final: 0.7456 (ttm) REVERT: J 154 GLU cc_start: 0.7951 (pp20) cc_final: 0.7604 (pp20) outliers start: 36 outliers final: 21 residues processed: 225 average time/residue: 0.1311 time to fit residues: 45.7900 Evaluate side-chains 218 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 215 ASN Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 191 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 32 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 16 optimal weight: 20.0000 chunk 25 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 190 optimal weight: 9.9990 chunk 192 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 GLN C 39 HIS ** C 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 ASN ** I 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 GLN J 44 GLN J 71 GLN ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.161199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.124332 restraints weight = 23571.451| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.46 r_work: 0.3334 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 17951 Z= 0.219 Angle : 1.293 89.090 24489 Z= 0.361 Chirality : 0.044 0.269 2687 Planarity : 0.005 0.111 2912 Dihedral : 17.561 163.049 2901 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.51 % Favored : 92.29 % Rotamer: Outliers : 2.46 % Allowed : 16.69 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.19), residues: 1985 helix: 1.64 (0.18), residues: 909 sheet: -0.02 (0.32), residues: 257 loop : -2.31 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 91 TYR 0.019 0.002 TYR C 320 PHE 0.022 0.002 PHE C 340 TRP 0.041 0.002 TRP D 165 HIS 0.005 0.001 HIS J 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.22 (17943) covalent geometry : angle 0.65009 / 0.35 (24465) hydrogen bonds : bond 0.05520 / 3.68 ( 840) hydrogen bonds : angle 4.34122 / 3.09 ( 2413) metal coordination : bond 0.02851 / 1.60 ( 8) metal coordination : angle 35.70999 / 22.42 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 194 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.5639 (tmm) cc_final: 0.5090 (tmm) REVERT: A 200 ASP cc_start: 0.5986 (t70) cc_final: 0.5647 (t70) REVERT: A 268 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7446 (mm-30) REVERT: B 125 ARG cc_start: 0.6862 (tmm-80) cc_final: 0.6522 (ttt90) REVERT: B 183 GLN cc_start: 0.6290 (OUTLIER) cc_final: 0.5882 (tm-30) REVERT: C 131 PRO cc_start: 0.8268 (Cg_endo) cc_final: 0.7952 (Cg_exo) REVERT: D 41 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8496 (mp) REVERT: D 125 ARG cc_start: 0.6514 (tpp-160) cc_final: 0.5671 (tmt170) REVERT: D 178 ASP cc_start: 0.7506 (t0) cc_final: 0.7164 (t0) REVERT: D 200 ASP cc_start: 0.7755 (m-30) cc_final: 0.6243 (p0) REVERT: D 330 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.6948 (mp) REVERT: D 342 TRP cc_start: 0.8481 (OUTLIER) cc_final: 0.7905 (m-10) REVERT: I 68 MET cc_start: 0.6507 (OUTLIER) cc_final: 0.5465 (tpt) REVERT: J 78 SER cc_start: 0.9160 (t) cc_final: 0.8959 (p) REVERT: J 154 GLU cc_start: 0.7988 (pp20) cc_final: 0.7640 (pp20) REVERT: J 217 LEU cc_start: 0.4239 (OUTLIER) cc_final: 0.3912 (mm) outliers start: 43 outliers final: 26 residues processed: 225 average time/residue: 0.1322 time to fit residues: 46.0218 Evaluate side-chains 222 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 0 SER Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain I residue 68 MET Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 191 ASN Chi-restraints excluded: chain J residue 217 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 31 optimal weight: 0.2980 chunk 108 optimal weight: 1.9990 chunk 101 optimal weight: 0.1980 chunk 163 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 56 optimal weight: 0.0040 chunk 2 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 140 optimal weight: 0.5980 chunk 120 optimal weight: 0.0970 chunk 86 optimal weight: 5.9990 overall best weight: 0.2390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 GLN A 73 ASN C 39 HIS ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 GLN ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.176316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.152323 restraints weight = 22094.258| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 1.44 r_work: 0.3610 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.082 17951 Z= 0.120 Angle : 1.124 80.067 24489 Z= 0.314 Chirality : 0.039 0.263 2687 Planarity : 0.004 0.111 2912 Dihedral : 17.376 165.698 2901 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.04 % Favored : 94.81 % Rotamer: Outliers : 1.66 % Allowed : 17.37 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.19), residues: 1985 helix: 1.95 (0.18), residues: 913 sheet: 0.12 (0.33), residues: 247 loop : -2.08 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 289 TYR 0.015 0.001 TYR D 255 PHE 0.017 0.001 PHE D 190 TRP 0.023 0.002 TRP D 165 HIS 0.013 0.001 HIS D 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 (17943) covalent geometry : angle 0.55871 / 0.30 (24465) hydrogen bonds : bond 0.03897 / 2.57 ( 840) hydrogen bonds : angle 3.97549 / 2.82 ( 2413) metal coordination : bond 0.01913 / 1.01 ( 8) metal coordination : angle 31.14647 / 19.66 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 202 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.6605 (tmm) cc_final: 0.6206 (tmm) REVERT: A 268 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8038 (mm-30) REVERT: B 12 GLN cc_start: 0.7849 (mp10) cc_final: 0.7573 (mp10) REVERT: B 125 ARG cc_start: 0.7511 (tmm-80) cc_final: 0.7024 (ttt90) REVERT: B 150 MET cc_start: 0.5559 (tpp) cc_final: 0.5221 (tpp) REVERT: B 183 GLN cc_start: 0.6493 (OUTLIER) cc_final: 0.6140 (tm-30) REVERT: C 131 PRO cc_start: 0.8234 (Cg_endo) cc_final: 0.7967 (Cg_exo) REVERT: D 125 ARG cc_start: 0.6999 (tpp-160) cc_final: 0.6264 (tmt170) REVERT: D 154 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.7305 (ttm-80) REVERT: D 200 ASP cc_start: 0.7578 (m-30) cc_final: 0.6621 (p0) REVERT: D 342 TRP cc_start: 0.8498 (OUTLIER) cc_final: 0.7780 (m-10) REVERT: I 48 LYS cc_start: 0.8145 (tptt) cc_final: 0.7412 (mttt) REVERT: J 154 GLU cc_start: 0.7610 (pp20) cc_final: 0.7383 (pp20) REVERT: J 217 LEU cc_start: 0.4491 (OUTLIER) cc_final: 0.4263 (mm) outliers start: 29 outliers final: 10 residues processed: 223 average time/residue: 0.1385 time to fit residues: 47.0788 Evaluate side-chains 205 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 191 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain J residue 217 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 130 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 154 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 GLN C 39 HIS C 306 HIS C 322 GLN ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN J 16 GLN ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.160112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.123306 restraints weight = 23650.471| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.46 r_work: 0.3322 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 17951 Z= 0.238 Angle : 1.220 87.568 24489 Z= 0.379 Chirality : 0.046 0.292 2687 Planarity : 0.005 0.111 2912 Dihedral : 17.639 164.441 2901 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.81 % Favored : 92.04 % Rotamer: Outliers : 2.00 % Allowed : 17.66 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.19), residues: 1985 helix: 1.60 (0.18), residues: 911 sheet: -0.11 (0.31), residues: 268 loop : -2.35 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 91 TYR 0.024 0.002 TYR D 255 PHE 0.027 0.002 PHE C 340 TRP 0.082 0.003 TRP D 165 HIS 0.006 0.001 HIS J 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.24 (17943) covalent geometry : angle 0.69812 / 0.37 (24465) hydrogen bonds : bond 0.05907 / 3.93 ( 840) hydrogen bonds : angle 4.33609 / 3.09 ( 2413) metal coordination : bond 0.03082 / 1.73 ( 8) metal coordination : angle 31.97028 / 20.48 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 194 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.5920 (tmm) cc_final: 0.5365 (tmm) REVERT: A 268 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7548 (mm-30) REVERT: B 125 ARG cc_start: 0.6883 (tmm-80) cc_final: 0.6524 (ttt90) REVERT: B 150 MET cc_start: 0.5726 (tpp) cc_final: 0.5318 (tpp) REVERT: B 183 GLN cc_start: 0.6387 (OUTLIER) cc_final: 0.5904 (tm-30) REVERT: C 131 PRO cc_start: 0.8243 (Cg_endo) cc_final: 0.7913 (Cg_exo) REVERT: D 41 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8472 (mp) REVERT: D 125 ARG cc_start: 0.6581 (tpp-160) cc_final: 0.5701 (tmt170) REVERT: D 154 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6969 (ttm-80) REVERT: D 178 ASP cc_start: 0.7511 (t0) cc_final: 0.7166 (t0) REVERT: D 200 ASP cc_start: 0.7790 (m-30) cc_final: 0.6290 (p0) REVERT: D 205 MET cc_start: 0.7778 (mtm) cc_final: 0.7496 (mtp) REVERT: D 255 TYR cc_start: 0.8355 (t80) cc_final: 0.7995 (t80) REVERT: D 342 TRP cc_start: 0.8580 (OUTLIER) cc_final: 0.8023 (m-10) REVERT: I 129 MET cc_start: 0.6854 (mtt) cc_final: 0.6646 (ttm) REVERT: J 154 GLU cc_start: 0.8051 (pp20) cc_final: 0.7693 (pp20) REVERT: J 217 LEU cc_start: 0.4275 (OUTLIER) cc_final: 0.3927 (mm) outliers start: 35 outliers final: 20 residues processed: 220 average time/residue: 0.1266 time to fit residues: 42.9901 Evaluate side-chains 214 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain J residue 191 ASN Chi-restraints excluded: chain J residue 217 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 95 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 110 optimal weight: 0.3980 chunk 107 optimal weight: 0.5980 chunk 145 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 GLN C 39 HIS ** C 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.172153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.146643 restraints weight = 22109.389| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 1.56 r_work: 0.3549 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 17951 Z= 0.130 Angle : 1.101 80.970 24489 Z= 0.322 Chirality : 0.040 0.274 2687 Planarity : 0.004 0.109 2912 Dihedral : 17.526 167.677 2901 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.59 % Favored : 94.21 % Rotamer: Outliers : 1.37 % Allowed : 18.46 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.19), residues: 1985 helix: 1.80 (0.18), residues: 914 sheet: 0.09 (0.33), residues: 245 loop : -2.17 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 258 TYR 0.016 0.001 TYR D 255 PHE 0.015 0.001 PHE D 190 TRP 0.042 0.002 TRP D 165 HIS 0.004 0.001 HIS D 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (17943) covalent geometry : angle 0.58005 / 0.31 (24465) hydrogen bonds : bond 0.04506 / 2.99 ( 840) hydrogen bonds : angle 4.07268 / 2.89 ( 2413) metal coordination : bond 0.02141 / 1.19 ( 8) metal coordination : angle 29.88835 / 19.10 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 198 time to evaluate : 0.669 Fit side-chains revert: symmetry clash REVERT: A 150 MET cc_start: 0.6665 (tmm) cc_final: 0.5995 (tmm) REVERT: A 268 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7991 (mm-30) REVERT: B 125 ARG cc_start: 0.7470 (tmm-80) cc_final: 0.6992 (ttt90) REVERT: B 149 MET cc_start: 0.7423 (ttp) cc_final: 0.7118 (tmm) REVERT: B 150 MET cc_start: 0.6112 (tpp) cc_final: 0.5774 (tpp) REVERT: B 180 MET cc_start: 0.5704 (mpp) cc_final: 0.4428 (mmt) REVERT: B 183 GLN cc_start: 0.6615 (OUTLIER) cc_final: 0.6181 (tm-30) REVERT: C 131 PRO cc_start: 0.8232 (Cg_endo) cc_final: 0.7927 (Cg_exo) REVERT: D 125 ARG cc_start: 0.7059 (tpp-160) cc_final: 0.6346 (tmt170) REVERT: D 154 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7362 (ttm-80) REVERT: D 178 ASP cc_start: 0.7690 (t0) cc_final: 0.7444 (t0) REVERT: D 180 MET cc_start: 0.7288 (mmm) cc_final: 0.6957 (tpp) REVERT: D 200 ASP cc_start: 0.7714 (m-30) cc_final: 0.6518 (p0) REVERT: D 255 TYR cc_start: 0.8182 (t80) cc_final: 0.7891 (t80) REVERT: D 342 TRP cc_start: 0.8606 (OUTLIER) cc_final: 0.7933 (m-10) REVERT: I 48 LYS cc_start: 0.8175 (tptt) cc_final: 0.7580 (ttmm) REVERT: I 68 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.6464 (tpt) REVERT: J 154 GLU cc_start: 0.7702 (pp20) cc_final: 0.7472 (pp20) REVERT: J 217 LEU cc_start: 0.4500 (OUTLIER) cc_final: 0.4241 (mm) outliers start: 24 outliers final: 14 residues processed: 215 average time/residue: 0.1314 time to fit residues: 43.2069 Evaluate side-chains 213 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 194 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain I residue 68 MET Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain J residue 217 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 201 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 193 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 GLN C 39 HIS ** C 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 GLN ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.168391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.141891 restraints weight = 22016.557| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.54 r_work: 0.3529 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 17951 Z= 0.204 Angle : 1.138 84.369 24489 Z= 0.351 Chirality : 0.044 0.292 2687 Planarity : 0.005 0.109 2912 Dihedral : 17.628 167.571 2901 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.71 % Favored : 92.14 % Rotamer: Outliers : 1.60 % Allowed : 18.23 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.19), residues: 1985 helix: 1.65 (0.18), residues: 913 sheet: -0.27 (0.30), residues: 284 loop : -2.34 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 23 TYR 0.023 0.001 TYR D 255 PHE 0.020 0.002 PHE C 340 TRP 0.025 0.002 TRP D 165 HIS 0.005 0.001 HIS D 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.20 (17943) covalent geometry : angle 0.64284 / 0.34 (24465) hydrogen bonds : bond 0.05321 / 3.54 ( 840) hydrogen bonds : angle 4.22833 / 3.00 ( 2413) metal coordination : bond 0.03056 / 1.71 ( 8) metal coordination : angle 29.98802 / 19.26 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 0.654 Fit side-chains REVERT: A 150 MET cc_start: 0.6642 (tmm) cc_final: 0.5936 (tmm) REVERT: A 268 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7971 (mm-30) REVERT: B 125 ARG cc_start: 0.7380 (tmm-80) cc_final: 0.6918 (ttt90) REVERT: B 149 MET cc_start: 0.7437 (ttp) cc_final: 0.7189 (tmm) REVERT: B 150 MET cc_start: 0.6222 (tpp) cc_final: 0.5930 (tpp) REVERT: B 180 MET cc_start: 0.5714 (mpp) cc_final: 0.4519 (mmt) REVERT: B 183 GLN cc_start: 0.6655 (OUTLIER) cc_final: 0.6264 (tm-30) REVERT: C 131 PRO cc_start: 0.8240 (Cg_endo) cc_final: 0.7923 (Cg_exo) REVERT: D 125 ARG cc_start: 0.7124 (tpp-160) cc_final: 0.6462 (tmt170) REVERT: D 178 ASP cc_start: 0.7717 (t0) cc_final: 0.7477 (t0) REVERT: D 180 MET cc_start: 0.7261 (mmm) cc_final: 0.6906 (tpp) REVERT: D 255 TYR cc_start: 0.8264 (t80) cc_final: 0.7978 (t80) REVERT: D 342 TRP cc_start: 0.8700 (OUTLIER) cc_final: 0.8074 (m-10) REVERT: I 68 MET cc_start: 0.7581 (OUTLIER) cc_final: 0.6463 (tpt) REVERT: J 154 GLU cc_start: 0.7756 (pp20) cc_final: 0.7539 (pp20) REVERT: J 217 LEU cc_start: 0.4513 (OUTLIER) cc_final: 0.4212 (mm) outliers start: 28 outliers final: 20 residues processed: 212 average time/residue: 0.1256 time to fit residues: 40.8764 Evaluate side-chains 211 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 233 MET Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain I residue 68 MET Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain J residue 217 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 104 optimal weight: 2.9990 chunk 105 optimal weight: 0.0770 chunk 192 optimal weight: 0.3980 chunk 186 optimal weight: 0.0770 chunk 150 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 101 optimal weight: 0.3980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 39 HIS ** C 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.173832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.149768 restraints weight = 22133.713| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.48 r_work: 0.3581 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 17951 Z= 0.121 Angle : 1.047 77.049 24489 Z= 0.315 Chirality : 0.039 0.278 2687 Planarity : 0.004 0.108 2912 Dihedral : 17.484 170.022 2901 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.84 % Favored : 94.01 % Rotamer: Outliers : 1.54 % Allowed : 18.34 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.19), residues: 1985 helix: 1.88 (0.18), residues: 915 sheet: -0.09 (0.31), residues: 272 loop : -2.18 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 163 TYR 0.017 0.001 TYR D 255 PHE 0.011 0.001 PHE D 190 TRP 0.015 0.001 TRP D 121 HIS 0.005 0.001 HIS C 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (17943) covalent geometry : angle 0.57203 / 0.31 (24465) hydrogen bonds : bond 0.04071 / 2.71 ( 840) hydrogen bonds : angle 3.97476 / 2.82 ( 2413) metal coordination : bond 0.02056 / 1.13 ( 8) metal coordination : angle 28.01532 / 17.95 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3711.15 seconds wall clock time: 64 minutes 30.25 seconds (3870.25 seconds total)