Starting phenix.real_space_refine on Sat Jul 4 00:47:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d3l_27159/07_2026/8d3l_27159.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d3l_27159/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8d3l_27159/07_2026/8d3l_27159.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d3l_27159/07_2026/8d3l_27159.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d3l_27159/07_2026/8d3l_27159.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d3l_27159/07_2026/8d3l_27159.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8d3l_27159/07_2026/8d3l_27159.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d3l_27159/07_2026/8d3l_27159.cif" } 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-dev-6108/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: 3.89, per 1000 atoms: 0.22 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: 1.61 Conformation dependent library (CDL) restraints added in 696.3 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: 1.90 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: 2.72 Time building geometry restraints manager: 2.10 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: 2.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.560 Find NCS groups from input model: 0.370 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: 0.010 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.770 ------------------------------------------------------------------------------- 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 : 1.669 84.418 24489 Z= 0.445 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 0.64594 / 0.42 (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 : 0.652 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: D 178 ASP cc_start: 0.7391 (t0) cc_final: 0.7070 (t0) REVERT: D 197 PRO cc_start: 0.3979 (Cg_exo) cc_final: 0.3654 (Cg_endo) REVERT: D 200 ASP cc_start: 0.6884 (m-30) cc_final: 0.6484 (p0) outliers start: 4 outliers final: 0 residues processed: 262 average time/residue: 0.1365 time to fit residues: 53.7733 Evaluate side-chains 200 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 = 0.4007 r_free = 0.4007 target = 0.173491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.137045 restraints weight = 23199.802| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.45 r_work: 0.3496 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.0999 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 : 1.579 82.865 24489 Z= 0.339 Chirality : 0.040 0.185 2687 Planarity : 0.005 0.116 2912 Dihedral : 16.946 157.495 2901 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.10 % Favored : 93.70 % Rotamer: Outliers : 0.80 % Allowed : 7.60 % Favored : 91.60 % 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: 0.13 (0.19), residues: 1985 helix: 1.86 (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 B 154 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 0.005 0.001 HIS C 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (17943) covalent geometry : angle 0.57392 / 0.31 (24465) hydrogen bonds : bond 0.04598 / 3.07 ( 840) hydrogen bonds : angle 4.50909 / 3.19 ( 2413) metal coordination : bond 0.02898 / 1.46 ( 8) metal coordination : angle 46.99498 / 27.58 ( 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 227 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 213 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 12 GLN cc_start: 0.7767 (mp10) cc_final: 0.7476 (mp10) REVERT: B 150 MET cc_start: 0.5329 (tpp) cc_final: 0.5011 (tpp) REVERT: B 180 MET cc_start: 0.5350 (mpp) cc_final: 0.3952 (mmt) REVERT: B 313 MET cc_start: 0.8338 (ptt) cc_final: 0.8048 (ptt) REVERT: C 248 MET cc_start: 0.7151 (tpt) cc_final: 0.6607 (ttt) REVERT: D 125 ARG cc_start: 0.6332 (tpp-160) cc_final: 0.5452 (tmt170) REVERT: D 126 MET cc_start: 0.8056 (tmm) cc_final: 0.7740 (tpp) REVERT: D 178 ASP cc_start: 0.7415 (t0) cc_final: 0.7057 (t0) REVERT: D 197 PRO cc_start: 0.3975 (Cg_exo) cc_final: 0.3694 (Cg_endo) REVERT: D 200 ASP cc_start: 0.7610 (m-30) cc_final: 0.6033 (p0) REVERT: D 336 GLU cc_start: 0.8399 (pm20) cc_final: 0.8156 (pm20) REVERT: E 62 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7964 (pm20) REVERT: I 48 LYS cc_start: 0.7447 (tptt) cc_final: 0.6649 (mttt) REVERT: J 44 GLN cc_start: 0.7848 (tp-100) cc_final: 0.7509 (tt0) REVERT: J 154 GLU cc_start: 0.7781 (pp20) cc_final: 0.7570 (pp20) REVERT: J 175 TYR cc_start: 0.7942 (m-10) cc_final: 0.7525 (m-10) outliers start: 14 outliers final: 10 residues processed: 220 average time/residue: 0.1305 time to fit residues: 43.9293 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 : 0.659 ------------------------------------------------------------------------------- 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: 0.1980 chunk 36 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 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: 5.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.3951 r_free = 0.3951 target = 0.167884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.131891 restraints weight = 23591.104| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.49 r_work: 0.3422 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 17951 Z= 0.171 Angle : 1.499 84.442 24489 Z= 0.343 Chirality : 0.041 0.224 2687 Planarity : 0.005 0.115 2912 Dihedral : 17.147 158.732 2901 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.75 % Favored : 93.10 % Rotamer: Outliers : 1.09 % Allowed : 11.94 % Favored : 86.97 % 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: 0.13 (0.19), residues: 1985 helix: 1.91 (0.18), residues: 910 sheet: -0.04 (0.33), residues: 250 loop : -2.10 (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 0.017 0.001 TRP D 342 HIS 0.004 0.001 HIS J 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (17943) covalent geometry : angle 0.60538 / 0.32 (24465) hydrogen bonds : bond 0.04981 / 3.32 ( 840) hydrogen bonds : angle 4.25405 / 3.01 ( 2413) metal coordination : bond 0.02979 / 1.53 ( 8) metal coordination : angle 43.80820 / 26.21 ( 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 220 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 201 time to evaluate : 0.703 Fit side-chains REVERT: A 150 MET cc_start: 0.5520 (tmm) cc_final: 0.5024 (tmm) REVERT: B 12 GLN cc_start: 0.7768 (mp10) cc_final: 0.7340 (mp10) REVERT: B 150 MET cc_start: 0.5344 (tpp) cc_final: 0.5047 (tpp) REVERT: B 180 MET cc_start: 0.5313 (mpp) cc_final: 0.4013 (mmt) REVERT: B 313 MET cc_start: 0.8237 (ptt) cc_final: 0.8022 (ptt) REVERT: C 126 MET cc_start: 0.8292 (tpp) cc_final: 0.8043 (tpp) REVERT: C 131 PRO cc_start: 0.8336 (Cg_endo) cc_final: 0.8045 (Cg_exo) REVERT: D 125 ARG cc_start: 0.6357 (tpp-160) cc_final: 0.5478 (tmt170) REVERT: D 126 MET cc_start: 0.8141 (tmm) cc_final: 0.7858 (tpp) REVERT: D 178 ASP cc_start: 0.7309 (t0) cc_final: 0.7065 (t0) REVERT: D 197 PRO cc_start: 0.3860 (Cg_exo) cc_final: 0.3583 (Cg_endo) REVERT: D 200 ASP cc_start: 0.7592 (m-30) cc_final: 0.6028 (p0) REVERT: D 201 ASN cc_start: 0.8018 (t0) cc_final: 0.7562 (t0) REVERT: D 342 TRP cc_start: 0.8242 (OUTLIER) cc_final: 0.7627 (m-10) REVERT: E 62 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7924 (pm20) REVERT: I 48 LYS cc_start: 0.7514 (tptt) cc_final: 0.6649 (mttt) REVERT: J 44 GLN cc_start: 0.7788 (tp-100) cc_final: 0.7492 (tt0) REVERT: J 129 MET cc_start: 0.7749 (mtp) cc_final: 0.7539 (ttm) REVERT: J 154 GLU cc_start: 0.7950 (pp20) cc_final: 0.7659 (pp20) outliers start: 19 outliers final: 9 residues processed: 211 average time/residue: 0.1398 time to fit residues: 45.1055 Evaluate side-chains 207 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 196 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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 284 MET Chi-restraints excluded: chain D residue 342 TRP 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: 1.9990 chunk 75 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 139 optimal weight: 0.8980 chunk 137 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 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 = 0.3891 r_free = 0.3891 target = 0.162140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.126366 restraints weight = 23760.966| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.49 r_work: 0.3348 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 17951 Z= 0.237 Angle : 1.431 88.518 24489 Z= 0.377 Chirality : 0.045 0.238 2687 Planarity : 0.005 0.113 2912 Dihedral : 17.467 162.038 2901 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.25 % Favored : 92.49 % Rotamer: Outliers : 1.89 % Allowed : 14.69 % Favored : 83.43 % 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: 1.60 (0.17), residues: 916 sheet: -0.03 (0.33), residues: 239 loop : -2.25 (0.19), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 91 TYR 0.021 0.002 TYR D 255 PHE 0.026 0.002 PHE C 340 TRP 0.020 0.002 TRP D 342 HIS 0.006 0.001 HIS J 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.24 (17943) covalent geometry : angle 0.67840 / 0.36 (24465) hydrogen bonds : bond 0.05737 / 3.84 ( 840) hydrogen bonds : angle 4.42367 / 3.15 ( 2413) metal coordination : bond 0.02761 / 1.56 ( 8) metal coordination : angle 40.24175 / 24.67 ( 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 226 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 0.564 Fit side-chains REVERT: A 150 MET cc_start: 0.5554 (tmm) cc_final: 0.5012 (tmm) REVERT: A 200 ASP cc_start: 0.5944 (t70) cc_final: 0.5610 (t70) REVERT: B 125 ARG cc_start: 0.6736 (tmm-80) cc_final: 0.6450 (ttt90) REVERT: B 150 MET cc_start: 0.5283 (tpp) cc_final: 0.4941 (tpp) REVERT: B 180 MET cc_start: 0.5297 (mpp) cc_final: 0.3966 (mmt) REVERT: C 30 GLN cc_start: 0.7832 (tp40) cc_final: 0.7563 (mp10) REVERT: C 131 PRO cc_start: 0.8284 (Cg_endo) cc_final: 0.7976 (Cg_exo) REVERT: D 125 ARG cc_start: 0.6318 (tpp-160) cc_final: 0.5467 (tmt170) REVERT: D 126 MET cc_start: 0.8315 (tmm) cc_final: 0.8027 (tpp) REVERT: D 178 ASP cc_start: 0.7345 (t0) cc_final: 0.7046 (t0) REVERT: D 197 PRO cc_start: 0.3980 (Cg_exo) cc_final: 0.3662 (Cg_endo) REVERT: D 200 ASP cc_start: 0.7736 (m-30) cc_final: 0.6209 (p0) REVERT: D 201 ASN cc_start: 0.8116 (t0) cc_final: 0.7605 (t0) REVERT: D 313 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7978 (mtm) REVERT: D 330 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.6817 (mp) REVERT: D 342 TRP cc_start: 0.8435 (OUTLIER) cc_final: 0.7842 (m-10) REVERT: I 147 ASN cc_start: 0.7970 (t0) cc_final: 0.7562 (t0) REVERT: J 71 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7670 (pp30) REVERT: J 129 MET cc_start: 0.7800 (mtp) cc_final: 0.7449 (ttm) REVERT: J 154 GLU cc_start: 0.7948 (pp20) cc_final: 0.7609 (pp20) outliers start: 33 outliers final: 20 residues processed: 215 average time/residue: 0.1275 time to fit residues: 42.4026 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 : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain B residue 176 VAL 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 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 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 Chi-restraints excluded: chain J residue 71 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 44 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 2 optimal weight: 8.9990 chunk 174 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 13 optimal weight: 20.0000 chunk 97 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 118 ASN ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 ASN 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 = 0.3902 r_free = 0.3902 target = 0.163195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.126272 restraints weight = 23379.652| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.46 r_work: 0.3360 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2119 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= 0.175 Angle : 1.319 88.260 24489 Z= 0.343 Chirality : 0.042 0.241 2687 Planarity : 0.004 0.112 2912 Dihedral : 17.467 163.744 2901 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.90 % Favored : 92.90 % Rotamer: Outliers : 2.57 % Allowed : 15.66 % Favored : 81.77 % 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: -0.08 (0.19), residues: 1985 helix: 1.72 (0.18), residues: 917 sheet: 0.03 (0.33), residues: 242 loop : -2.26 (0.19), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 91 TYR 0.016 0.001 TYR D 255 PHE 0.017 0.001 PHE C 340 TRP 0.017 0.002 TRP D 342 HIS 0.004 0.001 HIS D 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (17943) covalent geometry : angle 0.61039 / 0.33 (24465) hydrogen bonds : bond 0.05142 / 3.42 ( 840) hydrogen bonds : angle 4.25312 / 3.02 ( 2413) metal coordination : bond 0.02540 / 1.39 ( 8) metal coordination : angle 37.37244 / 23.16 ( 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 238 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 193 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: A 150 MET cc_start: 0.5648 (tmm) cc_final: 0.5317 (tmm) REVERT: A 200 ASP cc_start: 0.5958 (t70) cc_final: 0.5624 (t70) REVERT: A 268 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7447 (mm-30) REVERT: B 12 GLN cc_start: 0.7699 (mp10) cc_final: 0.7318 (mp10) REVERT: B 125 ARG cc_start: 0.6820 (tmm-80) cc_final: 0.6476 (ttt90) REVERT: B 150 MET cc_start: 0.5315 (tpp) cc_final: 0.5092 (tpp) REVERT: B 183 GLN cc_start: 0.6244 (OUTLIER) cc_final: 0.5903 (tm-30) REVERT: C 30 GLN cc_start: 0.7967 (tp40) cc_final: 0.7727 (tp40) REVERT: C 131 PRO cc_start: 0.8288 (Cg_endo) cc_final: 0.7969 (Cg_exo) REVERT: D 41 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8496 (mp) REVERT: D 125 ARG cc_start: 0.6475 (tpp-160) cc_final: 0.5603 (tmt170) REVERT: D 126 MET cc_start: 0.8325 (tmm) cc_final: 0.8077 (tpp) REVERT: D 178 ASP cc_start: 0.7409 (t0) cc_final: 0.7020 (t0) REVERT: D 200 ASP cc_start: 0.7796 (m-30) cc_final: 0.6291 (p0) REVERT: D 201 ASN cc_start: 0.8108 (t0) cc_final: 0.7598 (t0) REVERT: D 330 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.6919 (mp) REVERT: D 342 TRP cc_start: 0.8427 (OUTLIER) cc_final: 0.7763 (m-10) REVERT: I 48 LYS cc_start: 0.7552 (tptt) cc_final: 0.6708 (mttt) REVERT: I 147 ASN cc_start: 0.8017 (t0) cc_final: 0.7602 (t0) REVERT: J 154 GLU cc_start: 0.7962 (pp20) cc_final: 0.7627 (pp20) outliers start: 45 outliers final: 24 residues processed: 226 average time/residue: 0.1199 time to fit residues: 41.6934 Evaluate side-chains 216 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 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 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 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 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 0 SER Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 11 THR 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 Chi-restraints excluded: chain J residue 198 ILE 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: 0.0770 chunk 45 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 190 optimal weight: 8.9990 chunk 192 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 215 ASN E 35 GLN J 71 GLN ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.165447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.128608 restraints weight = 23329.677| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.46 r_work: 0.3390 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 17951 Z= 0.129 Angle : 1.222 86.046 24489 Z= 0.318 Chirality : 0.040 0.241 2687 Planarity : 0.004 0.111 2912 Dihedral : 17.399 164.570 2901 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.45 % Favored : 93.40 % Rotamer: Outliers : 1.49 % Allowed : 17.14 % Favored : 81.37 % 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: 0.11 (0.19), residues: 1985 helix: 1.89 (0.18), residues: 912 sheet: 0.08 (0.34), residues: 238 loop : -2.12 (0.20), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 331 TYR 0.014 0.001 TYR D 255 PHE 0.021 0.001 PHE D 190 TRP 0.015 0.001 TRP B 296 HIS 0.007 0.001 HIS D 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (17943) covalent geometry : angle 0.56000 / 0.30 (24465) hydrogen bonds : bond 0.04485 / 2.97 ( 840) hydrogen bonds : angle 4.10065 / 2.91 ( 2413) metal coordination : bond 0.02145 / 1.17 ( 8) metal coordination : angle 34.68952 / 21.68 ( 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 222 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 150 MET cc_start: 0.5775 (tmm) cc_final: 0.5205 (tmm) REVERT: A 200 ASP cc_start: 0.5896 (t70) cc_final: 0.5568 (t70) REVERT: A 268 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7466 (mm-30) REVERT: B 12 GLN cc_start: 0.7663 (mp10) cc_final: 0.7268 (mp10) REVERT: B 125 ARG cc_start: 0.6788 (tmm-80) cc_final: 0.6450 (ttt90) REVERT: B 183 GLN cc_start: 0.6141 (OUTLIER) cc_final: 0.5802 (tm-30) REVERT: C 131 PRO cc_start: 0.8271 (Cg_endo) cc_final: 0.7953 (Cg_exo) REVERT: D 125 ARG cc_start: 0.6286 (tpp-160) cc_final: 0.5432 (tmt170) REVERT: D 178 ASP cc_start: 0.7338 (t0) cc_final: 0.6980 (t0) REVERT: D 200 ASP cc_start: 0.7830 (m-30) cc_final: 0.6449 (p0) REVERT: D 201 ASN cc_start: 0.8030 (t0) cc_final: 0.7503 (t0) REVERT: I 48 LYS cc_start: 0.7534 (tptt) cc_final: 0.6713 (mttt) REVERT: I 68 MET cc_start: 0.6302 (OUTLIER) cc_final: 0.5288 (tpt) REVERT: J 49 LYS cc_start: 0.7480 (ttmm) cc_final: 0.7270 (ttpp) REVERT: J 154 GLU cc_start: 0.7969 (pp20) cc_final: 0.7615 (pp20) REVERT: J 217 LEU cc_start: 0.4249 (OUTLIER) cc_final: 0.3943 (mm) outliers start: 26 outliers final: 16 residues processed: 217 average time/residue: 0.1164 time to fit residues: 38.8901 Evaluate side-chains 211 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 192 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 105 THR Chi-restraints excluded: chain C residue 254 LEU 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 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 I residue 195 LEU Chi-restraints excluded: chain J residue 71 GLN 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: 0.8980 chunk 108 optimal weight: 1.9990 chunk 101 optimal weight: 0.0980 chunk 163 optimal weight: 0.4980 chunk 92 optimal weight: 0.4980 chunk 56 optimal weight: 0.0980 chunk 2 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 GLN A 73 ASN C 39 HIS ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 71 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 = 0.4009 r_free = 0.4009 target = 0.174700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.148754 restraints weight = 22226.581| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 1.57 r_work: 0.3580 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.081 17951 Z= 0.117 Angle : 1.145 83.614 24489 Z= 0.305 Chirality : 0.039 0.245 2687 Planarity : 0.004 0.111 2912 Dihedral : 17.338 165.111 2901 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.15 % Favored : 93.70 % Rotamer: Outliers : 2.00 % Allowed : 17.03 % 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: 0.24 (0.19), residues: 1985 helix: 2.00 (0.18), residues: 913 sheet: 0.03 (0.33), residues: 251 loop : -2.06 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 289 TYR 0.013 0.001 TYR D 255 PHE 0.021 0.001 PHE D 190 TRP 0.014 0.001 TRP D 165 HIS 0.005 0.001 HIS D 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (17943) covalent geometry : angle 0.53782 / 0.29 (24465) hydrogen bonds : bond 0.04076 / 2.70 ( 840) hydrogen bonds : angle 3.97802 / 2.83 ( 2413) metal coordination : bond 0.01932 / 1.04 ( 8) metal coordination : angle 32.30389 / 20.37 ( 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 227 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 192 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 150 MET cc_start: 0.6662 (tmm) cc_final: 0.6011 (tmm) REVERT: A 268 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7983 (mm-30) REVERT: B 12 GLN cc_start: 0.7830 (mp10) cc_final: 0.7530 (mp10) REVERT: B 125 ARG cc_start: 0.7510 (tmm-80) cc_final: 0.7060 (ttt90) REVERT: B 150 MET cc_start: 0.5894 (tpp) cc_final: 0.5590 (tpp) REVERT: B 183 GLN cc_start: 0.6494 (OUTLIER) cc_final: 0.6159 (tm-30) REVERT: D 125 ARG cc_start: 0.7069 (tpp-160) cc_final: 0.6240 (tmt170) REVERT: D 154 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.6970 (ttm-80) REVERT: D 200 ASP cc_start: 0.7774 (m-30) cc_final: 0.6638 (p0) REVERT: D 201 ASN cc_start: 0.8063 (t0) cc_final: 0.7736 (t0) REVERT: D 342 TRP cc_start: 0.8525 (OUTLIER) cc_final: 0.7838 (m-10) REVERT: I 48 LYS cc_start: 0.8162 (tptt) cc_final: 0.7371 (mttt) REVERT: J 154 GLU cc_start: 0.7639 (pp20) cc_final: 0.7427 (pp20) REVERT: J 217 LEU cc_start: 0.4532 (OUTLIER) cc_final: 0.4265 (mm) outliers start: 35 outliers final: 19 residues processed: 219 average time/residue: 0.1162 time to fit residues: 39.4596 Evaluate side-chains 213 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 190 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 153 ILE 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 248 MET 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 105 THR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 88 VAL 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 254 LEU 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 J residue 71 GLN 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: 3.9990 chunk 61 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 103 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 215 ASN ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 147 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.161492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.124556 restraints weight = 23613.942| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.47 r_work: 0.3340 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 17951 Z= 0.216 Angle : 1.190 86.767 24489 Z= 0.353 Chirality : 0.043 0.266 2687 Planarity : 0.005 0.111 2912 Dihedral : 17.521 165.841 2901 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.56 % Favored : 92.29 % Rotamer: Outliers : 2.17 % Allowed : 17.54 % Favored : 80.29 % 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: -0.10 (0.19), residues: 1985 helix: 1.73 (0.18), residues: 913 sheet: -0.19 (0.32), residues: 254 loop : -2.23 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 162 TYR 0.021 0.002 TYR D 255 PHE 0.023 0.002 PHE C 340 TRP 0.020 0.002 TRP D 342 HIS 0.005 0.001 HIS J 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.21 (17943) covalent geometry : angle 0.64293 / 0.34 (24465) hydrogen bonds : bond 0.05342 / 3.56 ( 840) hydrogen bonds : angle 4.21215 / 3.01 ( 2413) metal coordination : bond 0.02908 / 1.64 ( 8) metal coordination : angle 31.97887 / 20.40 ( 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 234 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 196 time to evaluate : 0.646 Fit side-chains revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7556 (mm-30) REVERT: B 125 ARG cc_start: 0.6894 (tmm-80) cc_final: 0.6520 (ttt90) REVERT: B 150 MET cc_start: 0.5512 (tpp) cc_final: 0.5197 (tpp) REVERT: B 183 GLN cc_start: 0.6367 (OUTLIER) cc_final: 0.5900 (tm-30) REVERT: C 131 PRO cc_start: 0.8272 (Cg_endo) cc_final: 0.7931 (Cg_exo) REVERT: D 125 ARG cc_start: 0.6500 (tpp-160) cc_final: 0.5690 (tmt170) REVERT: D 178 ASP cc_start: 0.7466 (t0) cc_final: 0.7150 (t0) REVERT: D 200 ASP cc_start: 0.7922 (m-30) cc_final: 0.6494 (p0) REVERT: D 201 ASN cc_start: 0.8120 (t0) cc_final: 0.7739 (t0) REVERT: D 255 TYR cc_start: 0.8223 (t80) cc_final: 0.7897 (t80) REVERT: D 342 TRP cc_start: 0.8480 (OUTLIER) cc_final: 0.7837 (m-10) REVERT: F 62 GLU cc_start: 0.8401 (pm20) cc_final: 0.8007 (pm20) REVERT: I 48 LYS cc_start: 0.7651 (tptt) cc_final: 0.6793 (mttt) REVERT: I 68 MET cc_start: 0.6526 (OUTLIER) cc_final: 0.5468 (tpt) REVERT: J 154 GLU cc_start: 0.7980 (pp20) cc_final: 0.7629 (pp20) REVERT: J 217 LEU cc_start: 0.4234 (OUTLIER) cc_final: 0.3896 (mm) outliers start: 38 outliers final: 25 residues processed: 222 average time/residue: 0.1180 time to fit residues: 40.8537 Evaluate side-chains 222 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 153 ILE 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 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 88 VAL Chi-restraints excluded: chain D residue 127 THR 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 342 TRP 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 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: 0.1980 chunk 107 optimal weight: 0.9990 chunk 145 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 215 ASN E 35 GLN J 71 GLN ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.171234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.146228 restraints weight = 22243.961| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.45 r_work: 0.3539 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 17951 Z= 0.140 Angle : 1.115 82.130 24489 Z= 0.321 Chirality : 0.040 0.255 2687 Planarity : 0.004 0.110 2912 Dihedral : 17.477 167.756 2901 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.30 % Favored : 93.55 % Rotamer: Outliers : 1.89 % Allowed : 17.94 % 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: 0.05 (0.19), residues: 1985 helix: 1.83 (0.18), residues: 914 sheet: -0.13 (0.32), residues: 255 loop : -2.14 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 91 TYR 0.021 0.001 TYR D 255 PHE 0.015 0.001 PHE D 190 TRP 0.017 0.001 TRP D 165 HIS 0.003 0.001 HIS D 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (17943) covalent geometry : angle 0.58128 / 0.31 (24465) hydrogen bonds : bond 0.04589 / 3.05 ( 840) hydrogen bonds : angle 4.07268 / 2.91 ( 2413) metal coordination : bond 0.02256 / 1.26 ( 8) metal coordination : angle 30.40258 / 19.40 ( 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 228 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8323 (mm-30) cc_final: 0.8033 (mm-30) REVERT: B 125 ARG cc_start: 0.7561 (tmm-80) cc_final: 0.7072 (ttt90) REVERT: B 149 MET cc_start: 0.7509 (ttp) cc_final: 0.7258 (tmm) REVERT: B 150 MET cc_start: 0.6041 (tpp) cc_final: 0.5800 (tpp) REVERT: B 183 GLN cc_start: 0.6628 (OUTLIER) cc_final: 0.6272 (tm-30) REVERT: D 125 ARG cc_start: 0.7187 (tpp-160) cc_final: 0.6492 (tmt170) REVERT: D 154 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.7290 (ttm-80) REVERT: D 178 ASP cc_start: 0.7676 (t0) cc_final: 0.7417 (t0) REVERT: D 200 ASP cc_start: 0.7751 (m-30) cc_final: 0.6715 (p0) REVERT: D 342 TRP cc_start: 0.8580 (OUTLIER) cc_final: 0.7880 (m-10) REVERT: E 61 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7787 (mm-30) REVERT: F 62 GLU cc_start: 0.8431 (pm20) cc_final: 0.8160 (pm20) REVERT: I 48 LYS cc_start: 0.8208 (tptt) cc_final: 0.7442 (mttt) REVERT: I 68 MET cc_start: 0.7553 (OUTLIER) cc_final: 0.6543 (tpt) REVERT: J 129 MET cc_start: 0.8528 (mmm) cc_final: 0.8299 (mtp) REVERT: J 154 GLU cc_start: 0.7700 (pp20) cc_final: 0.7495 (pp20) REVERT: J 217 LEU cc_start: 0.4506 (OUTLIER) cc_final: 0.4241 (mm) outliers start: 33 outliers final: 22 residues processed: 221 average time/residue: 0.1182 time to fit residues: 39.9964 Evaluate side-chains 217 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 153 ILE 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 105 THR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 88 VAL 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 215 ASN Chi-restraints excluded: chain D residue 254 LEU 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 I residue 195 LEU Chi-restraints excluded: chain J residue 71 GLN 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: 0.0970 chunk 36 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 157 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 GLN C 39 HIS ** C 201 ASN ** 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 J 71 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 = 0.3952 r_free = 0.3952 target = 0.169270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.142960 restraints weight = 22060.112| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.58 r_work: 0.3517 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 17951 Z= 0.194 Angle : 1.134 83.593 24489 Z= 0.342 Chirality : 0.042 0.265 2687 Planarity : 0.004 0.110 2912 Dihedral : 17.548 168.141 2901 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.15 % Favored : 92.70 % Rotamer: Outliers : 1.83 % Allowed : 18.11 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.19), residues: 1985 helix: 1.71 (0.18), residues: 914 sheet: -0.16 (0.32), residues: 259 loop : -2.23 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 91 TYR 0.023 0.001 TYR D 255 PHE 0.018 0.002 PHE C 340 TRP 0.018 0.002 TRP D 342 HIS 0.005 0.001 HIS D 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.19 (17943) covalent geometry : angle 0.62712 / 0.33 (24465) hydrogen bonds : bond 0.05065 / 3.36 ( 840) hydrogen bonds : angle 4.15721 / 2.97 ( 2413) metal coordination : bond 0.02739 / 1.54 ( 8) metal coordination : angle 30.19848 / 19.36 ( 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 219 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8009 (mm-30) REVERT: B 125 ARG cc_start: 0.7529 (tmm-80) cc_final: 0.7056 (ttt90) REVERT: B 149 MET cc_start: 0.7461 (ttp) cc_final: 0.7180 (tmm) REVERT: B 150 MET cc_start: 0.6197 (tpp) cc_final: 0.5985 (tpp) REVERT: B 183 GLN cc_start: 0.6602 (OUTLIER) cc_final: 0.6273 (tm-30) REVERT: C 131 PRO cc_start: 0.8271 (Cg_endo) cc_final: 0.7957 (Cg_exo) REVERT: D 125 ARG cc_start: 0.7190 (tpp-160) cc_final: 0.6523 (tmt170) REVERT: D 178 ASP cc_start: 0.7678 (t0) cc_final: 0.7420 (t0) REVERT: D 200 ASP cc_start: 0.7696 (m-30) cc_final: 0.6555 (p0) REVERT: D 342 TRP cc_start: 0.8631 (OUTLIER) cc_final: 0.7995 (m-10) REVERT: I 48 LYS cc_start: 0.8194 (tptt) cc_final: 0.7426 (mttt) REVERT: I 68 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.6454 (tpt) REVERT: J 154 GLU cc_start: 0.7754 (pp20) cc_final: 0.7535 (pp20) REVERT: J 217 LEU cc_start: 0.4524 (OUTLIER) cc_final: 0.4240 (mm) outliers start: 32 outliers final: 25 residues processed: 210 average time/residue: 0.1312 time to fit residues: 42.3195 Evaluate side-chains 216 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 153 ILE 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 105 THR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 215 ASN Chi-restraints excluded: chain D residue 233 MET Chi-restraints excluded: chain D residue 254 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 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 I residue 195 LEU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 71 GLN 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: 0.4980 chunk 105 optimal weight: 0.6980 chunk 192 optimal weight: 1.9990 chunk 186 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 101 optimal weight: 0.1980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 39 HIS ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 ASN 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 = 0.3968 r_free = 0.3968 target = 0.170782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.145697 restraints weight = 22229.546| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 1.44 r_work: 0.3523 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 17951 Z= 0.149 Angle : 1.117 82.863 24489 Z= 0.328 Chirality : 0.041 0.261 2687 Planarity : 0.004 0.109 2912 Dihedral : 17.530 168.966 2901 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.55 % Favored : 93.30 % Rotamer: Outliers : 2.06 % Allowed : 18.23 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.19), residues: 1985 helix: 1.78 (0.18), residues: 913 sheet: -0.21 (0.31), residues: 268 loop : -2.22 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 91 TYR 0.021 0.001 TYR D 255 PHE 0.014 0.001 PHE C 340 TRP 0.018 0.001 TRP D 165 HIS 0.004 0.001 HIS D 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (17943) covalent geometry : angle 0.59975 / 0.32 (24465) hydrogen bonds : bond 0.04711 / 3.13 ( 840) hydrogen bonds : angle 4.09602 / 2.92 ( 2413) metal coordination : bond 0.02715 / 1.50 ( 8) metal coordination : angle 30.10953 / 19.25 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3547.35 seconds wall clock time: 61 minutes 37.87 seconds (3697.87 seconds total)